pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] Morphing question

[Istvan K. <iko...@gm...>]

Hi,

I have a homo trimer protein structure in two different conformations.
However, one conformation has different atom ordering and an additional
residue. This has never been a problem, though, since align does sequence
alignment, so I am not sure why morphing (Pymol 2.5) gives completely crazy
morphing frames with atoms all over the place. The only difference is that
this is a homo trimer as opposed to a single chain protein. Could a homo
trimer somehow confuse the morphing algorithm?

As an example, I attached 3 PDB files. A.pdb can be morphed to B.pdb
perfectly fine, but morphing A2.pdb (which is very similar to A.pdb) to
B.pdb gives the crazy results I mentioned.

Thank you for your kind assistance.

Best regards,

   Istvan

Re: [PyMOL] separate two molecule as an object from a complex of four molecules

[Norbert S. <st...@bb...>]

Dear Shreya,

one further possibility is to create a new object using the named chains:

reinitialize
fetch 6ous
create trimer1, chain A+C+E+B+D+F
disable 6ous

alternatively, you could delete all other chains:

reinitialize
fetch 6ous
remove not chain A+C+E+B+D+F

It is usually necessary (or at least preferable) to make yourself 
familiar with the PyMOL selection algebra and some basic commands to 
show selected residues.

Working only with the GUI, you could use:
Menu: Display, Sequence Mode, Chain Identifiers
Menu: Display, Sequence

Next you select the chains you want to show (CTRL or Strg and left mouse 
click)
Finally you use the command buttons next to the selection (sele): A, 
copy to object, new

Best,

Norbert

Am 03.08.2023 um 09:57 schrieb Saurabh Gayali:
> Have you tried this:
> https://pymolwiki.org/index.php/Split_object
>
> ------------------------------------------------------------------------
> *Saurabh Gayali*
> Business Analyst [Excelra], Former Research Scientist [IGIB]
> sau...@gm... / +91 8800412916
> Bangalore, India
>
>
> Mailtrack 
> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&> 
> 	Sender notified by
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> 	03/08/23, 01:27:34 pm 	
>
>
> On Thu, Aug 3, 2023 at 8:15 AM Mukhopadhyay, Shreya via PyMOL-users 
> <pym...@li...> wrote:
>
>     Public
>
>
>     Hello All,
>
>     I am trying to separate out two molecules(one copy for each of
>     RSVF F1 and F2) from one pdb (6OUS). It’s a trimeric protein bound
>     to a Fab.
>
>     I want to separate out RSVF1 and F2 proteins as one object from
>     the bound antibody, ie create one object with only chains A,C,E
>     and B,D,F. If you could explain the commands to use that will be
>     really helpful to me.
>
>     Thanks,
>
>     Shreya
>
>     Shreya Mukhopadhyay, PhD.(She/Her)
>     *Post Doc Fellow (Infectious Diseases and Vaccines-Discovery)*
>
>     770 Sumneytown Pike, West Point B46, 2048-C,  PA 19486
>
>     This e-mail message, together with any attachments,
>     contains information of Merck & Co., Inc. (126 East Lincoln Ave.,
>     P.O. Box 2000, Rahway, NJ USA 07065) and/or its affiliates, that
>     may be confidential, proprietary copyrighted and/or legally
>     privileged.   (Direct contact information for affiliates is
>     available at - Contact us - MSD
>     <https://www.msd.com/contact-us/>.)  It is intended solely for the
>     use of the individual or entity named on this message. If you
>     are not the intended recipient, and have received this message in
>     error, please notify us immediately by reply e-mail and then
>     delete it from your system.
>
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-- 
-----------------------------------------------------------------------------
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Univ.-Prof. Dr. rer. nat.
Center for Biotechnology and Biomedicine
Institute of Bioanalytical Chemistry
Faculty of Chemistry and Mineralogy
Leipzig University
Deutscher Platz 5
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Re: [PyMOL] separate two molecule as an object from a complex of four molecules

[Saurabh G. <sau...@gm...>]

Have you tried this:
https://pymolwiki.org/index.php/Split_object

------------------------------

*Saurabh Gayali*
Business Analyst [Excelra], Former Research Scientist [IGIB]
sau...@gm... / +91 8800412916
<http://example.com/>Bangalore, India


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03/08/23,
01:27:34 pm

On Thu, Aug 3, 2023 at 8:15 AM Mukhopadhyay, Shreya via PyMOL-users <
pym...@li...> wrote:

> Public
>
> Hello All,
>
>
>
> I am trying to separate out two molecules(one copy for each of RSVF F1 and
> F2) from one pdb (6OUS). It’s a trimeric protein bound to a Fab.
>
>
>
> I want to separate out RSVF1 and F2 proteins as one object from the bound
> antibody, ie create one object with only chains A,C,E and B,D,F. If you
> could explain the commands to use that will be really helpful to me.
>
>
>
> Thanks,
>
> Shreya
>
>
>
>
>
> Shreya Mukhopadhyay, PhD. (She/Her)
> *Post Doc Fellow (Infectious Diseases and Vaccines-Discovery)*
>
> 770 Sumneytown Pike, West Point B46, 2048-C,  PA 19486
>
>
>
>
>
> This e-mail message, together with any attachments, contains information
> of Merck & Co., Inc. (126 East Lincoln Ave., P.O. Box 2000, Rahway, NJ USA
> 07065) and/or its affiliates, that may be confidential, proprietary
> copyrighted and/or legally privileged.   (Direct contact information for
> affiliates is available at - Contact us - MSD
> <https://www.msd.com/contact-us/>.)  It is intended solely for the use of
> the individual or entity named on this message. If you are not the intended
> recipient, and have received this message in error, please notify us
> immediately by reply e-mail and then delete it from your system.
>
> _______________________________________________
> PyMOL-users mailing list
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> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>

[PyMOL] separate two molecule as an object from a complex of four molecules

[Mukhopadhyay, S. <shr...@me...>]

Public

Hello All,

I am trying to separate out two molecules(one copy for each of RSVF F1 and F2) from one pdb (6OUS). It's a trimeric protein bound to a Fab.

I want to separate out RSVF1 and F2 proteins as one object from the bound antibody, ie create one object with only chains A,C,E and B,D,F. If you could explain the commands to use that will be really helpful to me.

Thanks,
Shreya


Shreya Mukhopadhyay, PhD. (She/Her)
Post Doc Fellow (Infectious Diseases and Vaccines-Discovery)
770 Sumneytown Pike, West Point B46, 2048-C,  PA 19486

[cid:image001.png@01D9C55F.2D2C6730]

This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (126 East Lincoln Ave., P.O. Box 2000, Rahway, NJ USA 07065) and/or its affiliates, that may be confidential, proprietary copyrighted and/or legally privileged.   (Direct contact information for affiliates is available at - Contact us - MSD<https://www.msd.com/contact-us/>.)  It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.

Re: [PyMOL] Map to cartoon

[Jarrett J. <jar...@sc...>]

Hi Mark,

Great question. I currently cannot see a way to do so. I think the color
command when providing a ramp should, by intention, color the cartoon, but
there may be a bug or this might not have been implemented yet (the cartoon
removes its color and is set to white). I have a workaround if the only
thing you need to do is color atoms by proximity to another object (using
the example from the `ramp_new` PyMOLWiki documentation). Note that the
color smoothing is not as good as using the `ramp_new` command:

from pymol import cmd

def set_property_proximity_to(obj, target, ramp='red yellow', minimum=None,
maximum=None):
    ligand_atoms = []
    cmd.iterate_state(0, target, 'ligand_atoms.append((x, y, z))', space=
locals())

    def find_nearest_dist(x, y, z):
        min2 = min((x - x1) ** 2 + (y - y1) ** 2 + (z - z1) ** 2
                   for x1, y1, z1 in ligand_atoms)
        return min2 ** 0.5

    nearest_ds = []
    cmd.alter_state(0, obj, 'nearest_ds.append(find_nearest_dist(x, y, z))',
space=locals())

    # Hijack 'b' property for closest distance
    cmd.alter(obj, 'b = nearest_ds[index-1]', space=locals())
    cmd.spectrum('b', palette='red yellow', selection=obj, minimum=minimum,
maximum=maximum)


cmd.fetch('1rx1')
cmd.extract('ligand', 'organic')
set_property_proximity_to('1rx1', 'ligand', ramp='red yellow', minimum=4,
maximum=8)
cmd.color('blue', 'ligand')
cmd.show('surface', 'ligand')

I'll do some investigation regarding why ramp coloring for cartoons isn't
working as intended (assuming there isn't something I'm missing already).

Hope this helps,

Jarrett J

On Mon, Jul 24, 2023 at 1:27 PM Foster, Mark <fos...@os...> wrote:

> Thanks Jarrett for the response.
>
>
>
> I think `spectrum` should work, but I can’t figure out how to access the
> proximity parameter calculated by `ramp_new` in order to use it directly
> (e.g., “p.prox”), or to map it to the b factor.
>
>
>
> Does ramp_new store the values in an array?
>
>
>
> -M
>
>
>
>
>
> *From: *Jarrett Johnson <jar...@sc...>
> *Date: *Monday, July 24, 2023 at 12:02 PM
> *To: *Foster, Mark <fos...@os...>
> *Cc: *pym...@li... <pym...@li...
> >
> *Subject: *Re: [PyMOL] Map to cartoon
>
> Hi Mark, Does the `spectrum` command cover your use case? https:
> //pymolwiki. org/index. php/Spectrum . You can specify an atomic property
> and map specified colors to a range of the given property. Hope that helps,
> Jarrett J. On Mon, Jul 24, 2023
>
> Hi Mark,
>
> Does the `spectrum` command cover your use case?
> https://pymolwiki.org/index.php/Spectrum
> <https://urldefense.com/v3/__https:/pymolwiki.org/index.php/Spectrum__;!!KGKeukY!2YCpuhVe5GRqx_4jegX3LkI02R8BJqaQz4vDGwiaUTk4P0DKAA-uma5ffkB7b706ohBs7I5Alp7QFqei3X8edZnW_j-ow-ipqQ$>
> . You can specify an atomic property and map specified colors to a range of
> the given property.
>
> Hope that helps,
> Jarrett J.
>
>
>
> On Mon, Jul 24, 2023 at 9:21 AM Foster, Mark <fos...@os...> wrote:
>
> PyMOL fans,
>
>
>
> Is possible to use ramp_new to color cartoons, in addition to atoms and
> surfaces?
>
>
>
> I assume ramp_new stores the property to be mapped in a variable that
> could be used for the CA atom color.
>
>
>
> color prox, (sele) sets the color of each atom, but not the cartoon.
>
>
>
> Thanks in advance,
>
>
>
> -M
>
>
>
>
>
> —
>
> Mark P. Foster, Professor, he/him
> Department of Chemistry and Biochemistry
> The Ohio State University
> 734 Riffe Building
> 484 West 12th Ave.
> Columbus, OH 43210-1214
> (614) 292-1377
> fos...@os...
> http://go.osu.edu/fosterlab
>
> ------------------------------------------------------
>
> Acknowledgement: The land that The Ohio State University occupies is the
> ancestral and contemporary territory of the Shawnee, Potawatomi, Delaware,
> Miami, Peoria, Seneca, Wyandotte, Ojibwe and Cherokee peoples. The
> university resides on land ceded in the 1795 Treaty of Greeneville and
> appropriated through the Indian Removal Act of 1830. As a land grant
> institution, we wish to honor the resiliency of these tribal nations and
> recognize the historical context that has and continues to affect the
> Indigenous peoples of this land.
>
>
>
> _______________________________________________
> PyMOL-users mailing list
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> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
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>
>
>
>
> --
>
> *Jarrett Johnson* | Senior Developer, PyMOL
>
> [image: Image removed by sender.]
>
>
>


-- 

*Jarrett Johnson* | Senior Developer, PyMOL

Re: [PyMOL] Map to cartoon

[Jarrett J. <jar...@sc...>]

Hi Mark,

Does the `spectrum` command cover your use case?
https://pymolwiki.org/index.php/Spectrum . You can specify an atomic
property and map specified colors to a range of the given property.

Hope that helps,
Jarrett J.

On Mon, Jul 24, 2023 at 9:21 AM Foster, Mark <fos...@os...> wrote:

> PyMOL fans,
>
>
>
> Is possible to use ramp_new to color cartoons, in addition to atoms and
> surfaces?
>
>
>
> I assume ramp_new stores the property to be mapped in a variable that
> could be used for the CA atom color.
>
>
>
> color prox, (sele) sets the color of each atom, but not the cartoon.
>
>
>
> Thanks in advance,
>
>
>
> -M
>
>
>
>
>
> —
>
> Mark P. Foster, Professor, he/him
> Department of Chemistry and Biochemistry
> The Ohio State University
> 734 Riffe Building
> 484 West 12th Ave.
> Columbus, OH 43210-1214
> (614) 292-1377
> fos...@os...
> http://go.osu.edu/fosterlab
>
> ------------------------------------------------------
>
> Acknowledgement: The land that The Ohio State University occupies is the
> ancestral and contemporary territory of the Shawnee, Potawatomi, Delaware,
> Miami, Peoria, Seneca, Wyandotte, Ojibwe and Cherokee peoples. The
> university resides on land ceded in the 1795 Treaty of Greeneville and
> appropriated through the Indian Removal Act of 1830. As a land grant
> institution, we wish to honor the resiliency of these tribal nations and
> recognize the historical context that has and continues to affect the
> Indigenous peoples of this land.
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>


-- 

*Jarrett Johnson* | Senior Developer, PyMOL

[PyMOL] Map to cartoon

[Foster, M. <fos...@os...>]

PyMOL fans,

Is possible to use ramp_new to color cartoons, in addition to atoms and surfaces?

I assume ramp_new stores the property to be mapped in a variable that could be used for the CA atom color.

color prox, (sele) sets the color of each atom, but not the cartoon.

Thanks in advance,

-M


—
Mark P. Foster, Professor, he/him
Department of Chemistry and Biochemistry
The Ohio State University
734 Riffe Building
484 West 12th Ave.
Columbus, OH 43210-1214
(614) 292-1377
fos...@os...<mailto:fos...@os...>
http://go.osu.edu/fosterlab
------------------------------------------------------
Acknowledgement: The land that The Ohio State University occupies is the ancestral and contemporary territory of the Shawnee, Potawatomi, Delaware, Miami, Peoria, Seneca, Wyandotte, Ojibwe and Cherokee peoples. The university resides on land ceded in the 1795 Treaty of Greeneville and appropriated through the Indian Removal Act of 1830. As a land grant institution, we wish to honor the resiliency of these tribal nations and recognize the historical context that has and continues to affect the Indigenous peoples of this land.

Re: [PyMOL] Question on residue selection in multiple PDB

[Neena S. E. <nee...@gm...>]

Thank you so much Jarrett, yes it works very well!

On Thu, 20 Jul 2023 at 08:51, Jarrett Johnson <
jar...@sc...> wrote:

> Sorry, typo. For the second approach, state should be `i + 1` and not `-1`"
>
> Jarrett J.
>
> On Thu, Jul 20, 2023 at 8:49 AM Jarrett Johnson <
> jar...@sc...> wrote:
>
>> Hi Neena,
>>
>> Is the split_states necessary? You can query the distance between atoms
>> on the state-level as well without having to break up your structure.
>> Here's two approaches that show either way; I recommend the second if
>> possible. You'll of course have to switch out the selection string to fit
>> your own atom pairs.
>>
>> from pymol import cmd
>>
>> # Approach 1: With splitting states
>>
>> cmd.fetch('1L2Y')
>> cmd.split_states('1L2Y')
>> for i in range(cmd.count_states('1L2Y')):
>>     nmr_frame = f"1L2Y_{i + 1:04d}"
>>     sele1 = f"/{nmr_frame}/A/A/ILE`4/O"
>>     sele2 = f"/{nmr_frame}/A/A/ASP`9/CA"
>>     dist = cmd.dist(f"dist_{nmr_frame}", sele1, sele2)
>>     print(dist)
>>
>> print("--------------------")
>>
>> # Approach 2: Without splitting states
>>
>> for i in range(cmd.count_states('1L2Y')):
>>     sele1 = "/1L2Y/A/A/ILE`4/O"
>>     sele2 = "/1L2Y/A/A/ASP`9/CA"
>>     dist = cmd.get_distance(sele1, sele2, state=-1)
>>     print(dist)
>>
>>
>> Hope that helps,
>> Jarrett J
>>
>>
>> On Wed, Jul 19, 2023 at 9:48 PM Neena Susan Eappen <
>> nee...@gm...> wrote:
>>
>>> Hello PyMOL users,
>>>
>>> Can I get some insight on how to approach this analysis?
>>>
>>> Many thanks,
>>> Neena
>>>
>>> On Wed, 5 Jul 2023 at 18:54, Neena Susan Eappen <nee...@gm...>
>>> wrote:
>>>
>>>> Hello PyMOL Team,
>>>>
>>>> I am studying a protein called Trp-cage (PDB code: 1L2Y); this PDB has
>>>> 38 NMR structures deposited in it.
>>>> Using split_states command, I can see all 38 structures.
>>>> I want to find polar contacts between same 3 residues in all these 38
>>>> structures and extract corresponding distance values for polar contacts.
>>>>
>>>> Question: Is there a single command to select 3 residues in all these
>>>> 38 structures and find polar contacts within this selection?
>>>>
>>>> Many thanks,
>>>> Neena
>>>>
>>> _______________________________________________
>>> PyMOL-users mailing list
>>> Archives: http://www.mail-archive.com/pym...@li...
>>> Unsubscribe:
>>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>>
>>
>>
>> --
>>
>> *Jarrett Johnson* | Senior Developer, PyMOL
>>
>>
>
> --
>
> *Jarrett Johnson* | Senior Developer, PyMOL
>
>

Re: [PyMOL] Question on residue selection in multiple PDB

[Jarrett J. <jar...@sc...>]

Sorry, typo. For the second approach, state should be `i + 1` and not `-1`"

Jarrett J.

On Thu, Jul 20, 2023 at 8:49 AM Jarrett Johnson <
jar...@sc...> wrote:

> Hi Neena,
>
> Is the split_states necessary? You can query the distance between atoms on
> the state-level as well without having to break up your structure. Here's
> two approaches that show either way; I recommend the second if possible.
> You'll of course have to switch out the selection string to fit your own
> atom pairs.
>
> from pymol import cmd
>
> # Approach 1: With splitting states
>
> cmd.fetch('1L2Y')
> cmd.split_states('1L2Y')
> for i in range(cmd.count_states('1L2Y')):
>     nmr_frame = f"1L2Y_{i + 1:04d}"
>     sele1 = f"/{nmr_frame}/A/A/ILE`4/O"
>     sele2 = f"/{nmr_frame}/A/A/ASP`9/CA"
>     dist = cmd.dist(f"dist_{nmr_frame}", sele1, sele2)
>     print(dist)
>
> print("--------------------")
>
> # Approach 2: Without splitting states
>
> for i in range(cmd.count_states('1L2Y')):
>     sele1 = "/1L2Y/A/A/ILE`4/O"
>     sele2 = "/1L2Y/A/A/ASP`9/CA"
>     dist = cmd.get_distance(sele1, sele2, state=-1)
>     print(dist)
>
>
> Hope that helps,
> Jarrett J
>
>
> On Wed, Jul 19, 2023 at 9:48 PM Neena Susan Eappen <
> nee...@gm...> wrote:
>
>> Hello PyMOL users,
>>
>> Can I get some insight on how to approach this analysis?
>>
>> Many thanks,
>> Neena
>>
>> On Wed, 5 Jul 2023 at 18:54, Neena Susan Eappen <nee...@gm...>
>> wrote:
>>
>>> Hello PyMOL Team,
>>>
>>> I am studying a protein called Trp-cage (PDB code: 1L2Y); this PDB has
>>> 38 NMR structures deposited in it.
>>> Using split_states command, I can see all 38 structures.
>>> I want to find polar contacts between same 3 residues in all these 38
>>> structures and extract corresponding distance values for polar contacts.
>>>
>>> Question: Is there a single command to select 3 residues in all these 38
>>> structures and find polar contacts within this selection?
>>>
>>> Many thanks,
>>> Neena
>>>
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>
>
> --
>
> *Jarrett Johnson* | Senior Developer, PyMOL
>
>

-- 

*Jarrett Johnson* | Senior Developer, PyMOL

Re: [PyMOL] Question on residue selection in multiple PDB

[Jarrett J. <jar...@sc...>]

Hi Neena,

Is the split_states necessary? You can query the distance between atoms on
the state-level as well without having to break up your structure. Here's
two approaches that show either way; I recommend the second if possible.
You'll of course have to switch out the selection string to fit your own
atom pairs.

from pymol import cmd

# Approach 1: With splitting states

cmd.fetch('1L2Y')
cmd.split_states('1L2Y')
for i in range(cmd.count_states('1L2Y')):
    nmr_frame = f"1L2Y_{i + 1:04d}"
    sele1 = f"/{nmr_frame}/A/A/ILE`4/O"
    sele2 = f"/{nmr_frame}/A/A/ASP`9/CA"
    dist = cmd.dist(f"dist_{nmr_frame}", sele1, sele2)
    print(dist)

print("--------------------")

# Approach 2: Without splitting states

for i in range(cmd.count_states('1L2Y')):
    sele1 = "/1L2Y/A/A/ILE`4/O"
    sele2 = "/1L2Y/A/A/ASP`9/CA"
    dist = cmd.get_distance(sele1, sele2, state=-1)
    print(dist)


Hope that helps,
Jarrett J


On Wed, Jul 19, 2023 at 9:48 PM Neena Susan Eappen <nee...@gm...>
wrote:

> Hello PyMOL users,
>
> Can I get some insight on how to approach this analysis?
>
> Many thanks,
> Neena
>
> On Wed, 5 Jul 2023 at 18:54, Neena Susan Eappen <nee...@gm...>
> wrote:
>
>> Hello PyMOL Team,
>>
>> I am studying a protein called Trp-cage (PDB code: 1L2Y); this PDB has 38
>> NMR structures deposited in it.
>> Using split_states command, I can see all 38 structures.
>> I want to find polar contacts between same 3 residues in all these 38
>> structures and extract corresponding distance values for polar contacts.
>>
>> Question: Is there a single command to select 3 residues in all these 38
>> structures and find polar contacts within this selection?
>>
>> Many thanks,
>> Neena
>>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe



-- 

*Jarrett Johnson* | Senior Developer, PyMOL

Re: [PyMOL] Distance measure between pseudo atoms does not update over states

[Istvan K. <iko...@gm...>]

Hi Jarrett,

Thank you very much for the fix, it works perfectly.

Best regards,

   Istvan


On Wed, Jul 19, 2023 at 9:02 PM Jarrett Johnson <
jar...@sc...> wrote:

> Hi Istvan,
>
> I can reproduce the same issue. Seems to be some unintended behavior with
> how this multistate pseudoatom object is created. I've attached a modified
> center_of_mass.py script so that it should behave the way you expect. Let
> me know if this works for you.
>
> Example that I tried with this:
>
> fetch 1nmr
> run center_of_mass_states_joined.py
> com 1nmr, object=COM
> wizard distance
> # created distances between traj atom and pseudoatom
>
> Hope that helps,
> Jarrett J.
>
> On Tue, Jul 18, 2023 at 12:52 PM Istvan Kolossvary <iko...@gm...>
> wrote:
>
>> Hi,
>>
>> I have a simulation trajectory loaded in Pymol and I want to display
>> certain interatomic distances interactively. This works perfectly fine with
>> normal atoms, I can see how these selected distances change over the course
>> of the simulation using the wizard and playing the movie. However, it seems
>> that this feature doesn't work with pseudo atoms. I defined a couple of
>> center-of-mass pseudo atoms using this script
>> http://www.pymolwiki.org/index.php/center_of_mass. The script creates
>> separate objects corresponding to the different COMs and each COM object
>> has the same number of states as the trajectory object. I can use the
>> wizard, select the distances, which show on the display, but when I play
>> the movie, the distance values are not updated while the pseudo atoms do
>> move around. The first thing I figured was that maybe the COM objects
>> should be merged in a single object. So, I did that but to no avail, the
>> distances are not updated while I play the movie. I must be overlooking
>> something, can you tell me why this is not working?
>>
>> Thank you very much,
>>
>>    Istvan
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>
>
> --
>
> *Jarrett Johnson* | Senior Developer, PyMOL
>
>

Re: [PyMOL] Question on residue selection in multiple PDB

[Neena S. E. <nee...@gm...>]

Hello PyMOL users,

Can I get some insight on how to approach this analysis?

Many thanks,
Neena

On Wed, 5 Jul 2023 at 18:54, Neena Susan Eappen <nee...@gm...>
wrote:

> Hello PyMOL Team,
>
> I am studying a protein called Trp-cage (PDB code: 1L2Y); this PDB has 38
> NMR structures deposited in it.
> Using split_states command, I can see all 38 structures.
> I want to find polar contacts between same 3 residues in all these 38
> structures and extract corresponding distance values for polar contacts.
>
> Question: Is there a single command to select 3 residues in all these 38
> structures and find polar contacts within this selection?
>
> Many thanks,
> Neena
>

Re: [PyMOL] Distance measure between pseudo atoms does not update over states

[Jarrett J. <jar...@sc...>]

Hi Istvan,

I can reproduce the same issue. Seems to be some unintended behavior with
how this multistate pseudoatom object is created. I've attached a modified
center_of_mass.py script so that it should behave the way you expect. Let
me know if this works for you.

Example that I tried with this:

fetch 1nmr
run center_of_mass_states_joined.py
com 1nmr, object=COM
wizard distance
# created distances between traj atom and pseudoatom

Hope that helps,
Jarrett J.

On Tue, Jul 18, 2023 at 12:52 PM Istvan Kolossvary <iko...@gm...>
wrote:

> Hi,
>
> I have a simulation trajectory loaded in Pymol and I want to display
> certain interatomic distances interactively. This works perfectly fine with
> normal atoms, I can see how these selected distances change over the course
> of the simulation using the wizard and playing the movie. However, it seems
> that this feature doesn't work with pseudo atoms. I defined a couple of
> center-of-mass pseudo atoms using this script
> http://www.pymolwiki.org/index.php/center_of_mass. The script creates
> separate objects corresponding to the different COMs and each COM object
> has the same number of states as the trajectory object. I can use the
> wizard, select the distances, which show on the display, but when I play
> the movie, the distance values are not updated while the pseudo atoms do
> move around. The first thing I figured was that maybe the COM objects
> should be merged in a single object. So, I did that but to no avail, the
> distances are not updated while I play the movie. I must be overlooking
> something, can you tell me why this is not working?
>
> Thank you very much,
>
>    Istvan
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe



-- 

*Jarrett Johnson* | Senior Developer, PyMOL

[PyMOL] Distance measure between pseudo atoms does not update over states

[Istvan K. <iko...@gm...>]

Hi,

I have a simulation trajectory loaded in Pymol and I want to display
certain interatomic distances interactively. This works perfectly fine with
normal atoms, I can see how these selected distances change over the course
of the simulation using the wizard and playing the movie. However, it seems
that this feature doesn't work with pseudo atoms. I defined a couple of
center-of-mass pseudo atoms using this script
http://www.pymolwiki.org/index.php/center_of_mass. The script creates
separate objects corresponding to the different COMs and each COM object
has the same number of states as the trajectory object. I can use the
wizard, select the distances, which show on the display, but when I play
the movie, the distance values are not updated while the pseudo atoms do
move around. The first thing I figured was that maybe the COM objects
should be merged in a single object. So, I did that but to no avail, the
distances are not updated while I play the movie. I must be overlooking
something, can you tell me why this is not working?

Thank you very much,

   Istvan

[PyMOL] Question on residue selection in multiple PDB

[Neena S. E. <nee...@gm...>]

Hello PyMOL Team,

I am studying a protein called Trp-cage (PDB code: 1L2Y); this PDB has 38
NMR structures deposited in it.
Using split_states command, I can see all 38 structures.
I want to find polar contacts between same 3 residues in all these 38
structures and extract corresponding distance values for polar contacts.

Question: Is there a single command to select 3 residues in all these 38
structures and find polar contacts within this selection?

Many thanks,
Neena

[PyMOL] No email received

[Luke W. <lw...@ca...>]

Hello,

I have submitted the form to obtain an educational license for PyMOL (as I am a full-time student) but did not receive an email in response. Any help would be appreciated.

Best wishes,
Luke

Re: [PyMOL] Help with selecting interface residues between two structures

[Zhou, Y. <yin...@no...>]

Hi, Jarrett

This is more than helpful! I just need to fix my own mistake in the selection

cmd.select(base_interface, "byres((not (/base//H+L) & base) within 10 of /base//H+L)")

Maybe one more question:

Selection: “not (/base//H+L)” returns all residues in pred, as well as the P chain of base. I understand this.
However, why “not /base//H+L” returns an empty selection?

Thanks!

From: Jarrett Johnson <jar...@sc...>
Sent: Thursday, June 29, 2023 6:31 AM
To: Zhou, Yingyao <yin...@no...>
Cc: pym...@li...
Subject: Re: [PyMOL] Help with selecting interface residues between two structures


This Message is from an External Sender. Do not click links or open attachments unless you trust the sender.
Hi,

There might be a cleaner way to do this, but I propose creating a mapping of your chains from base to pred and use the `iterate` command to get the relevant identifiers and map them back to the prediction. Here is a full script that pulls from the PDB that attempts this idea.

from pymol
import cmd



# our reference

cmd.fetch('3hfm',
'base')

# dummy prediction

cmd.copy('pred',
'base')



# Heavy & Light chains in 3hfm are named L and H

# Antigen is Y so lets rename to A to simulate your case

cmd.alter('base & chain Y',
'chain="A"')



# change chain to emulate same residues different chain names

cmd.alter('pred & chain L',
'chain="A"')

cmd.alter('pred & chain H',
'chain="B"')

cmd.alter('pred & chain Y',
'chain="C"')



base_interface
= 'int_base'

cmd.select(base_interface,
'byres(base & (/base//H+L around 5))')



# After preparation:

# create a mapping of chains from base to pred

base_to_pred_chains
= {'L':
'A', 'H':
'B', 'A':
'C'}



# Create a list of identifiers in the interface from the selection

myspace
= {'int_set':
set()}

cmd.iterate(base_interface,
'int_set.add((chain, resi, resn))', space=myspace)



# Map them to a new selection onto the prediction

pred_interface
= 'int_pred'

cmd.select(pred_interface,
'none')

for
chain, resi,
resn in
myspace['int_set']:

    new_chain
= base_to_pred_chains[chain]

    # Add each pred residue to the selection

    cmd.select(pred_interface,

               f'pred & chain
{new_chain} & resi
{resi} & resn
{resn}',

               merge=1)


Hope that helps,
Jarrett J

On Thu, Jun 29, 2023 at 12:59 AM Zhou, Yingyao via PyMOL-users <pym...@li...<mailto:pym...@li...>> wrote:
I am a relatively new PyMOL user and would like to get some helps from the community.

I have two structures for the same antibody-antigen complex (with three chains: light chain L, heavy chain H, and an antigen chain A) .
Structure “base” is the experimental true structure, structure “pred” is the predicted structure. My goal is to determine how close the predicted interface is w.r.t. the experimental truth.

I first select the interface residues as defined by “base”

load base.pdb
load pred.pdb
select int_base, byres(base & (/base//H+L around 5))

How do I select the same corresponding residues in object “pred”?

In addition, what if in the pred structure, chains are named A, B, and C, corresponding to base structure L, H, A, respectively, how will I handle that?
(I was planning to rename the chains, if there is no nice trick to transfer the selections from base to pred)

Thanks!


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--

Jarrett Johnson | Senior Developer, PyMOL
[https://drive.google.com/uc?id=1zOlB9fluGZyuInRUQgKsdjtjpR5L9z6R&export=download]

Re: [PyMOL] Help with selecting interface residues between two structures

[Jarrett J. <jar...@sc...>]

Hi,

There might be a cleaner way to do this, but I propose creating a mapping
of your chains from base to pred and use the `iterate` command to get the
relevant identifiers and map them back to the prediction. Here is a full
script that pulls from the PDB that attempts this idea.

from pymol import cmd

# our reference
cmd.fetch('3hfm', 'base')
# dummy prediction
cmd.copy('pred', 'base')

# Heavy & Light chains in 3hfm are named L and H
# Antigen is Y so lets rename to A to simulate your case
cmd.alter('base & chain Y', 'chain="A"')

# change chain to emulate same residues different chain names
cmd.alter('pred & chain L', 'chain="A"')
cmd.alter('pred & chain H', 'chain="B"')
cmd.alter('pred & chain Y', 'chain="C"')

base_interface = 'int_base'
cmd.select(base_interface, 'byres(base & (/base//H+L around 5))')

# After preparation:
# create a mapping of chains from base to pred
base_to_pred_chains = {'L': 'A', 'H': 'B', 'A': 'C'}

# Create a list of identifiers in the interface from the selection
myspace = {'int_set': set()}
cmd.iterate(base_interface, 'int_set.add((chain, resi, resn))', space=
myspace)

# Map them to a new selection onto the prediction
pred_interface = 'int_pred'
cmd.select(pred_interface, 'none')
for chain, resi, resn in myspace['int_set']:
    new_chain = base_to_pred_chains[chain]
    # Add each pred residue to the selection
    cmd.select(pred_interface,
               f'pred & chain {new_chain} & resi {resi} & resn {resn}',
               merge=1)

Hope that helps,
Jarrett J

On Thu, Jun 29, 2023 at 12:59 AM Zhou, Yingyao via PyMOL-users <
pym...@li...> wrote:

> I am a relatively new PyMOL user and would like to get some helps from the
> community.
>
>
>
> I have two structures for the same antibody-antigen complex (with three
> chains: light chain L, heavy chain H, and an antigen chain A) .
>
> Structure “base” is the experimental true structure, structure “pred” is
> the predicted structure. My goal is to determine how close the predicted
> interface is w.r.t. the experimental truth.
>
>
>
> I first select the interface residues as defined by “base”
>
>
>
> load base.pdb
>
> load pred.pdb
>
> select int_base, byres(base & (/base//H+L around 5))
>
>
>
> How do I select the same corresponding residues in object “pred”?
>
>
>
> In addition, what if in the pred structure, chains are named A, B, and C,
> corresponding to base structure L, H, A, respectively, how will I handle
> that?
>
> (I was planning to rename the chains, if there is no nice trick to
> transfer the selections from base to pred)
>
>
>
> Thanks!
>
>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>


-- 

*Jarrett Johnson* | Senior Developer, PyMOL

[PyMOL] Help with selecting interface residues between two structures

[Zhou, Y. <yin...@no...>]

I am a relatively new PyMOL user and would like to get some helps from the community.

I have two structures for the same antibody-antigen complex (with three chains: light chain L, heavy chain H, and an antigen chain A) .
Structure "base" is the experimental true structure, structure "pred" is the predicted structure. My goal is to determine how close the predicted interface is w.r.t. the experimental truth.

I first select the interface residues as defined by "base"

load base.pdb
load pred.pdb
select int_base, byres(base & (/base//H+L around 5))

How do I select the same corresponding residues in object "pred"?

In addition, what if in the pred structure, chains are named A, B, and C, corresponding to base structure L, H, A, respectively, how will I handle that?
(I was planning to rename the chains, if there is no nice trick to transfer the selections from base to pred)

Thanks!

[PyMOL] hydrogen bond detection via the dist command and mode=2 option

[Norbert S. <st...@bb...>]

Dear PyMOL users and experts,

I wonder if anybody has insight into the following problem concerning 
the determination of hydrogen bonding interactions in PyMOL via the dist 
command with the mode=2 option. For an upcoming local PyMOL workshop, 
which I organize for PhD students, I tried to find a way to detect 
hydrogen bonding interactions of a ligand with its receptor within PyMOL.

This is described to some extent in
https://pymol.org/dokuwiki/doku.php?id=setting:h_bond
or
https://pymolwiki.org/index.php/Displaying_Biochemical_Properties#Hydrogen_bonds_and_Polar_Contacts

The documentation suggests that if resonable positions of the polar 
hydrogens are available, one can detect hydrogen bonds using distance 
and donor angle criteria. I added hydrogen bonds using Protoss of the 
ProteinPlus webserver to the structure 4eiy. However, when analyzing the 
environment of the ligand, I notice that many hydrogen bonds are 
detected quite fine, but there are many others, which are not displayed, 
although they have quite perfect geometry. Furthermore, for some 
hydrogen bonds, the heavy atoms are connected, in contrast to the 
settings (and the correct display of many other interactions).

If somebody wants to test, the pdb file is available here: 
https://research.uni-leipzig.de/straeter/pymol/data/4eiy_protoss.pdb

and these are the commands:

load 4eiy_protoss.pdb
hide all
zoom resn ZMA
clip slab, 8
show sticks
dist hbonds, all, all, mode=2

For example, for water molecules 2522 or 2527 in the vicinity of the 
ligand, the non-hydrogen atoms are connected by the H-bond. Waters 2584, 
2514 and Tyr-9 OH are well set for a hydrogen bonding interaction, but 
this is not detected.

I wonder, what the cause of these apparent inconsistencies might be. Is 
it the algorithm or the detection of the donor/acceptor functionalities?

If the hydrogens are deleted before the running the dist command, these 
hydrogen bonds are shown, but also others which are only very weak based 
on the deviations from donor angle linearity.

Best regards,

Norbert

Re: [PyMOL] Edu-PyMOL for master thesis

[Jarrett J. <jar...@sc...>]

Hello,

Using PyMOL's figures for the purpose of fulfilling academic requirements
such as a thesis or a dissertation is permissible.

Best,
Jarrett J.

On Wed, Jun 14, 2023 at 10:59 AM deniz tunalıer <den...@gm...>
wrote:

> Hi PyMOL users,
>
> I'm using Edu-PyMOL and I'm wondering if I can use figures that I created
> with it in my master's thesis? Or do I need to buy a license? Thanks in
> advance. Looking forward to your response.
>
> Best wishes,
> Deniz
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe



-- 

*Jarrett Johnson* | Senior Developer, PyMOL

[PyMOL] Need Download Credentials for Educational PyMOL

[Mr. P. T. <par...@cg...>]

Hi PyMOL Support Team

I'm having trouble getting the download credentials for the PyMOL educational version. I completed the registration process on 20/06/23 and verified my educational status, but haven't received any email with the credentials or instructions. Can you please assist me with this issue?

Thanks, Parinya

[PyMOL] Custom Functions are blocking

[Simon D. <ha...@si...>]

I am currently working on a plugin for PyMol that should continuously add
new structures to the PyMol view while the function is running.

This is some demo code:
import time
from pymol import cmd

@cmd.extend
def custom_function(inp):
    for i in range(len(inp)):
        time.sleep(2)
        print(i) # here we would load the structures

However, this doesn't work. It prints in the system console just in time
but not in the Pymol console (and if I call e.g cmd.load("somepdb") also
the structure doesn't get added to the view) until the function has
completed running.

Is there a way around this ?

Thanks,
Simon

*Simon Dürr*
in...@si...
https://simonduerr.eu

[PyMOL] You're invited to Educator's Week 2023

[Teaching w. S. <tea...@sc...>]

Hi,

The Schrödinger Education team is hosting a free event from June 13-16th
called Educator's Week 2023 <https://events.bizzabo.com/467368>, connecting
educators from all over the world to discuss the growing role of
educational technology in the classroom and integrating computational
molecular modeling into modern science curricula.

*June 13-15, 2023*
11:00 AM to 2:00 PM ET
Virtual conference with live presentations

*Register for the free event. <https://events.bizzabo.com/467368>*

We're very excited that* Noeris Salam from Schrödinger *will be giving a
virtual talk today, June 14th, on *PyMOL 3.0 Beta* and will discuss the new
movie-making features. We'll also be hosting several teachers and
professors who will highlight how PyMOL and molecular modeling are
revolutionizing elementary school science, among other chemistry and
biology teachers and college-level professors.

Hope to see you there!

Best,

Schrödinger Education Team | Teaching

[PyMOL] Edu-PyMOL for master thesis

[deniz t. <den...@gm...>]

Hi PyMOL users,

I'm using Edu-PyMOL and I'm wondering if I can use figures that I created
with it in my master's thesis? Or do I need to buy a license? Thanks in
advance. Looking forward to your response.

Best wishes,
Deniz