pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] [EXTERNAL] Valence_Mode issue

[Dr. V. M. <vij...@gm...>]

Thank you, Dr. Ali Kusay and Dr. Blaine Mooers
I will try this.

With Warm Regards
*Dr. Vijay H. Masand*
Department of Chemistry,
Vidya Bharati College, Amravati, 444 602
Maharashtra, India.
Phone number- +91-9403312628
https://sites.google.com/site/vijaymasand/



On Sun, Jun 21, 2020 at 10:08 PM Mooers, Blaine H.M. (HSC) <
Bla...@ou...> wrote:

> Hi Ali,
>
> Thank you for the follow-up explanation!
>
> I forgot that you can specify valence in a sdf file.
> This is something that you cannot do in a pdb file.
>
> Best regards,
>
> Blaine
>
> Blaine Mooers, Ph.D.
> Associate Professor
> Department of Biochemistry and Molecular Biology
> College of Medicine
> University of Oklahoma Health Sciences Center
> S.L. Young Biomedical Research Center (BRC) Rm. 466
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
>
> ________________________________________
> From: Ali Kusay [aku...@un...]
> Sent: Sunday, June 21, 2020 7:41 AM
> To: Mooers, Blaine H.M.  (HSC); Vijay Masand
> Cc: pym...@li...
> Subject: Re: [PyMOL] [EXTERNAL]  Valence_Mode issue
>
> Hi Vijar and Blaine,
>
> >>> Had to send this message again since it was flagged by the image size
> restriction <<<
>
>  Thank you for showing me all these possibilities, I am convinced that
> PyMOL is excellent for 2D molecules!
>
> I have found similar similar Blaine as far as manually setting bonds:
> I have managed to change delocalised bonds to “bonds inside” by directly
> setting the bond order between 2 atoms using the “bond” command and
> “valence” commands. Both are not perfect solutions, documentation in
> https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_Valence&d=DwIGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=-qnBLebfMbB7OaVmSmuM3mfuMu_2_k8OZvs_xQ_Xm88&s=sV8ovzxIsDWSl0uoHo1BUdChLeAdw_h5R5-BeBtHkN0&e=
> .
>
> Its perhaps easiest to edit the bonds from the files itself (or load one
> with the right bonds order), see attached images of file difference between
> left (valence between atoms 5-6 and 5-7 bond set to 4 delocalised) and
> right (valence between atoms 5-6 and 5-7 bond set to 1 and 2 bonds inside),
> PyMOL image in the same order.
>
> BTW this is aspirin from
> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.drugbank.ca_drugs_DB00945&d=DwIGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=-qnBLebfMbB7OaVmSmuM3mfuMu_2_k8OZvs_xQ_Xm88&s=fe5TrhAFsg6zZY9iAHu1aINfqUuQ91KvQFo8gQiSa8o&e=
> , in the downloaded sdf file it already has the non-delocalised bond and I
> made delocalised using the valence command with the guess option, its just
> hard to go the other way around!
>
> Kind regards,
>
> Ali
>
> Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
> The University of Sydney School of Pharmacy | Faculty of Medicine and
> Health
> 424, Brain and Mind Centre | The University of Sydney | NSW 2050
> Email: aku...@un...
>
>
> On 21/6/20, 10:32 pm, "Mooers, Blaine H.M.  (HSC)" <
> Bla...@ou...> wrote:
>
>     Hi Vijay,
>
>     It is unlikely that PyMOL can correctly interpret the atom names in
> your ligand.
>     I suspect that you have to manually unbound and then bond each pair of
> atoms
>     of interest in your ligand. You can do so by pasting a pair of
> commands like
>     the following on the command line at the PyMOL> prompt below the
> command history window.
>
>     unbond name CBE, name CBF;bond name CBE, name CBF, 2
>
>     See the  attached images for a ligand after applying the above two
> commands.
>     The Ball-and-Stick representation is found in the Presets under the A
> menu
>     in the internal gui on the right.
>
>     You can get the atom names printed to the command history window
>     by switching the selection mode in the lower right hand corner to
> 'Atoms' and
>     then left-click on the atom of interest.
>
>
>     Explanation:
>
>     One would hope that the following command would work:
>
>     set valence, 1, ligand; set valence_mode, 1, ligamd
>
>     See
> https://urldefense.proofpoint.com/v2/url?u=https-3A__protect-2Dau.mimecast.com_s_fNQtC2xMQzin5pN4UnwJ-5FQ-3Fdomain-3Dpymolwiki.org&d=DwIGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=-qnBLebfMbB7OaVmSmuM3mfuMu_2_k8OZvs_xQ_Xm88&s=II8Q6vB36GagQ-ygUFTK6ybIZsN6DIfSjl0ytoVurhU&e=
>
>     A work around would be to add the ligand atoms of interest the
> wonderful script by Andreas Warnecke:
>
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__protect-2Dau.mimecast.com_s_KbvGC3QNPBiLDp5PSqeXG3-3Fdomain-3Draw.githubusercontent.com&d=DwIGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=-qnBLebfMbB7OaVmSmuM3mfuMu_2_k8OZvs_xQ_Xm88&s=S_bEV5e15l4ZTM263lAHuxIKRG4onVuWMeGlvXD_YF4&e=
>
>     This will require edits in several locations, but it would provide a
> longer term solution.
>     See
> https://urldefense.proofpoint.com/v2/url?u=https-3A__protect-2Dau.mimecast.com_s_jWHFC4QOPEiL4BpnSBL3lk-3Fdomain-3Dpymolwiki.org&d=DwIGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=-qnBLebfMbB7OaVmSmuM3mfuMu_2_k8OZvs_xQ_Xm88&s=55G8zMnSza8lxpwMY204KzRDFduU4QYBr1_vVMVB_S8&e=
>
>     Best regards,
>
>     Blaine
>
>     Blaine Mooers, Ph.D.
>     Associate Professor
>     Department of Biochemistry and Molecular Biology
>     College of Medicine
>     University of Oklahoma Health Sciences Center
>     S.L. Young Biomedical Research Center (BRC) Rm. 466
>     975 NE 10th Street, BRC 466
>     Oklahoma City, OK 73104-5419
>
>     ________________________________________
>     From: Dr. Vijay Masand [vij...@gm...]
>     Sent: Sunday, June 21, 2020 2:53 AM
>     To: pymol-users
>     Subject: [EXTERNAL] [PyMOL] Valence_Mode issue
>
>     Dear All
>     I am trying to get a nice 2D- like representation for a small molecule
> using PyMOL.
>
>     I am using PyMOL 2.4 (Windows 10, Python3). I tried to set valence and
> valence_mode to get 'bonds inside' using the following commands:
>
>     set valence, 1
>     set valence_mode, 1
>
>     Unfortunately, I am getting 'delocalized bonds' for a small molecule.
> Please see the attached figure. How to activate valence_mode?
>     [Pymol-Issue-Valence-Mode.jpg]
>
>     With Warm Regards
>     Dr. Vijay H. Masand
>     Department of Chemistry,
>     Vidya Bharati College, Amravati, 444 602
>     Maharashtra, India.
>     Phone number- +91-9403312628
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__protect-2Dau.mimecast.com_s_5UqYC5QPXJiqkZVzs2DXxq-3Fdomain-3Dsites.google.com&d=DwIGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=-qnBLebfMbB7OaVmSmuM3mfuMu_2_k8OZvs_xQ_Xm88&s=BC3gq6JqpYp36Fvo1wYIKytH83HmQiOliRmJKAA_XxY&e=
> <
> https://urldefense.proofpoint.com/v2/url?u=https-3A__protect-2Dau.mimecast.com_s_Mh47C6XQ4LfQLrngTxJNJp-3Fdomain-3Durldefense.proofpoint.com&d=DwIGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=-qnBLebfMbB7OaVmSmuM3mfuMu_2_k8OZvs_xQ_Xm88&s=bX1f_BrDYaN_2GLjXqmyl3JC_xv8khukhFxEwiSCYdU&e=
> >
>
>
>

Re: [PyMOL] Help! figure (ligand in cavity)

[Vertika G. <var...@gm...>]

Thank you!

On Mon, Jun 22, 2020, 10:20 AM Joel Tyndall <joe...@ot...>
wrote:

> Dear Vertika,
>
>
>
> There are probably a few tutorials around to help you with this, but
> briefly you will probably need to extract the ligand to a new object,
> create surface of your protein and that will do it. Colour the objects, as
> you prefer
>
>
>
> Hope this helps
>
>
>
> J
>
>
>
> *From:* Vertika Gautam <var...@gm...>
> *Sent:* Monday, 22 June 2020 2:55 AM
> *To:* pym...@li...
> *Subject:* [PyMOL] Help! figure (ligand in cavity)
>
>
>
> Hello everyone
>
>
>
> I am trying to make a figure showing the potential surface and binding
> pocket as shown in the attached figure. Can anyone help me with the
> commands?
>
> Thanks in advance for your help!
>
> [image: image.png]
>
>
>
> --
>
> Vertika Gautam
>
> Research Assistant
>
> Drug Design and Development Research Group (DDDRG)
>
> Department of Chemistry, Faculty of Science
>
> University of Malaya
>
>
>
> *e-mail address: var...@gm... <var...@gm...>
>                           var...@ho...
> <var...@ho...>                           01112294191 *
>
>

Re: [PyMOL] Help! figure (ligand in cavity)

[Joel T. <joe...@ot...>]

Dear Vertika,

There are probably a few tutorials around to help you with this, but briefly you will probably need to extract the ligand to a new object, create surface of your protein and that will do it. Colour the objects, as you prefer

Hope this helps

J

From: Vertika Gautam <var...@gm...>
Sent: Monday, 22 June 2020 2:55 AM
To: pym...@li...
Subject: [PyMOL] Help! figure (ligand in cavity)

Hello everyone

I am trying to make a figure showing the potential surface and binding pocket as shown in the attached figure. Can anyone help me with the commands?
Thanks in advance for your help!
[image.png]


--
Vertika Gautam

Research Assistant
Drug Design and Development Research Group (DDDRG)
Department of Chemistry, Faculty of Science
University of Malaya
e-mail address: var...@gm...<mailto:var...@gm...>
                          var...@ho...<mailto:var...@ho...>
                          01112294191

Re: [PyMOL] [EXTERNAL] Valence_Mode issue

[Mooers, B. H.M. (HSC) <Bla...@ou...>]

Hi Ali,

Thank you for the follow-up explanation!

I forgot that you can specify valence in a sdf file.
This is something that you cannot do in a pdb file.

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419

________________________________________
From: Ali Kusay [aku...@un...]
Sent: Sunday, June 21, 2020 7:41 AM
To: Mooers, Blaine H.M.  (HSC); Vijay Masand
Cc: pym...@li...
Subject: Re: [PyMOL] [EXTERNAL]  Valence_Mode issue

Hi Vijar and Blaine,

>>> Had to send this message again since it was flagged by the image size restriction <<<

 Thank you for showing me all these possibilities, I am convinced that PyMOL is excellent for 2D molecules!

I have found similar similar Blaine as far as manually setting bonds:
I have managed to change delocalised bonds to “bonds inside” by directly setting the bond order between 2 atoms using the “bond” command and “valence” commands. Both are not perfect solutions, documentation in https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_Valence&d=DwIGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=-qnBLebfMbB7OaVmSmuM3mfuMu_2_k8OZvs_xQ_Xm88&s=sV8ovzxIsDWSl0uoHo1BUdChLeAdw_h5R5-BeBtHkN0&e= .

Its perhaps easiest to edit the bonds from the files itself (or load one with the right bonds order), see attached images of file difference between left (valence between atoms 5-6 and 5-7 bond set to 4 delocalised) and right (valence between atoms 5-6 and 5-7 bond set to 1 and 2 bonds inside), PyMOL image in the same order.

BTW this is aspirin from https://urldefense.proofpoint.com/v2/url?u=https-3A__www.drugbank.ca_drugs_DB00945&d=DwIGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=-qnBLebfMbB7OaVmSmuM3mfuMu_2_k8OZvs_xQ_Xm88&s=fe5TrhAFsg6zZY9iAHu1aINfqUuQ91KvQFo8gQiSa8o&e= , in the downloaded sdf file it already has the non-delocalised bond and I made delocalised using the valence command with the guess option, its just hard to go the other way around!

Kind regards,

Ali

Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
The University of Sydney School of Pharmacy | Faculty of Medicine and Health
424, Brain and Mind Centre | The University of Sydney | NSW 2050
Email: aku...@un...


On 21/6/20, 10:32 pm, "Mooers, Blaine H.M.  (HSC)" <Bla...@ou...> wrote:

    Hi Vijay,

    It is unlikely that PyMOL can correctly interpret the atom names in your ligand.
    I suspect that you have to manually unbound and then bond each pair of atoms
    of interest in your ligand. You can do so by pasting a pair of commands like
    the following on the command line at the PyMOL> prompt below the command history window.

    unbond name CBE, name CBF;bond name CBE, name CBF, 2

    See the  attached images for a ligand after applying the above two commands.
    The Ball-and-Stick representation is found in the Presets under the A menu
    in the internal gui on the right.

    You can get the atom names printed to the command history window
    by switching the selection mode in the lower right hand corner to 'Atoms' and
    then left-click on the atom of interest.


    Explanation:

    One would hope that the following command would work:

    set valence, 1, ligand; set valence_mode, 1, ligamd

    See https://urldefense.proofpoint.com/v2/url?u=https-3A__protect-2Dau.mimecast.com_s_fNQtC2xMQzin5pN4UnwJ-5FQ-3Fdomain-3Dpymolwiki.org&d=DwIGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=-qnBLebfMbB7OaVmSmuM3mfuMu_2_k8OZvs_xQ_Xm88&s=II8Q6vB36GagQ-ygUFTK6ybIZsN6DIfSjl0ytoVurhU&e=

    A work around would be to add the ligand atoms of interest the wonderful script by Andreas Warnecke:

    https://urldefense.proofpoint.com/v2/url?u=https-3A__protect-2Dau.mimecast.com_s_KbvGC3QNPBiLDp5PSqeXG3-3Fdomain-3Draw.githubusercontent.com&d=DwIGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=-qnBLebfMbB7OaVmSmuM3mfuMu_2_k8OZvs_xQ_Xm88&s=S_bEV5e15l4ZTM263lAHuxIKRG4onVuWMeGlvXD_YF4&e=

    This will require edits in several locations, but it would provide a longer term solution.
    See https://urldefense.proofpoint.com/v2/url?u=https-3A__protect-2Dau.mimecast.com_s_jWHFC4QOPEiL4BpnSBL3lk-3Fdomain-3Dpymolwiki.org&d=DwIGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=-qnBLebfMbB7OaVmSmuM3mfuMu_2_k8OZvs_xQ_Xm88&s=55G8zMnSza8lxpwMY204KzRDFduU4QYBr1_vVMVB_S8&e=

    Best regards,

    Blaine

    Blaine Mooers, Ph.D.
    Associate Professor
    Department of Biochemistry and Molecular Biology
    College of Medicine
    University of Oklahoma Health Sciences Center
    S.L. Young Biomedical Research Center (BRC) Rm. 466
    975 NE 10th Street, BRC 466
    Oklahoma City, OK 73104-5419

    ________________________________________
    From: Dr. Vijay Masand [vij...@gm...]
    Sent: Sunday, June 21, 2020 2:53 AM
    To: pymol-users
    Subject: [EXTERNAL] [PyMOL] Valence_Mode issue

    Dear All
    I am trying to get a nice 2D- like representation for a small molecule using PyMOL.

    I am using PyMOL 2.4 (Windows 10, Python3). I tried to set valence and valence_mode to get 'bonds inside' using the following commands:

    set valence, 1
    set valence_mode, 1

    Unfortunately, I am getting 'delocalized bonds' for a small molecule. Please see the attached figure. How to activate valence_mode?
    [Pymol-Issue-Valence-Mode.jpg]

    With Warm Regards
    Dr. Vijay H. Masand
    Department of Chemistry,
    Vidya Bharati College, Amravati, 444 602
    Maharashtra, India.
    Phone number- +91-9403312628
    https://urldefense.proofpoint.com/v2/url?u=https-3A__protect-2Dau.mimecast.com_s_5UqYC5QPXJiqkZVzs2DXxq-3Fdomain-3Dsites.google.com&d=DwIGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=-qnBLebfMbB7OaVmSmuM3mfuMu_2_k8OZvs_xQ_Xm88&s=BC3gq6JqpYp36Fvo1wYIKytH83HmQiOliRmJKAA_XxY&e= <https://urldefense.proofpoint.com/v2/url?u=https-3A__protect-2Dau.mimecast.com_s_Mh47C6XQ4LfQLrngTxJNJp-3Fdomain-3Durldefense.proofpoint.com&d=DwIGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=-qnBLebfMbB7OaVmSmuM3mfuMu_2_k8OZvs_xQ_Xm88&s=bX1f_BrDYaN_2GLjXqmyl3JC_xv8khukhFxEwiSCYdU&e= >

[PyMOL] Help! figure (ligand in cavity)

[Vertika G. <var...@gm...>]

 Hello everyone

I am trying to make a figure showing the potential surface and binding
pocket as shown in the attached figure. Can anyone help me with the
commands?
Thanks in advance for your help!
[image: image.png]


-- 
Vertika Gautam

Research Assistant
Drug Design and Development Research Group (DDDRG)
Department of Chemistry, Faculty of Science
University of Malaya



*e-mail address: var...@gm...
<var...@gm...>
var...@ho... <var...@ho...>
    01112294191*

Re: [PyMOL] [EXTERNAL] Valence_Mode issue

[Ali K. <aku...@un...>]

Hi Vijar and Blaine,

>>> Had to send this message again since it was flagged by the image size restriction <<<

 Thank you for showing me all these possibilities, I am convinced that PyMOL is excellent for 2D molecules! 
 
I have found similar similar Blaine as far as manually setting bonds:
I have managed to change delocalised bonds to “bonds inside” by directly setting the bond order between 2 atoms using the “bond” command and “valence” commands. Both are not perfect solutions, documentation in https://pymolwiki.org/index.php/Valence.
 
Its perhaps easiest to edit the bonds from the files itself (or load one with the right bonds order), see attached images of file difference between left (valence between atoms 5-6 and 5-7 bond set to 4 delocalised) and right (valence between atoms 5-6 and 5-7 bond set to 1 and 2 bonds inside), PyMOL image in the same order.
 
BTW this is aspirin from https://www.drugbank.ca/drugs/DB00945, in the downloaded sdf file it already has the non-delocalised bond and I made delocalised using the valence command with the guess option, its just hard to go the other way around!

Kind regards,
 
Ali
 
Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
The University of Sydney School of Pharmacy | Faculty of Medicine and Health
424, Brain and Mind Centre | The University of Sydney | NSW 2050
Email: aku...@un...


On 21/6/20, 10:32 pm, "Mooers, Blaine H.M.  (HSC)" <Bla...@ou...> wrote:

    Hi Vijay,

    It is unlikely that PyMOL can correctly interpret the atom names in your ligand. 
    I suspect that you have to manually unbound and then bond each pair of atoms
    of interest in your ligand. You can do so by pasting a pair of commands like 
    the following on the command line at the PyMOL> prompt below the command history window.

    unbond name CBE, name CBF;bond name CBE, name CBF, 2

    See the  attached images for a ligand after applying the above two commands.
    The Ball-and-Stick representation is found in the Presets under the A menu
    in the internal gui on the right.

    You can get the atom names printed to the command history window 
    by switching the selection mode in the lower right hand corner to 'Atoms' and 
    then left-click on the atom of interest.


    Explanation:

    One would hope that the following command would work:

    set valence, 1, ligand; set valence_mode, 1, ligamd

    See https://protect-au.mimecast.com/s/fNQtC2xMQzin5pN4UnwJ_Q?domain=pymolwiki.org

    A work around would be to add the ligand atoms of interest the wonderful script by Andreas Warnecke:

    https://protect-au.mimecast.com/s/KbvGC3QNPBiLDp5PSqeXG3?domain=raw.githubusercontent.com

    This will require edits in several locations, but it would provide a longer term solution.
    See https://protect-au.mimecast.com/s/jWHFC4QOPEiL4BpnSBL3lk?domain=pymolwiki.org

    Best regards,

    Blaine

    Blaine Mooers, Ph.D.
    Associate Professor
    Department of Biochemistry and Molecular Biology
    College of Medicine
    University of Oklahoma Health Sciences Center
    S.L. Young Biomedical Research Center (BRC) Rm. 466
    975 NE 10th Street, BRC 466
    Oklahoma City, OK 73104-5419

    ________________________________________
    From: Dr. Vijay Masand [vij...@gm...]
    Sent: Sunday, June 21, 2020 2:53 AM
    To: pymol-users
    Subject: [EXTERNAL] [PyMOL] Valence_Mode issue

    Dear All
    I am trying to get a nice 2D- like representation for a small molecule using PyMOL.

    I am using PyMOL 2.4 (Windows 10, Python3). I tried to set valence and valence_mode to get 'bonds inside' using the following commands:

    set valence, 1
    set valence_mode, 1

    Unfortunately, I am getting 'delocalized bonds' for a small molecule. Please see the attached figure. How to activate valence_mode?
    [Pymol-Issue-Valence-Mode.jpg]

    With Warm Regards
    Dr. Vijay H. Masand
    Department of Chemistry,
    Vidya Bharati College, Amravati, 444 602
    Maharashtra, India.
    Phone number- +91-9403312628
    https://protect-au.mimecast.com/s/5UqYC5QPXJiqkZVzs2DXxq?domain=sites.google.com<https://protect-au.mimecast.com/s/Mh47C6XQ4LfQLrngTxJNJp?domain=urldefense.proofpoint.com>

Re: [PyMOL] [EXTERNAL] Valence_Mode issue

[Mooers, B. H.M. (HSC) <Bla...@ou...>]

Hi Vijay,

It is unlikely that PyMOL can correctly interpret the atom names in your ligand. 
I suspect that you have to manually unbound and then bond each pair of atoms
of interest in your ligand. You can do so by pasting a pair of commands like 
the following on the command line at the PyMOL> prompt below the command history window.

unbond name CBE, name CBF;bond name CBE, name CBF, 2

See the  attached images for a ligand after applying the above two commands.
The Ball-and-Stick representation is found in the Presets under the A menu
in the internal gui on the right.

You can get the atom names printed to the command history window 
by switching the selection mode in the lower right hand corner to 'Atoms' and 
then left-click on the atom of interest.


Explanation:

One would hope that the following command would work:

set valence, 1, ligand; set valence_mode, 1, ligamd

See https://pymolwiki.org/index.php/Valence

A work around would be to add the ligand atoms of interest the wonderful script by Andreas Warnecke:

https://raw.githubusercontent.com/Pymol-Scripts/Pymol-script-repo/master/format_bonds.py

This will require edits in several locations, but it would provide a longer term solution.
See https://pymolwiki.org/index.php/Format_bonds

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419

________________________________________
From: Dr. Vijay Masand [vij...@gm...]
Sent: Sunday, June 21, 2020 2:53 AM
To: pymol-users
Subject: [EXTERNAL] [PyMOL] Valence_Mode issue

Dear All
I am trying to get a nice 2D- like representation for a small molecule using PyMOL.

I am using PyMOL 2.4 (Windows 10, Python3). I tried to set valence and valence_mode to get 'bonds inside' using the following commands:

set valence, 1
set valence_mode, 1

Unfortunately, I am getting 'delocalized bonds' for a small molecule. Please see the attached figure. How to activate valence_mode?
[Pymol-Issue-Valence-Mode.jpg]

With Warm Regards
Dr. Vijay H. Masand
Department of Chemistry,
Vidya Bharati College, Amravati, 444 602
Maharashtra, India.
Phone number- +91-9403312628
https://sites.google.com/site/vijaymasand/<https://urldefense.proofpoint.com/v2/url?u=https-3A__sites.google.com_site_vijaymasand_&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9MKqEVQDvZHvSVvXmAO0iMXc1SCkh4ZQH2hhrRwy6XE&s=qmWnnUG9myB1HzBx_ttJjOPs1FaJRMYe3F8xI6qvmrU&e=>

Re: [PyMOL] Valence_Mode issue

[Ali K. <aku...@un...>]

Hi Vijay,

I have never through to use PyMOL to look at 2D molecules, its an interesting idea but software like chemdraw will offer you more functionality for situation like this.

Have you tried applying the valuence_mode command to a selection, i.e.:

Set valuence_mode, 1, testing # applies it to the “testing” object in the PyMOL session

Kind regards,

Ali

From: "Dr. Vijay Masand" <vij...@gm...>
Date: Sunday, 21 June 2020 at 5:58 pm
To: pymol-users <pym...@li...>
Subject: [PyMOL] Valence_Mode issue

Dear All
I am trying to get a nice 2D- like representation for a small molecule using PyMOL.

I am using PyMOL 2.4 (Windows 10, Python3). I tried to set valence and valence_mode to get 'bonds inside' using the following commands:

set valence, 1
set valence_mode, 1

Unfortunately, I am getting 'delocalized bonds' for a small molecule. Please see the attached figure. How to activate valence_mode?
[cid:image001.jpg@01D647FD.0528DB70]

With Warm Regards
Dr. Vijay H. Masand
Department of Chemistry,
Vidya Bharati College, Amravati, 444 602
Maharashtra, India.
Phone number- +91-9403312628
https://sites.google.com/site/vijaymasand/<https://protect-au.mimecast.com/s/822SCWLVXkUl8Vm3t6wWP3?domain=sites.google.com/>

[PyMOL] Valence_Mode issue

[Dr. V. M. <vij...@gm...>]

Dear All
I am trying to get a nice 2D- like representation for a small molecule
using PyMOL.

I am using PyMOL 2.4 (Windows 10, Python3). I tried to set valence and
valence_mode to get 'bonds inside' using the following commands:

set valence, 1
set valence_mode, 1

Unfortunately, I am getting 'delocalized bonds' for a small molecule.
Please see the attached figure. How to activate valence_mode?
[image: Pymol-Issue-Valence-Mode.jpg]

With Warm Regards
*Dr. Vijay H. Masand*
Department of Chemistry,
Vidya Bharati College, Amravati, 444 602
Maharashtra, India.
Phone number- +91-9403312628
https://sites.google.com/site/vijaymasand/

Re: [PyMOL] Install license file from CLI

[Thomas H. <tho...@sc...>]

That's unexpected. Can you send the output of the following command?

pymol -cd diagnostics

This will report the exact installation location, and also if a license file was found.


> On Jun 19, 2020, at 10:33 AM, Antonio Serrano <ase...@uc...> wrote:
> 
> I changed the name of the license file as you said, but the warning message keeps popping:
> 
> <current_pos.png>
> 
> 
> 
> 
> 
> 
> El jue., 18 jun. 2020 a las 20:16, Thomas Holder (<tho...@sc...>) escribió:
> Hi Antonio,
> 
> Rename the file to "license.lic".
> 
> Cheers,
>   Thomas
> 
> > On Jun 18, 2020, at 6:08 PM, Antonio Serrano <ase...@uc...> wrote:
> > 
> > Hi Thomas. Thanks for your quick response. I installed Miniconda, so I put the license file (pymol-edu-license.lic) in the following path:  $HOME/miniconda3/share/pymol/ . But a warning text stating "No License File - For evaluation Only (0 days remaining)" still appears when rendering PNG files with PyMol. Any suggestions?
> > 
> > El jue., 18 jun. 2020 a las 12:44, Thomas Holder (<tho...@sc...>) escribió:
> > Hi Antonio,
> > 
> > Did you install PyMOL into $HOME/anaconda3 ? If you installed into a different location, then that path to the license file will differ of course. Basically, path-to-pymol-dir/share/pymol/license.lic is the path.
> > 
> > Cheers,
> >   Thomas
> > 
> > > On Jun 17, 2020, at 2:15 PM, Antonio Serrano <ase...@uc...> wrote:
> > > 
> > > Hi:
> > > 
> > > I'm working with PyMol installed on a remote server, so I don't have access to the GUI. I already have an educational license. According to your FAQ at https://pymol.org/2/support.html?, the license file should be placed in $HOME/anaconda3/share/pymol/license.lic on a Linux computer. I already did it but PyMol isn't still activated. Any idea on how to completely install the license file using only the Command Line Interface? Many thx.
> > > 
> > > BR,
> > > Antonio Serrano
> 
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
> 
> 
> 
> -- 
> Antonio Serrano 
> Predoctoral researcher - Contratado predoctoral
> 
> UCAM Universidad Católica de Murcia
> Phone:  +34 968 278 821
> Email:    ase...@uc...

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] Install license file from CLI

[Antonio S. <ase...@uc...>]

I changed the name of the license file as you said, but the warning message
keeps popping:

[image: current_pos.png]






El jue., 18 jun. 2020 a las 20:16, Thomas Holder (<
tho...@sc...>) escribió:

> Hi Antonio,
>
> Rename the file to "license.lic".
>
> Cheers,
>   Thomas
>
> > On Jun 18, 2020, at 6:08 PM, Antonio Serrano <ase...@uc...> wrote:
> >
> > Hi Thomas. Thanks for your quick response. I installed Miniconda, so I
> put the license file (pymol-edu-license.lic) in the following path:
> $HOME/miniconda3/share/pymol/ . But a warning text stating "No License File
> - For evaluation Only (0 days remaining)" still appears when rendering PNG
> files with PyMol. Any suggestions?
> >
> > El jue., 18 jun. 2020 a las 12:44, Thomas Holder (<
> tho...@sc...>) escribió:
> > Hi Antonio,
> >
> > Did you install PyMOL into $HOME/anaconda3 ? If you installed into a
> different location, then that path to the license file will differ of
> course. Basically, path-to-pymol-dir/share/pymol/license.lic is the path.
> >
> > Cheers,
> >   Thomas
> >
> > > On Jun 17, 2020, at 2:15 PM, Antonio Serrano <ase...@uc...>
> wrote:
> > >
> > > Hi:
> > >
> > > I'm working with PyMol installed on a remote server, so I don't have
> access to the GUI. I already have an educational license. According to your
> FAQ at https://pymol.org/2/support.html?, the license file should be
> placed in $HOME/anaconda3/share/pymol/license.lic on a Linux computer. I
> already did it but PyMol isn't still activated. Any idea on how to
> completely install the license file using only the Command Line Interface?
> Many thx.
> > >
> > > BR,
> > > Antonio Serrano
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>

-- 
Antonio Serrano
Predoctoral researcher - Contratado predoctoral

*UCAM Universidad Católica de Murcia*

Phone:  +34 968 278 821
Email:    ase...@uc... <//ase...@uc...>

<https://scholar.google.es/citations?user=ZEJJCuUAAAAJ&hl=en&authuser=1>
<https://orcid.org/0000-0002-8121-5032>
<https://www.researchgate.net/profile/Antonio_Serrano9?ev=hdr_xprf>

-- 

"Este mensaje es privado y confidencial y se dirige exclusivamente a su 
destinatario. Si usted recibe este mensaje por error, no debe revelar, 
distribuir o copiar este e-mail. Por favor, comuníquelo al remitente y 
borre el mensaje y los archivos adjuntos de su sistema. No hay renuncia a 
la confidencialidad ni a ningún privilegio a causa de una transmisión 
errónea o por mal funcionamiento". 


"This message is private and 
confidential and it is intended exclusively for the addressee. If your 
receive this message by mistake, you should not disseminate, distribute or 
copy this e-mail. Please inform the sender and delete the message and 
attachments from your system. No confidentiality or any privilege regarding 
the information is waived or lost by any mistransmission or malfunction".



No me imprimas si no es necesario.Don't print me unless it's necessary.

[PyMOL] transparent electron density silhouette

[Daniel P F. <da...@uw...>]

Hello,
I'm working with some cryo-EM density and I'm trying to get my isosurface
or volume (whichever's easier) to display transparent except for the curves
and turns of the density.
similar to this (done in chimeraX) https://imgur.com/a/lZuG8gD

Does anyone know if this is possible?

thanks
~Dan

Re: [PyMOL] Install license file from CLI

[Thomas H. <tho...@sc...>]

Hi Antonio,

Rename the file to "license.lic".

Cheers,
  Thomas

> On Jun 18, 2020, at 6:08 PM, Antonio Serrano <ase...@uc...> wrote:
> 
> Hi Thomas. Thanks for your quick response. I installed Miniconda, so I put the license file (pymol-edu-license.lic) in the following path:  $HOME/miniconda3/share/pymol/ . But a warning text stating "No License File - For evaluation Only (0 days remaining)" still appears when rendering PNG files with PyMol. Any suggestions?
> 
> El jue., 18 jun. 2020 a las 12:44, Thomas Holder (<tho...@sc...>) escribió:
> Hi Antonio,
> 
> Did you install PyMOL into $HOME/anaconda3 ? If you installed into a different location, then that path to the license file will differ of course. Basically, path-to-pymol-dir/share/pymol/license.lic is the path.
> 
> Cheers,
>   Thomas
> 
> > On Jun 17, 2020, at 2:15 PM, Antonio Serrano <ase...@uc...> wrote:
> > 
> > Hi:
> > 
> > I'm working with PyMol installed on a remote server, so I don't have access to the GUI. I already have an educational license. According to your FAQ at https://pymol.org/2/support.html?, the license file should be placed in $HOME/anaconda3/share/pymol/license.lic on a Linux computer. I already did it but PyMol isn't still activated. Any idea on how to completely install the license file using only the Command Line Interface? Many thx.
> > 
> > BR,
> > Antonio Serrano

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] Install license file from CLI

[Antonio S. <ase...@uc...>]

Hi Thomas. Thanks for your quick response. I installed Miniconda, so I put
the license file (pymol-edu-license.lic) in the following path:
$HOME/miniconda3/share/pymol/ . But a warning text stating "No License File
- For evaluation Only (0 days remaining)" still appears when rendering PNG
files with PyMol. Any suggestions?

El jue., 18 jun. 2020 a las 12:44, Thomas Holder (<
tho...@sc...>) escribió:

> Hi Antonio,
>
> Did you install PyMOL into $HOME/anaconda3 ? If you installed into a
> different location, then that path to the license file will differ of
> course. Basically, path-to-pymol-dir/share/pymol/license.lic is the path.
>
> Cheers,
>   Thomas
>
> > On Jun 17, 2020, at 2:15 PM, Antonio Serrano <ase...@uc...> wrote:
> >
> > Hi:
> >
> > I'm working with PyMol installed on a remote server, so I don't have
> access to the GUI. I already have an educational license. According to your
> FAQ at https://pymol.org/2/support.html?, the license file should be
> placed in $HOME/anaconda3/share/pymol/license.lic on a Linux computer. I
> already did it but PyMol isn't still activated. Any idea on how to
> completely install the license file using only the Command Line Interface?
> Many thx.
> >
> > BR,
> > Antonio Serrano
> >
> >
> > "Este mensaje es privado y confidencial y se dirige exclusivamente a su
> destinatario. Si usted recibe este mensaje por error, no debe revelar,
> distribuir o copiar este e-mail. Por favor, comuníquelo al remitente y
> borre el mensaje y los archivos adjuntos de su sistema. No hay renuncia a
> la confidencialidad ni a ningún privilegio a causa de una transmisión
> errónea o por mal funcionamiento".
> >
> > "This message is private and confidential and it is intended exclusively
> for the addressee. If your receive this message by mistake, you should not
> disseminate, distribute or copy this e-mail. Please inform the sender and
> delete the message and attachments from your system. No confidentiality or
> any privilege regarding the information is waived or lost by any
> mistransmission or malfunction".
> >
> > No me imprimas si no es necesario.
> > Don't print me unless it's necessary.
> >
> > _______________________________________________
> > PyMOL-users mailing list
> > Archives: http://www.mail-archive.com/pym...@li...
> > Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>

-- 

"Este mensaje es privado y confidencial y se dirige exclusivamente a su 
destinatario. Si usted recibe este mensaje por error, no debe revelar, 
distribuir o copiar este e-mail. Por favor, comuníquelo al remitente y 
borre el mensaje y los archivos adjuntos de su sistema. No hay renuncia a 
la confidencialidad ni a ningún privilegio a causa de una transmisión 
errónea o por mal funcionamiento". 


"This message is private and 
confidential and it is intended exclusively for the addressee. If your 
receive this message by mistake, you should not disseminate, distribute or 
copy this e-mail. Please inform the sender and delete the message and 
attachments from your system. No confidentiality or any privilege regarding 
the information is waived or lost by any mistransmission or malfunction".



No me imprimas si no es necesario.Don't print me unless it's necessary.

[PyMOL] color by index

[Chen, Q. <qi...@pi...>]

Will spectrum just works for your purpose?

spectrum count, blue red, yourprotein, byres=1

you can switch off byres if you really want color by atom index.
 
Charles

> hello everyone!
>  I am trying to color an explicit distribution by color (say blue to red)
> pls help me with the command color by index

> On Jun 18, 2020, at 12:20 AM, pym...@li... wrote:
> 
> Send PyMOL-users mailing list submissions to
> 	pym...@li...
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> 	https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fpymol-users&data=02%7C01%7Cqic8%40pitt.edu%7Ce118586bf6ff40e8fb8508d8133ee536%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637280508154218214&sdata=wvtOxRB5m%2Bg7ASumbPcJ%2BB%2BtJzO92NpCWEvtHb7bxsI%3D&reserved=0
> or, via email, send a message with subject or body 'help' to
> 	pym...@li...
> 
> You can reach the person managing the list at
> 	pym...@li...
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of PyMOL-users digest..."
> 
> 
> Today's Topics:
> 
>   1. Re: Effect of different align method (Robert Campbell)
>   2. Color by index (Vertika Gautam)
>   3. help (Vertika Gautam)
>   4. help (Vertika Gautam)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Wed, 17 Jun 2020 16:49:52 -0400
> From: Robert Campbell <rob...@qu...>
> To: pym...@li...
> Subject: Re: [PyMOL] Effect of different align method
> Message-ID: <202...@ad...>
> Content-Type: text/plain; charset=UTF-8
> 
> Hello Sunyeping,
> 
> I would first point out that if you align on chain A of each molecule, then chain B of ASFV aligns with chain C of MTUB and vice versa.  In other words you don't have the same assignment of chain ids in your trimer.  The alignment of just alpha carbons of chain A with "align" gives an RMSD of 1.78 ? for 81 atoms and for "super" gives an RMSD of 1.746 ? for 81 atoms. That may be the best that you can do, but if you want to align the whole trimer than you need to rename chain B to chain C and chain C to chain B for one of your molecules.
> 
> You can do that renaming within PyMOL with these commands:
> 
> PyMOL>alter MTUB_trimer & c. B, chain="D"
> PyMOL>alter MTUB_trimer & c. C, chain="B"
> PyMOL>alter MTUB_trimer & c. D, chain="C"
> 
> (I'm just using "D" as an intermediate name here)
> 
> If you do that, then aligning all alpha carbons gives an RMSD of 2.189 ? for "align" and 1.845 ? for "super".
> 
> Cheers,
> Rob
> 
> On Wed, 2020-06-17 21:04  +0800,  sunyeping via PyMOL-users <pym...@li...> wrote:
> 
>> Hello Julien Capp?le,
>>   Thank you for your response. I didn't mean to keep the input file
>> in secrete. I have changed the access right to them, so you can
>> download them freely. Best, Yeping Sun
>> ------------------------------------------------------------------
>> From:Julien CAPPELE <jul...@un...>
>> Sent At:2020 Jun. 17 (Wed.) 17:05
>> To:??? <sun...@al...>
>> Subject:Re: [PyMOL] Effect of different align method
>> 
>> Hello Sunyeping,
>> 
>> I would suggest you to try TM-align, and a very good way to use it
>> for multi-protein alignment is to use their server mTM-align.
>> TM-align is a very robust alignment tool that will in most of the
>> case, give you a better structural based alignment with low to zero
>> input from the sequence.
>> https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fyanglab.nankai.edu.cn%2FmTM-align%2F&amp;data=02%7C01%7Cqic8%40pitt.edu%7Ce118586bf6ff40e8fb8508d8133ee536%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637280508154218214&amp;sdata=isejknGXC9BfuPHsGXhYBsux0pWwNIBGuiZntSyR2BY%3D&amp;reserved=0 
>> 
>> Also, if you are not working on secret stuff, you can give me access
>> so I can rework the output files from mTM-align server to give you a
>> RMSD-colored alignment in PyMOL.
>> 
>> On PyMOL only, I didn't try to implement TM-align because I use
>> Windows, but the developers said that a linux implementation could be
>> possible if you are a bit familiar with compiling softwares.
>> 
>> ---------------------------------------------
>> Julien Capp?le
>> Doctorant - 2?me ann?e - ED C2MP
>> Universit? de Lorraine
>> CRM? - UMR CNRS 7036
>> jul...@un...
>> Tel: (+33)6 99 18 59 03
>> ---------------------------------------------
>> 
>> Le mer. 17 juin 2020 ? 05:06, sunyeping via PyMOL-users
>> <pym...@li...> a ?crit : Dear pymol users,
>> 
>> I am trying to align two very similar trimeric molecules. I tried
>> different alignment commands including "align", "cealign" and
>> "super", but none of them gives satisfying effect. Athough the
>> backbone conformations and orientations of two two molecules look
>> very similar, there are obvious displacements between them after
>> alignment with these three commands. The rmsd of the two molecules
>> for these three methods are 2.250, 4.682, 2.206 and 2.206,
>> respectively. I wonder whether there is any better alignment command
>> or there are any parameters that can be passed to these three
>> alignment commands to improve the effects. Could you help me check
>> this? The pdb files of these two molecules, the image for the two
>> molecules after using "super" command, and the alignment effect in
>> the publication I mentioned can be found at the following link.
>> 
>> https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F1ff3XgTexgdul-SezUz75dVoCx2cL5YPL%2Fview%3Fusp%3Dsharing&amp;data=02%7C01%7Cqic8%40pitt.edu%7Ce118586bf6ff40e8fb8508d8133ee536%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637280508154218214&amp;sdata=dCFxgp3VTqywcrbc5b3ID4VcKcMMvOBKqqB2oXrwrTE%3D&amp;reserved=0
>> 
>> With many thanks.
>> 
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives:
>> https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fpymol-users%40lists.sourceforge.net&amp;data=02%7C01%7Cqic8%40pitt.edu%7Ce118586bf6ff40e8fb8508d8133ee536%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637280508154218214&amp;sdata=nldC9GskvF2yZFhsem7WE%2Fw5zp%2BYen9p0Rb8LBfrdEU%3D&amp;reserved=0
>> Unsubscribe:
>> https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fpymol%2Flists%2Fpymol-users%2Funsubscribe&amp;data=02%7C01%7Cqic8%40pitt.edu%7Ce118586bf6ff40e8fb8508d8133ee536%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637280508154218214&amp;sdata=%2Bx7ToQjAdGcCO%2BLYE538mCL8nA%2FDzrj%2FMIAejis7jYo%3D&amp;reserved=0
>> 
> 
> 
> 
> -- 
> Robert L. Campbell, Ph.D.
> Academic Advisor, BHSc Program
> Assistant Professor, Dept. of Biomedical & Molecular Sciences, 
> Queen's University, Kingston, ON K7L 3N6  Canada
> Botterell Hall Rm 644     Tel: 613-533-6821
> <rob...@qu...>  https://nam05.safelinks.protection.outlook.com/?url=http:%2F%2Fpldserver1.biochem.queensu.ca%2F~rlc&amp;data=02%7C01%7Cqic8%40pitt.edu%7Ce118586bf6ff40e8fb8508d8133ee536%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637280508154218214&amp;sdata=FDbdIfTMBWfhWcD6HBL3EDIlexLk84hM8qQwypQRu18%3D&amp;reserved=0
> 
> 
> 
> ------------------------------
> 
> Message: 2
> Date: Thu, 18 Jun 2020 12:05:06 +0800
> From: Vertika Gautam <var...@gm...>
> To: pym...@li...
> Subject: [PyMOL] Color by index
> Message-ID:
> 	<CAD...@ma...>
> Content-Type: text/plain; charset="utf-8"
> 
> hello everyone!
>  I am trying to color an explicit distribution by color (say blue to red)
> pls help me with the command color by index
> 
> 
> thanks!
> Vertika Gautam
> 
> Research Assistant
> Drug Design and Development Research Group (DDDRG)
> Department of Chemistry, Faculty of Science
> University of Malaya
> 
> 
> 
> *e-mail address: var...@gm...
> <var...@gm...>
> var...@ho... <var...@ho...>
>    01112294191*
> -------------- next part --------------
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> ------------------------------
> 
> Message: 3
> Date: Thu, 18 Jun 2020 12:08:45 +0800
> From: Vertika Gautam <var...@gm...>
> To: pym...@li...
> Subject: [PyMOL] help
> Message-ID:
> 	<CAD2fjZe=FPV...@ma...>
> Content-Type: text/plain; charset="utf-8"
> 
> hello everyone!
>  I am trying to color an explicit distribution by color (say blue to red)
> pls help me with the command color by index
> 
> 
> thanks!
> 
> -- 
> Vertika Gautam
> 
> Research Assistant
> Drug Design and Development Research Group (DDDRG)
> Department of Chemistry, Faculty of Science
> University of Malaya
> 
> 
> 
> *e-mail address: var...@gm...
> <var...@gm...>
> var...@ho... <var...@ho...>
>    01112294191*
> -------------- next part --------------
> An HTML attachment was scrubbed...
> 
> ------------------------------
> 
> Message: 4
> Date: Thu, 18 Jun 2020 12:19:15 +0800
> From: Vertika Gautam <var...@gm...>
> To: pym...@li...
> Subject: [PyMOL] help
> Message-ID:
> 	<CAD2fjZdt6x3E=JYQrcfwhddMYkGDkTqfEwyD9Kni=u6v...@ma...>
> Content-Type: text/plain; charset="utf-8"
> 
> Hello everyone
> 
> I am trying to make a figure showing the potential surface and binding
> pocket as shown in the attached figure. Can anyone help me with the
> commands?
> Thanks in advance for your help!
> [image: image.png]
> -- 
> Vertika Gautam
> 
> Research Assistant
> Drug Design and Development Research Group (DDDRG)
> Department of Chemistry, Faculty of Science
> University of Malaya
> 
> 
> 
> *e-mail address: var...@gm...
> <var...@gm...>
> var...@ho... <var...@ho...>
>    01112294191*
> -------------- next part --------------
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> 
> ------------------------------
> 
> 
> 
> ------------------------------
> 
> Subject: Digest Footer
> 
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
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> 
> ------------------------------
> 
> End of PyMOL-users Digest, Vol 169, Issue 32
> ********************************************

Re: [PyMOL] Install license file from CLI

[Thomas H. <tho...@sc...>]

Hi Antonio,

Did you install PyMOL into $HOME/anaconda3 ? If you installed into a different location, then that path to the license file will differ of course. Basically, path-to-pymol-dir/share/pymol/license.lic is the path.

Cheers,
  Thomas

> On Jun 17, 2020, at 2:15 PM, Antonio Serrano <ase...@uc...> wrote:
> 
> Hi:
> 
> I'm working with PyMol installed on a remote server, so I don't have access to the GUI. I already have an educational license. According to your FAQ at https://pymol.org/2/support.html?, the license file should be placed in $HOME/anaconda3/share/pymol/license.lic on a Linux computer. I already did it but PyMol isn't still activated. Any idea on how to completely install the license file using only the Command Line Interface? Many thx.
> 
> BR,
> Antonio Serrano
> 
> 
> "Este mensaje es privado y confidencial y se dirige exclusivamente a su destinatario. Si usted recibe este mensaje por error, no debe revelar, distribuir o copiar este e-mail. Por favor, comuníquelo al remitente y borre el mensaje y los archivos adjuntos de su sistema. No hay renuncia a la confidencialidad ni a ningún privilegio a causa de una transmisión errónea o por mal funcionamiento". 
> 
> "This message is private and confidential and it is intended exclusively for the addressee. If your receive this message by mistake, you should not disseminate, distribute or copy this e-mail. Please inform the sender and delete the message and attachments from your system. No confidentiality or any privilege regarding the information is waived or lost by any mistransmission or malfunction".
> 
> No me imprimas si no es necesario.
> Don't print me unless it's necessary.
> 
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

[PyMOL] help

[Vertika G. <var...@gm...>]

Hello everyone

I am trying to make a figure showing the potential surface and binding
pocket as shown in the attached figure. Can anyone help me with the
commands?
Thanks in advance for your help!
[image: image.png]
-- 
Vertika Gautam

Research Assistant
Drug Design and Development Research Group (DDDRG)
Department of Chemistry, Faculty of Science
University of Malaya



*e-mail address: var...@gm...
<var...@gm...>
var...@ho... <var...@ho...>
    01112294191*

[PyMOL] help

[Vertika G. <var...@gm...>]

hello everyone!
  I am trying to color an explicit distribution by color (say blue to red)
pls help me with the command color by index


thanks!

-- 
Vertika Gautam

Research Assistant
Drug Design and Development Research Group (DDDRG)
Department of Chemistry, Faculty of Science
University of Malaya



*e-mail address: var...@gm...
<var...@gm...>
var...@ho... <var...@ho...>
    01112294191*

[PyMOL] Color by index

[Vertika G. <var...@gm...>]

hello everyone!
  I am trying to color an explicit distribution by color (say blue to red)
pls help me with the command color by index


thanks!
Vertika Gautam

Research Assistant
Drug Design and Development Research Group (DDDRG)
Department of Chemistry, Faculty of Science
University of Malaya



*e-mail address: var...@gm...
<var...@gm...>
var...@ho... <var...@ho...>
    01112294191*

Re: [PyMOL] Effect of different align method

[Robert C. <rob...@qu...>]

Hello Sunyeping,

I would first point out that if you align on chain A of each molecule, then chain B of ASFV aligns with chain C of MTUB and vice versa.  In other words you don't have the same assignment of chain ids in your trimer.  The alignment of just alpha carbons of chain A with "align" gives an RMSD of 1.78 Å for 81 atoms and for "super" gives an RMSD of 1.746 Å for 81 atoms. That may be the best that you can do, but if you want to align the whole trimer than you need to rename chain B to chain C and chain C to chain B for one of your molecules.

You can do that renaming within PyMOL with these commands:

PyMOL>alter MTUB_trimer & c. B, chain="D"
PyMOL>alter MTUB_trimer & c. C, chain="B"
PyMOL>alter MTUB_trimer & c. D, chain="C"

(I'm just using "D" as an intermediate name here)

If you do that, then aligning all alpha carbons gives an RMSD of 2.189 Å for "align" and 1.845 Å for "super".

Cheers,
Rob

On Wed, 2020-06-17 21:04  +0800,  sunyeping via PyMOL-users <pym...@li...> wrote:

> Hello Julien Cappèle,
>    Thank you for your response. I didn't mean to keep the input file
> in secrete. I have changed the access right to them, so you can
> download them freely. Best, Yeping Sun
> ------------------------------------------------------------------
> From:Julien CAPPELE <jul...@un...>
> Sent At:2020 Jun. 17 (Wed.) 17:05
> To:孙业平 <sun...@al...>
> Subject:Re: [PyMOL] Effect of different align method
> 
> Hello Sunyeping,
> 
> I would suggest you to try TM-align, and a very good way to use it
> for multi-protein alignment is to use their server mTM-align.
> TM-align is a very robust alignment tool that will in most of the
> case, give you a better structural based alignment with low to zero
> input from the sequence.
> https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fyanglab.nankai.edu.cn%2FmTM-align%2F&amp;data=02%7C01%7Crobert.campbell%40queensu.ca%7C4e290e0f1c4044d3b1fc08d812bf8cca%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637279961201881850&amp;sdata=EOgyXD4A%2FemFaZHj6eRrx1h3nc%2BoCOHr94cFzpmIE3o%3D&amp;reserved=0 
> 
> Also, if you are not working on secret stuff, you can give me access
> so I can rework the output files from mTM-align server to give you a
> RMSD-colored alignment in PyMOL.
> 
> On PyMOL only, I didn't try to implement TM-align because I use
> Windows, but the developers said that a linux implementation could be
> possible if you are a bit familiar with compiling softwares.
> 
> ---------------------------------------------
> Julien Cappèle
> Doctorant - 2ème année - ED C2MP
> Université de Lorraine
> CRM² - UMR CNRS 7036
> jul...@un...
> Tel: (+33)6 99 18 59 03
> ---------------------------------------------
> 
> Le mer. 17 juin 2020 à 05:06, sunyeping via PyMOL-users
> <pym...@li...> a écrit : Dear pymol users,
> 
> I am trying to align two very similar trimeric molecules. I tried
> different alignment commands including "align", "cealign" and
> "super", but none of them gives satisfying effect. Athough the
> backbone conformations and orientations of two two molecules look
> very similar, there are obvious displacements between them after
> alignment with these three commands. The rmsd of the two molecules
> for these three methods are 2.250, 4.682, 2.206 and 2.206,
> respectively. I wonder whether there is any better alignment command
> or there are any parameters that can be passed to these three
> alignment commands to improve the effects. Could you help me check
> this? The pdb files of these two molecules, the image for the two
> molecules after using "super" command, and the alignment effect in
> the publication I mentioned can be found at the following link.
> 
> https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F1ff3XgTexgdul-SezUz75dVoCx2cL5YPL%2Fview%3Fusp%3Dsharing&amp;data=02%7C01%7Crobert.campbell%40queensu.ca%7C4e290e0f1c4044d3b1fc08d812bf8cca%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637279961201881850&amp;sdata=72dx0AyAPoHLvV4iXbEhmoGY18cXymzJRRWUqC7gdjE%3D&amp;reserved=0
> 
> With many thanks.
> 
> _______________________________________________
>  PyMOL-users mailing list
>  Archives:
> https://can01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fpymol-users%40lists.sourceforge.net&amp;data=02%7C01%7Crobert.campbell%40queensu.ca%7C4e290e0f1c4044d3b1fc08d812bf8cca%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637279961201881850&amp;sdata=PS%2BRq2rFtONyOjTtIS59OZnLnYEAG2spdQJXLzlpGzA%3D&amp;reserved=0
> Unsubscribe:
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> 



-- 
Robert L. Campbell, Ph.D.
Academic Advisor, BHSc Program
Assistant Professor, Dept. of Biomedical & Molecular Sciences, 
Queen's University, Kingston, ON K7L 3N6  Canada
Botterell Hall Rm 644     Tel: 613-533-6821
<rob...@qu...>  http://pldserver1.biochem.queensu.ca/~rlc

Re: [PyMOL] hydrogen bond list for a series of files

[Robert C. <rob...@qu...>]

Hi,

I would make one minor change to your script -- the command "run list_hb.py" needs to be run only once at the beginning of the script so:

# multiple_hb.py
from pymol import cmd
from glob import glob
cmd.do("run list_hb.py")

for file in glob("model.000.*.pdb"):
print(file)
#file_list = [f'{m:02d}'  for m in  list(range(0,30,1))]
cmd.load(file)
obj=cmd.get_object_list('all')
print(obj)
#chains=[('A','F'),('B', 'F'),('C','F'),('D','F'),('E','F')]
cmd.do("list_hb chain F, chain A:E,
write_distances_file=hb_"+str(obj[0])+".txt") cmd.delete("all”)

Cheers,
Rob

On Tue, 2020-06-16 20:23  +0000,  "Chen, Qiang" <qi...@pi...> wrote:

> This script will have a memory issue. My pymol will stuck if I have
> more than 3 files be processed. file_list = [f'{m:02d}'  for m in
> list(range(1,30,1))] [cmd.do("load
> model.000."+str(k)+"_minimized.pdb") for k in file_list]
> object_list=cmd.get_object_list('(model.000.*_minimized)')
> chains=[('A','F'),('B', 'F'),('C','F'),('D','F'),('E','F')] run
> C:\Users\user\AppData\Local\Programs\Python\Python38\lib\site-packages\pymol\pymol_path\Pymol-script-repo\list_hb.py
> [cmd.do("list_hb chain F, chain A:E,
> write_distances_file=hb_"+str(file)+".txt") for file in object_list ]
> 
> I modified from the sample script here
> 
> https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.pymolwiki.org%2Findex.php%2FProcess_All_Files_In_Directory&amp;data=02%7C01%7Crobert.campbell%40queensu.ca%7C5a300643d81e4d7ea3f608d812359b34%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637279368764004254&amp;sdata=p5tXmvSD1QCS%2BdIXyJv58rEBk9GCIRtl8BFSnamwoNs%3D&amp;reserved=0
> 
> Save the following lines in a file named as, eg. multiple_hb.py and
> make sure list_hb.py in the working directory of searching directory.
> 
> Then run multiple_hb.py in the pymol command line.
> 
> from pymol import cmd
> from glob import glob
> 
> for file in glob("model.000.*.pdb"):
> print(file)
> #file_list = [f'{m:02d}'  for m in  list(range(0,30,1))]
> cmd.load(file)
> obj=cmd.get_object_list('all')
> print(obj)
> #chains=[('A','F'),('B', 'F'),('C','F'),('D','F'),('E','F')]
> cmd.do("run list_hb.py")
> cmd.do("list_hb chain F, chain A:E,
> write_distances_file=hb_"+str(obj[0])+".txt") cmd.delete("all”)
> 
> 
> On Jun 16, 2020, at 11:15 AM,
> pym...@li...<mailto:pym...@li...>
> wrote:
> 
> Send PyMOL-users mailing list submissions to
> pym...@li...<mailto:pym...@li...>
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fpymol-users&amp;data=02%7C01%7Crobert.campbell%40queensu.ca%7C5a300643d81e4d7ea3f608d812359b34%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637279368764004254&amp;sdata=9UIjcsPwiUC9PmwQ4mcTi1%2F4%2BIGx9jQKarXsh7dfpGk%3D&amp;reserved=0
> or, via email, send a message with subject or body 'help' to
> pym...@li...
> 
> You can reach the person managing the list at
> pym...@li...
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of PyMOL-users digest..."
> 
> 
> Today's Topics:
> 
>   1. Re: hydrogen bond list for a series of files
>      (Mooers, Blaine H.M.  (HSC))
>   2. Re: hydrogen bond list for a series of files (Chen, Qiang)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Tue, 16 Jun 2020 14:51:38 +0000
> From: "Mooers, Blaine H.M.  (HSC)" <Bla...@ou...>
> To: "Chen, Qiang" <qi...@pi...>, "pym...@li..."
> <pym...@li...>
> Subject: Re: [PyMOL] hydrogen bond list for a series of files
> Message-ID:
> <87D...@CO...>
> Content-Type: text/plain; charset="Windows-1252"
> 
> Hi Charlie,
> 
> This will give the desired list.
> 
> file_list = [f'{m:02d}'  for m in  list(range(1,30,1))]
> print(file_list)
> 
> Best regards,
> 
> Blaine
> 
> Blaine Mooers, Ph.D.
> Associate Professor
> Department of Biochemistry and Molecular Biology
> College of Medicine
> University of Oklahoma Health Sciences Center
> S.L. Young Biomedical Research Center (BRC) Rm. 466
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
> 
> ________________________________________
> From: Chen, Qiang [qi...@pi...]
> Sent: Tuesday, June 16, 2020 9:26 AM
> To: Mooers, Blaine H.M.  (HSC); pym...@li...
> Subject: [EXTERNAL] Re: hydrogen bond list for a series of files
> 
> Hi, Blaine,
> 
> Then the question becomes how to generate a list with 30 or 300
> numbers.
> 
> Will this work?
> file_list=list(range(00, 30))
> 
> Thanks!
> 
> Charles
> 
> 
> ________________________________
> From: Mooers, Blaine H.M. (HSC) <Bla...@ou...>
> Sent: Tuesday, June 16, 2020 9:57 AM
> To: Chen, Qiang <qi...@pi...>; pym...@li...
> <pym...@li...> Subject: RE: hydrogen bond list
> for a series of files
> 
> Hi Charles,
> 
> You are right and I am wrong about the files needing to be loaded.
> 
> The object name has the pesky pdb file extension stripped off, so
> lets use the object name instead of using Python to strip it off for
> us. We no longer need to use glob. We do need to the create a list of
> strings that encode the indexing of the files. This code worked for
> me with two files. Adapt to your 30 or 300 files.
> 
> file_list = ['01','02']
> [cmd.do("load model.000."+str(k)+"_minimized.pdb") for k in file_list]
> object_list=cmd.get_object_list('(model.000.*_minimized)')
> chains=[('A','F'),('B', 'F'),('C','F'),('D','F'),('E','F')]
> run
> C:\Users\user\AppData\Local\Programs\Python\Python38\lib\site-packages\pymol\pymol_path\Pymol-script-repo\list_hb.py
> [cmd.do("list_hb chain F, chain A:E,
> write_distances_file=hb_"+str(file)+".txt") for file in object_list ]
> 
> 
> Best regards,
> 
> Blaine
> 
> Blaine Mooers, Ph.D.
> Associate Professor
> Department of Biochemistry and Molecular Biology
> College of Medicine
> University of Oklahoma Health Sciences Center
> S.L. Young Biomedical Research Center (BRC) Rm. 466
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
> 
> ________________________________________
> From: Chen, Qiang [qi...@pi...]
> Sent: Monday, June 15, 2020 10:18 PM
> To: Mooers, Blaine H.M.  (HSC); pym...@li...
> Subject: [EXTERNAL] Re: hydrogen bond list for a series of files
> 
> Thanks, Dr. Mooers.
> 
> I modified a little.
> 
> It seems the pdb files need be loaded.
> 
> I put all the following lines in a file multifile_hb.pml
> 
> run
> C:\Users\user\AppData\Local\Programs\Python\Python38\lib\site-packages\pymol\pymol_path\Pymol-script-repo\list_hb.py
> import glob load model.000.*_minimized.pdb
> #chains=[('A','F'),('B', 'F'),('C','F'),('D','F'),('E','F')]
> [cmd.do("list_hb chain F, chain A:E,
> write_distances_file=hb_"+str(file)+".txt") for file in
> glob.glob("model.000.??_minimized.pdb")]
> 
> A little not so perfect is that the output file,
> 
> hb_model.000.??_minimized.pdb.txt
> 
> Is is possible to do something like this
> write_distances_file=hb_"+basename(file)+".txt"
> 
> Then the output will be
> hb_model.000.??_minimized.txt
> 
> I tried, and this simple thing does not work.
> 
> Any suggestion?
> 
> Thanks!
> 
> Charles
> ________________________________
> From: Mooers, Blaine H.M. (HSC) <Bla...@ou...>
> Sent: Monday, June 15, 2020 9:44 PM
> To: Chen, Qiang <qi...@pi...>; pym...@li...
> <pym...@li...> Subject: RE: hydrogen bond list
> for a series of files
> 
> Hi Charles,
> 
> Make sure that PyMOL's present working directory is where the pdb
> files are stored. Copy and paste each of the four lines below one at
> a time on the command line in PyMOL.
> 
> 
> run
> list_hb.py<https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__list-5Fhb.py%26d%3DDwQF-g%26c%3DVjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY%26r%3Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks%26m%3DX2B3s7D21CBjGtOAQJ2noNR7vnKXPiHiT2eLIRiSC18%26s%3DKYQX_tOI8_HnmseLbJRMv7UTirG78evoaztp35Gg74E%26e%3D&amp;data=02%7C01%7Crobert.campbell%40queensu.ca%7C5a300643d81e4d7ea3f608d812359b34%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637279368764004254&amp;sdata=NvuLHnhUNs8SbnVriI5mzDDHt%2FTOAYkCszgvxCLf3%2BA%3D&amp;reserved=0<https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__nam05.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Furldefense.proofpoint.com-252Fv2-252Furl-253Fu-253Dhttp-2D3A-5F-5Flist-2D5Fhb.py-2526d-253DDwQF-2Dg-2526c-253DVjzId-2DSM5S6aVB-5FcCGQ0d3uo9UfKByQ3sI6Audoy6dY-2526r-253Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks-2526m-253DX2B3s7D21CBjGtOAQJ2noNR7vnKXPiHiT2eLIRiSC18-2526s-253DKYQX-5FtOI8-5FHnmseLbJRMv7UTirG78evoaztp35Gg74E-2526e-253D-26amp-3Bdata-3D02-257C01-257Cqic8-2540pitt.edu-257C2ea32a0b061443a37f1908d811fd40fd-257C9ef9f489e0a04eeb87cc3a526112fd0d-257C1-257C0-257C637279126707606574-26amp-3Bsdata-3D8VnRodmeEUrqQfFm7fe0gqd02cYPsKv8VxPcb09RIkQ-253D-26amp-3Breserved-3D0%26d%3DDwMF-g%26c%3DVjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY%26r%3Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks%26m%3DQ6LxvA7WaglxixxzDsbpjU7pbOFqJPXxmweHw0k_x7I%26s%3D6cyeevFFP1ip0quoSgRLS9fqrvVtj8JlnLJWMpJWqFg%26e%3D&amp;data=02%7C01%7Crobert.campbell%40queensu.ca%7C5a300643d81e4d7ea3f608d812359b34%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637279368764004254&amp;sdata=Wvtb4FDbK8ph8tIPtB3XZwSj8GR%2FaKTwqu%2FFxqwGsS8%3D&amp;reserved=0>>
> import glob chains = [('A','B'), ('A','C'), ('A','D'), ('A','E'),
> ('B','C'), ('B','D'), ('B','E'), ('C','D'), ('C','E'), ('D','E') ]
> [[cmd.do("list_hb chain "+ str(i) +", chain " +str(j) + ",
> write_distances_file=hb_"+ str(file) + "_" + str(i) + "_" +str( j) +
> "_001.txt") for i, j in chains] for file in glob.glob("model.??.pdb")]
> 
> Note that you do not have to load the pdb files into PyMOL.
> If you want to analyze more than 99 files and less than 999 files,
> add a third question mark to the argument of glob.glob().
> 
> Best regards,
> 
> Blaine
> 
> Blaine Mooers, Ph.D.
> Associate Professor
> Department of Biochemistry and Molecular Biology
> College of Medicine
> University of Oklahoma Health Sciences Center
> S.L. Young Biomedical Research Center (BRC) Rm. 466
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
> 
> ________________________________________
> From: Chen, Qiang [qi...@pi...]
> Sent: Monday, June 15, 2020 2:53 PM
> To: pym...@li...
> Subject: [EXTERNAL] [PyMOL] hydrogen bond list for a series of files
> 
> Hi, Pymol users
> 
> Could you help me do this in an efficient way?
> 
> Let me describe the task I try to do.
> 
> I have a series of numerically ordered files, say model00.pdb
> model.01.pdb ?? model.30.pdb
> 
> All the pdb have the same protein composition, chain A, B, C, D, and
> E. Their relative position is different in each file.
> 
> I would like to check the hydrogen bonds between, say, chain A and B.
> 
> Thanks to Prof. Robert L. Campbell, I can list the hydrogen bonds in
> one pdb and print the list as the follows
> 
> list_hb chain A, chain B, write_distances_file=hb_A_B_01.txt
> 
> How can I process the 30 files in an efficient way? what if I have
> 300 pdb files?
> 
> Shell script, python, or anything else?
> 
> 
> Thanks!
> Charles Chen
> 
> 
> 
> 
> _______________________________________________
> PyMOL-users mailing list
> Archives:
> https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net%26d%3DDwIGaQ%26c%3DVjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY%26r%3Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks%26m%3DxyAmhZRZYDjhbBLdiMRRk6wCJ14kA5UeQYC4urBFvQw%26s%3DaOpeSOw9Gqop8KF8Xf_lkPoBC_MSbb5i0cKlRaIAulI%26e%3D&amp;data=02%7C01%7Crobert.campbell%40queensu.ca%7C5a300643d81e4d7ea3f608d812359b34%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637279368764014248&amp;sdata=yZqQXrkiZ9xi%2Fq0wQYI02RrH2QfUStm2IhKPBTPLzcY%3D&amp;reserved=0<https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__nam05.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Furldefense.proofpoint.com-252Fv2-252Furl-253Fu-253Dhttp-2D3A-5F-5Fwww.mail-2D2Darchive.com-5Fpymol-2D2Dusers-2D40lists.sourceforge.net-2526d-253DDwIGaQ-2526c-253DVjzId-2DSM5S6aVB-5FcCGQ0d3uo9UfKByQ3sI6Audoy6dY-2526r-253Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks-2526m-253DxyAmhZRZYDjhbBLdiMRRk6wCJ14kA5UeQYC4urBFvQw-2526s-253DaOpeSOw9Gqop8KF8Xf-5FlkPoBC-5FMSbb5i0cKlRaIAulI-2526e-253D-26amp-3Bdata-3D02-257C01-257Cqic8-2540pitt.edu-257C01a30e93a2ca4a40b37308d81196d7ba-257C9ef9f489e0a04eeb87cc3a526112fd0d-257C1-257C0-257C637278686852886299-26amp-3Bsdata-3DH-252BbXZ7ylGnf8aHeqS8UfkWyeYYuKCLZv1GikWVh2gAM-253D-26amp-3Breserved-3D0%26d%3DDwMF-g%26c%3DVjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY%26r%3Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks%26m%3DX2B3s7D21CBjGtOAQJ2noNR7vnKXPiHiT2eLIRiSC18%26s%3DUml8pWJGL1VV1FRsRqY0A8xQ-ZVcOqvXJIUCvJgGjSY%26e%3D&amp;data=02%7C01%7Crobert.campbell%40queensu.ca%7C5a300643d81e4d7ea3f608d812359b34%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637279368764014248&amp;sdata=xtvWDb4Qm9z9PC21dmPn7%2BpLdpmHSKtRYyuGwA7yP3c%3D&amp;reserved=0>
> Unsubscribe:
> https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe%26d%3DDwIGaQ%26c%3DVjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY%26r%3Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks%26m%3DxyAmhZRZYDjhbBLdiMRRk6wCJ14kA5UeQYC4urBFvQw%26s%3DPY-g0XYMB9DqXC06Iixbjxfqf8jB9Pb_GFu8zClx3oY%26e%3D&amp;data=02%7C01%7Crobert.campbell%40queensu.ca%7C5a300643d81e4d7ea3f608d812359b34%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637279368764014248&amp;sdata=DPsvHWHcmU74LFh%2FTC1PJ5eURwVcW%2FGN%2BYE5Ip73QzU%3D&amp;reserved=0<https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__nam05.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Furldefense.proofpoint.com-252Fv2-252Furl-253Fu-253Dhttps-2D3A-5F-5Fsourceforge.net-5Fprojects-5Fpymol-5Flists-5Fpymol-2D2Dusers-5Funsubscribe-2526d-253DDwIGaQ-2526c-253DVjzId-2DSM5S6aVB-5FcCGQ0d3uo9UfKByQ3sI6Audoy6dY-2526r-253Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks-2526m-253DxyAmhZRZYDjhbBLdiMRRk6wCJ14kA5UeQYC4urBFvQw-2526s-253DPY-2Dg0XYMB9DqXC06Iixbjxfqf8jB9Pb-5FGFu8zClx3oY-2526e-253D-26amp-3Bdata-3D02-257C01-257Cqic8-2540pitt.edu-257C01a30e93a2ca4a40b37308d81196d7ba-257C9ef9f489e0a04eeb87cc3a526112fd0d-257C1-257C0-257C637278686852886299-26amp-3Bsdata-3Do1asKPIbwdAFwN-252FCJSTCXDg-252BndmmLXC8VJW8z48Y-252BAA-253D-26amp-3Breserved-3D0%26d%3DDwMF-g%26c%3DVjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY%26r%3Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks%26m%3DX2B3s7D21CBjGtOAQJ2noNR7vnKXPiHiT2eLIRiSC18%26s%3D52GYpWEgXcbl5EqO1gYdzX31C41KuEUPECZU1zDR_TU%26e%3D&amp;data=02%7C01%7Crobert.campbell%40queensu.ca%7C5a300643d81e4d7ea3f608d812359b34%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637279368764014248&amp;sdata=%2FwsE8dTQEIVGqA5dEK5Vxy1a9RycJ1MHZAZ4DjckGWA%3D&amp;reserved=0>
> 
> 
> 
> ------------------------------
> 
> Message: 2
> Date: Tue, 16 Jun 2020 15:15:11 +0000
> From: "Chen, Qiang" <qi...@pi...>
> To: "Mooers, Blaine H.M.  (HSC)" <Bla...@ou...>,
> "pym...@li..."
> <pym...@li...>
> Subject: Re: [PyMOL] hydrogen bond list for a series of files
> Message-ID:
> <BL0...@BL...>
> 
> Content-Type: text/plain; charset="windows-1252"
> 
> Great, thanks!
> 
> Really appreciate your help!
> 
> Charles
> ________________________________
> From: Mooers, Blaine H.M. (HSC) <Bla...@ou...>
> Sent: Tuesday, June 16, 2020 10:51 AM
> To: Chen, Qiang <qi...@pi...>; pym...@li...
> <pym...@li...> Subject: RE: hydrogen bond list
> for a series of files
> 
> Hi Charlie,
> 
> This will give the desired list.
> 
> file_list = [f'{m:02d}'  for m in  list(range(1,30,1))]
> print(file_list)
> 
> Best regards,
> 
> Blaine
> 
> Blaine Mooers, Ph.D.
> Associate Professor
> Department of Biochemistry and Molecular Biology
> College of Medicine
> University of Oklahoma Health Sciences Center
> S.L. Young Biomedical Research Center (BRC) Rm. 466
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
> 
> ________________________________________
> From: Chen, Qiang [qi...@pi...]
> Sent: Tuesday, June 16, 2020 9:26 AM
> To: Mooers, Blaine H.M.  (HSC); pym...@li...
> Subject: [EXTERNAL] Re: hydrogen bond list for a series of files
> 
> Hi, Blaine,
> 
> Then the question becomes how to generate a list with 30 or 300
> numbers.
> 
> Will this work?
> file_list=list(range(00, 30))
> 
> Thanks!
> 
> Charles
> 
> 
> ________________________________
> From: Mooers, Blaine H.M. (HSC) <Bla...@ou...>
> Sent: Tuesday, June 16, 2020 9:57 AM
> To: Chen, Qiang <qi...@pi...>; pym...@li...
> <pym...@li...> Subject: RE: hydrogen bond list
> for a series of files
> 
> Hi Charles,
> 
> You are right and I am wrong about the files needing to be loaded.
> 
> The object name has the pesky pdb file extension stripped off, so
> lets use the object name instead of using Python to strip it off for
> us. We no longer need to use glob. We do need to the create a list of
> strings that encode the indexing of the files. This code worked for
> me with two files. Adapt to your 30 or 300 files.
> 
> file_list = ['01','02']
> [cmd.do("load model.000."+str(k)+"_minimized.pdb") for k in file_list]
> object_list=cmd.get_object_list('(model.000.*_minimized)')
> chains=[('A','F'),('B', 'F'),('C','F'),('D','F'),('E','F')]
> run
> C:\Users\user\AppData\Local\Programs\Python\Python38\lib\site-packages\pymol\pymol_path\Pymol-script-repo\list_hb.py
> [cmd.do("list_hb chain F, chain A:E,
> write_distances_file=hb_"+str(file)+".txt") for file in object_list ]
> 
> 
> Best regards,
> 
> Blaine
> 
> Blaine Mooers, Ph.D.
> Associate Professor
> Department of Biochemistry and Molecular Biology
> College of Medicine
> University of Oklahoma Health Sciences Center
> S.L. Young Biomedical Research Center (BRC) Rm. 466
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
> 
> ________________________________________
> From: Chen, Qiang [qi...@pi...]
> Sent: Monday, June 15, 2020 10:18 PM
> To: Mooers, Blaine H.M.  (HSC); pym...@li...
> Subject: [EXTERNAL] Re: hydrogen bond list for a series of files
> 
> Thanks, Dr. Mooers.
> 
> I modified a little.
> 
> It seems the pdb files need be loaded.
> 
> I put all the following lines in a file multifile_hb.pml
> 
> run
> C:\Users\user\AppData\Local\Programs\Python\Python38\lib\site-packages\pymol\pymol_path\Pymol-script-repo\list_hb.py
> import glob load model.000.*_minimized.pdb
> #chains=[('A','F'),('B', 'F'),('C','F'),('D','F'),('E','F')]
> [cmd.do("list_hb chain F, chain A:E,
> write_distances_file=hb_"+str(file)+".txt") for file in
> glob.glob("model.000.??_minimized.pdb")]
> 
> A little not so perfect is that the output file,
> 
> hb_model.000.??_minimized.pdb.txt
> 
> Is is possible to do something like this
> write_distances_file=hb_"+basename(file)+".txt"
> 
> Then the output will be
> hb_model.000.??_minimized.txt
> 
> I tried, and this simple thing does not work.
> 
> Any suggestion?
> 
> Thanks!
> 
> Charles
> ________________________________
> From: Mooers, Blaine H.M. (HSC) <Bla...@ou...>
> Sent: Monday, June 15, 2020 9:44 PM
> To: Chen, Qiang <qi...@pi...>; pym...@li...
> <pym...@li...> Subject: RE: hydrogen bond list
> for a series of files
> 
> Hi Charles,
> 
> Make sure that PyMOL's present working directory is where the pdb
> files are stored. Copy and paste each of the four lines below one at
> a time on the command line in PyMOL.
> 
> 
> run
> list_hb.py<https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__list-5Fhb.py%26d%3DDwQF-g%26c%3DVjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY%26r%3Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks%26m%3DX2B3s7D21CBjGtOAQJ2noNR7vnKXPiHiT2eLIRiSC18%26s%3DKYQX_tOI8_HnmseLbJRMv7UTirG78evoaztp35Gg74E%26e%3D&amp;data=02%7C01%7Crobert.campbell%40queensu.ca%7C5a300643d81e4d7ea3f608d812359b34%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637279368764014248&amp;sdata=mRQt8S4QlPA4%2FO%2FNvifhW54IYOXxpnv1IFvOqPpOeIg%3D&amp;reserved=0<https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__nam05.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Furldefense.proofpoint.com-252Fv2-252Furl-253Fu-253Dhttp-2D3A-5F-5Flist-2D5Fhb.py-2526d-253DDwQF-2Dg-2526c-253DVjzId-2DSM5S6aVB-5FcCGQ0d3uo9UfKByQ3sI6Audoy6dY-2526r-253Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks-2526m-253DX2B3s7D21CBjGtOAQJ2noNR7vnKXPiHiT2eLIRiSC18-2526s-253DKYQX-5FtOI8-5FHnmseLbJRMv7UTirG78evoaztp35Gg74E-2526e-253D-26amp-3Bdata-3D02-257C01-257Cqic8-2540pitt.edu-257C2ea32a0b061443a37f1908d811fd40fd-257C9ef9f489e0a04eeb87cc3a526112fd0d-257C1-257C0-257C637279126707606574-26amp-3Bsdata-3D8VnRodmeEUrqQfFm7fe0gqd02cYPsKv8VxPcb09RIkQ-253D-26amp-3Breserved-3D0%26d%3DDwMF-g%26c%3DVjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY%26r%3Dk0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks%26m%3DQ6LxvA7WaglxixxzDsbpjU7pbOFqJPXxmweHw0k_x7I%26s%3D6cyeevFFP1ip0quoSgRLS9fqrvVtj8JlnLJWMpJWqFg%26e%3D&amp;data=02%7C01%7Crobert.campbell%40queensu.ca%7C5a300643d81e4d7ea3f608d812359b34%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637279368764024242&amp;sdata=xcUVp%2FkLfWCbq%2FWAF6rakqELuj4V9snyTM5Cxpl20yg%3D&amp;reserved=0>>
> import glob chains = [('A','B'), ('A','C'), ('A','D'), ('A','E'),
> ('B','C'), ('B','D'), ('B','E'), ('C','D'), ('C','E'), ('D','E') ]
> [[cmd.do("list_hb chain "+ str(i) +", chain " +str(j) + ",
> write_distances_file=hb_"+ str(file) + "_" + str(i) + "_" +str( j) +
> "_001.txt") for i, j in chains] for file in glob.glob("model.??.pdb")]
> 
> Note that you do not have to load the pdb files into PyMOL.
> If you want to analyze more than 99 files and less than 999 files,
> add a third question mark to the argument of glob.glob().
> 
> Best regards,
> 
> Blaine
> 
> Blaine Mooers, Ph.D.
> Associate Professor
> Department of Biochemistry and Molecular Biology
> College of Medicine
> University of Oklahoma Health Sciences Center
> S.L. Young Biomedical Research Center (BRC) Rm. 466
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
> 
> ________________________________________
> From: Chen, Qiang [qi...@pi...]
> Sent: Monday, June 15, 2020 2:53 PM
> To: pym...@li...
> Subject: [EXTERNAL] [PyMOL] hydrogen bond list for a series of files
> 
> Hi, Pymol users
> 
> Could you help me do this in an efficient way?
> 
> Let me describe the task I try to do.
> 
> I have a series of numerically ordered files, say model00.pdb
> model.01.pdb ?? model.30.pdb
> 
> All the pdb have the same protein composition, chain A, B, C, D, and
> E. Their relative position is different in each file.
> 
> I would like to check the hydrogen bonds between, say, chain A and B.
> 
> Thanks to Prof. Robert L. Campbell, I can list the hydrogen bonds in
> one pdb and print the list as the follows
> 
> list_hb chain A, chain B, write_distances_file=hb_A_B_01.txt
> 
> How can I process the 30 files in an efficient way? what if I have
> 300 pdb files?
> 
> Shell script, python, or anything else?
> 
> 
> Thanks!
> Charles Chen
> 
> 
> 
> 
> _______________________________________________
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-- 
Robert L. Campbell, Ph.D.
Academic Advisor, BHSc Program
Assistant Professor, Dept. of Biomedical & Molecular Sciences, 
Queen's University, Kingston, ON K7L 3N6  Canada
Botterell Hall Rm 644     Tel: 613-533-6821
<rob...@qu...>  http://pldserver1.biochem.queensu.ca/~rlc

[PyMOL] Write the number of molecules for each state in a file

[ABEL S. <Ste...@ce...>]

Hello PyMOLers

I have PDB file that contains different frames ( or state or models) extracted from a MD simulation and I would like to select the number the water near (say 3.5 Angstroms) a protein for each state and write the results in the file.

For instance like this where resid is a list of the water that satisfy the cut off below

Frame 0 : residX, residY, ...., 
Frame 1:  residZ, residY, ...., 

In the pml script I have selected the water molecules near the protein within the pymol commands below

### 

select GrA_Channel, (id 1-267+277-542) and name CA+C+O+N
select water_channel, resname SOL within 3.5 of GrA_Channel

f=open("toto.txt","w")

iterate_state 0, water_channel, state + ':' + water_channel ")   ## How to use this command

f.close()

but I do not know to use the iterate_state for each frame with above selected command

Can you help me ?

Thank you in advance

Stéphane

[PyMOL] Install license file from CLI

[Antonio S. <ase...@uc...>]

Hi:

I'm working with PyMol installed on a remote server, so I don't have access
to the GUI. I already have an educational license. According to your FAQ at
https://pymol.org/2/support.html?, the license file should be placed
in $HOME/anaconda3/share/pymol/license.lic
on a Linux computer. I already did it but PyMol isn't still activated. Any
idea on how to completely install the license file using only the Command
Line Interface? Many thx.

BR,
Antonio Serrano

-- 

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confidential and it is intended exclusively for the addressee. If your 
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No me imprimas si no es necesario.Don't print me unless it's necessary.

Re: [PyMOL] Effect of different align method

[sunyeping <sun...@al...>]

Hello Julien Cappèle,
   Thank you for your response. I didn't mean to keep the input file in secrete. I have changed the access right to them, so you can download them freely.
Best,
Yeping Sun
------------------------------------------------------------------
From:Julien CAPPELE <jul...@un...>
Sent At:2020 Jun. 17 (Wed.) 17:05
To:孙业平 <sun...@al...>
Subject:Re: [PyMOL] Effect of different align method

Hello Sunyeping,

I would suggest you to try TM-align, and a very good way to use it for multi-protein alignment is to use their server mTM-align. TM-align is a very robust alignment tool that will in most of the case, give you a better structural based alignment with low to zero input from the sequence. https://yanglab.nankai.edu.cn/mTM-align/ 

Also, if you are not working on secret stuff, you can give me access so I can rework the output files from mTM-align server to give you a RMSD-colored alignment in PyMOL.

On PyMOL only, I didn't try to implement TM-align because I use Windows, but the developers said that a linux implementation could be possible if you are a bit familiar with compiling softwares.

---------------------------------------------
Julien Cappèle
Doctorant - 2ème année - ED C2MP
Université de Lorraine
CRM² - UMR CNRS 7036
jul...@un...
Tel: (+33)6 99 18 59 03
---------------------------------------------

Le mer. 17 juin 2020 à 05:06, sunyeping via PyMOL-users <pym...@li...> a écrit :
Dear pymol users,

I am trying to align two very similar trimeric molecules. I tried different alignment commands including "align", "cealign" and "super", but none of them gives satisfying effect. Athough the backbone conformations and orientations of two two molecules look very similar, there are obvious displacements between them after alignment with these three commands. The rmsd of the two molecules for these three methods are 2.250, 4.682, 2.206 and 2.206, respectively. I wonder whether there is any better alignment command or there are any parameters that can be passed to these three alignment commands to improve the effects. Could you help me check this?
The pdb files of these two molecules, the image for the two molecules after using "super" command, and the alignment effect in the publication I mentioned can be found at the following link.

https://drive.google.com/file/d/1ff3XgTexgdul-SezUz75dVoCx2cL5YPL/view?usp=sharing

With many thanks.

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Re: [PyMOL] APBS plugin for Sugars

[Mario G. U. <ma...@cm...>]

Thank you so much for your quick answer!

Now I can access the file and I was wondering how to get amber data for specific molecules. I know that the GLYCAM parameters exist, but as far as I understand I can see only bond information. If, for alanine, the amber.dat file has the following:

ALA	N	-0.415700	1.8240	N
ALA	H	0.271900	0.6000	H
ALA	CA	0.033700	1.9080	CT
ALA	HA	0.082300	1.3870	H1
ALA	CB	-0.182500	1.9080	CT
ALA	HB1	0.060300	1.4870	HC
ALA	HB2	0.060300	1.4870	HC
ALA	HB3	0.060300	1.4870	HC
ALA	C	0.597300	1.9080	C
ALA	O	-0.567900	1.6612	O

I was wondering how I could get this info for SIA (Sialic Acid). Is there any library where I could get it in this format? Or maybe some tool to get them from pdb information (if feasible, I am brainstorming!)

Thanks again for your help and for your help in advance,

Mario

-----Original Message-----
From: Thomas Holder <tho...@sc...> 
Sent: Monday, June 15, 2020 9:37 AM
To: Mario Garcia Urena <ma...@cm...>
Cc: pym...@li...
Subject: Re: [PyMOL] APBS plugin for Sugars

Hi Mario,

Incentive PyMOL 2.x includes regular APBS and PDB2QPR. You should be able to manually edit the files there as well. For example with PyMOL 2.4.0 on Linux, the AMBER force field data files can be found like this:

$ find . -name "AMBER.*"
./lib/python3.7/site-packages/src/dat/AMBER.names
./lib/python3.7/site-packages/src/dat/AMBER.DAT


Hope that helps.

Cheers,
  Thomas


> On Jun 14, 2020, at 6:35 PM, Mario Garcia Urena <ma...@cm...> wrote:
> 
> Hi all,
>  
> I was trying to generate dipole moments with pymol using the APBS plugin. For proteins I adapted a code and the dipole moments are correct and work just fine, but for sugars it does not. I am well aware that the problem is that many of the residues are not present in the AMBER force field data (or the force field I want to use.) In APBS it is relatively easy to adapt and introduce the sugars’ information manually, however in the APBS plugin for pymol gets a little bit thorny. I cannot seem to find the files where I should store the sugar information. Has anybody done this before? Any alternatives with other programs or approaches are also welcome.
>  
> Thank you in advance,
>  
> Mario
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--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.