pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] Blur text

[Yijie L. <yij...@br...>]

Hi!

I found all the text in PyMol interface became blur, could you help me to figure it out?

It happens after I set the GPU from the integrated video card to the external video card.

Thanks!

[cid:ec1ee628-a6d0-4b8c-90d7-8025edc0f138]

[PyMOL] Loading chempy objects into PyMOL 2.4.0

[R M. <rau...@us...>]

Dear all,

I am trying to implement a reader for a trajectory format.
I use cmd.get_model to get the "reference" structure, and then iterate over
the trajectory frames, everytime replacing the coordinates of my model with
the ones from the trajectory, and then loading the modified model back into
PyMOL with cmd.load_model, changing the state every time.

The issue is, I can't get the sequence view to work correctly (i.e. to
display the one-letter code of each residue). This happens even if I don't
modify the coordinates at all, like here:

#This doesn't display the sequence
for i in range(9):
   m=cmd.get_model("sele")
   cmd.load_model(m,"sele2",state=i+1)

On the other hand, if I load only one state for the object, the sequence is
displayed correctly:

#this DOES display the sequence
for i in range(1):
   m=cmd.get_model("sele")
   cmd.load_model(m,"sele2",state=i+1)



I have tried with the Wiki help and even looking at the cmd code, but I
can't find any way of getting this to work. The options for load_model, for
instance, have no effect. What I _can_ do is to use:

cmd.set("seq_view_discrete_by_state",0)

Which will show the sequence correctly (apparently, the first state always
gets the sequence, the others don't).  It is not a good solution, though,
as you can't use that sequence to select residues (it will only select them
on the first state, _and_ it will take you back to that state).

Is this possible at all to do? Is it an issue with my PyMOL version? (I am
using PyMOL on Fedora [Linux], and it i the version from the Fedora 32
repositories, by the way, although I don't think I am doing anything
OS-dependent).

Thanks!

Raul


-- 

Prof. Dr. Raúl Mera Adasme

Facultad de Química y Biología ,
Universidad de Santiago de Chile (USACH).

Re: [PyMOL] Complement or Inverse Selection in Pymol

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

Hi Gret,

No worries,

In regards to the selection: “resi 25 and object”

Its more so to ensure that you don’t accidently select “resi 25” from multiple chains or objects

Like if you load two pdb files into PyMOL (say obj01 and obj02) and both have a resi 25, then resi 25 from both objects will be selected if you don’t include the object in the selection.

On the other hand, If you:

select chA, resi 25 and obj01

Then the chA selection will only contain resi 25 from obj01 and ignore obj02.

Its more of a note about selections that you might already be familiar with

Cheers,

Ali

From: Gert Kruger <KR...@uk...>
Date: Saturday, 27 November 2021 at 5:05 pm
To: Ali Saad Kusay <aku...@un...>
Cc: "pym...@li..." <pym...@li...>
Subject: Re: [PyMOL] Complement or Inverse Selection in Pymol

Dear Ali,

Many thanks for your kind and very helpfull reply!  One question:

You wrote:  "Doing something like resi 25 and object is safer".

Do you mean: select chA, resi 25

And will that reflect as follows in my requirement:

select other_waters, br. (resn WAT beyond 5 of chA, resi 25)

Best wishes
Gert Kruger

On Fri, 2021-11-26 at 15:09 +0000, Ali Saad Kusay wrote:
Hi Gert,

These selection commands will generate a selection object called "other_waters "

See https://pymolwiki.org/index.php/Selection_Algebra<https://protect-au.mimecast.com/s/h0hkCQnMBZfkPgpznSPf8vp?domain=protect-za.mimecast.com>

You can do:
select other_waters, br. (resn WAT and not sele) # after you make the selection in your email
or
select other_waters, br. (resn WAT beyond 5 of resi 25)

A few notes:
1) you need to select by residue otherwise your selection will yield incomplete water molecules i.e. waters with 1-2 atoms in the selection as opposed to all 3 atoms. To do this use "br."
2) Be careful of selections like resi 25 since if you have multiple chains or objects with "resi 25", all will be included in the selection. Doing something like resi 25 and object is safer, object is the name in the object list in PyMOL

To remove the unwanted water atoms, do:

remove other_waters

Cheers,

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

On 27/11/21, 1:57 am, "Gert Kruger" <KR...@uk...> wrote:

Dear All,

Apologies for my ignorance. I need to know which solvent molecules are
in the active site of an enzyme (HIV-PR). I use "tleap" in Amber to
create a solvent waterbox in and around the enzyme.

I found the following command that seems to find the Water molecules in
the active site:

> sele resn WAT within 5 sele resi 25

(ASP25 is in the active site).

Now I want to remove ALL other water/solvent molecules (those that are
not selected).

Is there a method to achieve a complement or inverse selection (to
hightlight ALL other watermolecules that are not currently selected?)

I am able save the selection, but that is a bit more tedious.

Question: Is there an easy way in Pymol to achieve a "complement" or
"inverse" selection of waters in a solvent box?
Thanks alot and best wishes
Gert Kruger

UKZN email disclaimer:
The contents of this e-mail may contain personal information, and/or privileged information, and/or confidential information. The information contained herein is therefore only meant for consumption by the recipient mentioned and for the purpose as specified in the body of the e-mail. Should you receive this e-mail in error kindly inform the sender of such by responding to the sender via a response e-mail and thereafter please delete the original e-mail received as well as the response e-mail. The University of KwaZulu-Natal e-mail platform is meant for business purposes (of the University) only and the University therefore does not accept any liability whatsoever that may arise from instances where such platform is utilised for personal reasons. Any views or opinions expressed in this e-mail represent those of the author and may not necessarily be binding on the University. The author of the e-mail may also not bind the University in any manner that may be construed from the contents of the e-mail unless such sender has been granted the requisite authority to do so by the University.

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Re: [PyMOL] Complement or Inverse Selection in Pymol

[Gert K. <KR...@uk...>]

Dear Ali,

Many thanks for your kind and very helpfull reply!  One question:

You wrote:  "Doing something like resi 25 and object is safer".

Do you mean: select chA, resi 25

And will that reflect as follows in my requirement:

select other_waters, br. (resn WAT beyond 5 of chA, resi 25)

Best wishes
Gert Kruger

On Fri, 2021-11-26 at 15:09 +0000, Ali Saad Kusay wrote:
Hi Gert,

These selection commands will generate a selection object called "other_waters "

See https://pymolwiki.org/index.php/Selection_Algebra<https://protect-za.mimecast.com/s/zlwlCX6Vp3CG2Y35ukvxhi?domain=pymolwiki.org>

You can do:
select other_waters, br. (resn WAT and not sele) # after you make the selection in your email
or
select other_waters, br. (resn WAT beyond 5 of resi 25)

A few notes:
1) you need to select by residue otherwise your selection will yield incomplete water molecules i.e. waters with 1-2 atoms in the selection as opposed to all 3 atoms. To do this use "br."
2) Be careful of selections like resi 25 since if you have multiple chains or objects with "resi 25", all will be included in the selection. Doing something like resi 25 and object is safer, object is the name in the object list in PyMOL

To remove the unwanted water atoms, do:

remove other_waters

Cheers,

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

On 27/11/21, 1:57 am, "Gert Kruger" <KR...@uk...> wrote:

Dear All,

Apologies for my ignorance. I need to know which solvent molecules are
in the active site of an enzyme (HIV-PR). I use "tleap" in Amber to
create a solvent waterbox in and around the enzyme.

I found the following command that seems to find the Water molecules in
the active site:

> sele resn WAT within 5 sele resi 25

(ASP25 is in the active site).

Now I want to remove ALL other water/solvent molecules (those that are
not selected).

Is there a method to achieve a complement or inverse selection (to
hightlight ALL other watermolecules that are not currently selected?)

I am able save the selection, but that is a bit more tedious.

Question: Is there an easy way in Pymol to achieve a "complement" or
"inverse" selection of waters in a solvent box?
Thanks alot and best wishes
Gert Kruger

UKZN email disclaimer:
The contents of this e-mail may contain personal information, and/or privileged information, and/or confidential information. The information contained herein is therefore only meant for consumption by the recipient mentioned and for the purpose as specified in the body of the e-mail. Should you receive this e-mail in error kindly inform the sender of such by responding to the sender via a response e-mail and thereafter please delete the original e-mail received as well as the response e-mail. The University of KwaZulu-Natal e-mail platform is meant for business purposes (of the University) only and the University therefore does not accept any liability whatsoever that may arise from instances where such platform is utilised for personal reasons. Any views or opinions expressed in this e-mail represent those of the author and may not necessarily be binding on the University. The author of the e-mail may also not bind the University in any manner that may be construed from the contents of the e-mail unless such sender has been granted the requisite authority to do so by the University.

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Re: [PyMOL] Complement or Inverse Selection in Pymol

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

Hi Gert, 

These selection commands will generate a selection object called "other_waters "

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

You can do:
select other_waters, br. (resn WAT and not sele) # after you make the selection in your email
or
select other_waters, br. (resn WAT beyond 5 of resi 25)

A few notes:
1) you need to select by residue otherwise your selection will yield incomplete water molecules i.e. waters with 1-2 atoms in the selection as opposed to all 3 atoms. To do this use "br."
2) Be careful of selections like resi 25 since if you have multiple chains or objects with "resi 25", all will be included in the selection. Doing something like resi 25 and object is safer, object is the name in the object list in PyMOL

To remove the unwanted water atoms, do:

remove other_waters

Cheers, 

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

On 27/11/21, 1:57 am, "Gert Kruger" <KR...@uk...> wrote:

    Dear All,

    Apologies for my ignorance.  I need to know which solvent molecules are
    in the active site of an enzyme (HIV-PR).  I use "tleap" in Amber to
    create a solvent waterbox in and around the enzyme.

    I found the following command that seems to find the Water molecules in
    the active site:

    > sele resn WAT within 5 sele resi 25

    (ASP25 is in the active site).

    Now I want to remove ALL other water/solvent molecules (those that are
    not selected).

    Is there a method to achieve a complement or inverse selection (to
    hightlight ALL other watermolecules that are not currently selected?)

    I am able save the selection, but that is a bit more tedious.

    Question:  Is there an easy way in Pymol to achieve a "complement" or
    "inverse" selection of waters in a solvent box?
    Thanks alot and best wishes
    Gert Kruger

    UKZN email disclaimer:
    The contents of this e-mail may contain personal information, and/or privileged information, and/or confidential information. The information contained herein is therefore only meant for consumption by the recipient mentioned and for the purpose as specified in the body of the e-mail. Should you receive this e-mail in error kindly inform the sender of such by responding to the sender via a response e-mail and thereafter please delete the original e-mail received as well as the response e-mail. The University of KwaZulu-Natal e-mail platform is meant for business purposes (of the University) only and the University therefore does not accept any liability whatsoever that may arise from instances where such platform is utilised for personal reasons. Any views or opinions expressed in this e-mail represent those of the author and may not necessarily be binding on the University. The author of the e-mail may also not bind the University in any manner that may be construed from the contents of the e-mail unless such sender has been granted the requisite authority to do so by the University.

    _______________________________________________
    PyMOL-users mailing list
    Archives: https://protect-au.mimecast.com/s/G7JzCXLW2mUXKGn89c6nIX_?domain=mail-archive.com
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[PyMOL] Complement or Inverse Selection in Pymol

[Gert K. <KR...@uk...>]

Dear All,

Apologies for my ignorance.  I need to know which solvent molecules are
in the active site of an enzyme (HIV-PR).  I use "tleap" in Amber to
create a solvent waterbox in and around the enzyme.

I found the following command that seems to find the Water molecules in
the active site:

> sele resn WAT within 5 sele resi 25

(ASP25 is in the active site).

Now I want to remove ALL other water/solvent molecules (those that are
not selected).

Is there a method to achieve a complement or inverse selection (to
hightlight ALL other watermolecules that are not currently selected?)

I am able save the selection, but that is a bit more tedious.

Question:  Is there an easy way in Pymol to achieve a "complement" or
"inverse" selection of waters in a solvent box?
Thanks alot and best wishes
Gert Kruger

UKZN email disclaimer:
The contents of this e-mail may contain personal information, and/or privileged information, and/or confidential information. The information contained herein is therefore only meant for consumption by the recipient mentioned and for the purpose as specified in the body of the e-mail. Should you receive this e-mail in error kindly inform the sender of such by responding to the sender via a response e-mail and thereafter please delete the original e-mail received as well as the response e-mail. The University of KwaZulu-Natal e-mail platform is meant for business purposes (of the University) only and the University therefore does not accept any liability whatsoever that may arise from instances where such platform is utilised for personal reasons. Any views or opinions expressed in this e-mail represent those of the author and may not necessarily be binding on the University. The author of the e-mail may also not bind the University in any manner that may be construed from the contents of the e-mail unless such sender has been granted the requisite authority to do so by the University.

Re: [PyMOL] fusing structures

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

Have you tried superimposing the loop (or the main chain of the terminal fragments? You could then export the moved loop and edit the pdb

J

From: zeinab masoomi <zei...@gm...>
Sent: Monday, 22 November 2021 9:52 PM
To: pym...@li...
Subject: [PyMOL] fusing structures

Hi
I want to fuse a modeled loop into a protein structure, is this possible? how can I merge two structures into one file to put them close enough and fuse them?
structures are attached below
thank you.

[PyMOL] fusing structures

[zeinab m. <zei...@gm...>]

Hi
I want to fuse a modeled loop into a protein structure, is this possible?
how can I merge two structures into one file to put them close enough and
fuse them?
structures are attached below
thank you.

[PyMOL] fusing structures

[zeinab m. <zei...@gm...>]

Hi
I want to fuse a modeled loop into a protein structure, is this possible?
how can I merge two structures into one file to put them close enough and
fuse them?
thank you.

Re: [PyMOL] [EXTERNAL] create a 26 bp RNA from a 13 bp system

[Xiang-Jun Lu <3d...@gm...>]

On Fri, Nov 12, 2021 at 11:15 AM amirhossein taghavi <
tag...@gm...> wrote:

> Hi Xiang-Jun,
>
> Sorry to bother. I meant if I can do the same thing you have done with
> DSSR pro with free version of x3dna-dssr, as I am getting some error
> messages:
>

No, as made clear in my previous response to Blaine: "The duplicated model
was generated with following DSSR Pro commands:"

Best regards,

Xiang-Jun


> x3dna-dssr -i=model.pdb --frame-pair=last -o=model1-ref-last.pdb
> Processing file 'model.pdb'
> total number of nucleotides: 26
> [e] no matched residue for option --frame
>
> Thanks for your help.
>
> Best,
> Amir
>
>
> On Fri, Nov 12, 2021 at 11:00 AM Xiang-Jun Lu <3d...@gm...> wrote:
>
>> Hi Amir,
>>
>> Please have a look at the announcement "No more grant funding for
>> 3DNA/DSSR" (
>> http://forum.x3dna.org/site-announcements/no-more-grant-funding-for-3dnadssr/)
>> on the 3DNA Forum. DSSR results are reproduced, period.
>>
>> Best wishes,
>>
>> Xiang-Jun
>>
>> --
>> Xiang-Jun Lu (Ph.D.)
>> Email: xia...@x3...
>> Web: http://x3dna.org/
>> Forum: http://forum.x3dna.org/
>>
>>
>> On Fri, Nov 12, 2021 at 10:51 AM amirhossein taghavi <
>> tag...@gm...> wrote:
>>
>>> Hello Dr. Xiang-Jun Lu,
>>>
>>> Thanks a lot for your help. The model you have duplicated is exactly
>>> what I am looking for (checked it with VMD). Unfortunately I do not have
>>> access to DSSR-Pro. Is there any way that I can reproduce your procedure
>>> with x3dna-dssr?
>>> I need to create different numbers of duplicates (2,4,6,5,8) for
>>> different systems and this will be very helpful.
>>>
>>> Thanks in advance.
>>>
>>> Best regards,
>>> Amir
>>>
>>> On Fri, Nov 12, 2021 at 10:33 AM Xiang-Jun Lu <3d...@gm...> wrote:
>>>
>>>> Dear Blaine,
>>>>
>>>> On Fri, Nov 12, 2021 at 10:14 AM Mooers, Blaine H.M. (HSC) <
>>>> Bla...@ou...> wrote:
>>>>
>>>>> Hi Xiang-Jun Lu,
>>>>>
>>>>> Thanks for proving me wrong. Congratulations on your duplicated model!
>>>>> Please share the commands that you used with DSSR to generate the
>>>>> duplicated helix.
>>>>>
>>>>
>>>> The duplicated model was generated with following DSSR Pro commands:
>>>>
>>>> ```
>>>> x3dna-dssr tasks -i=model.pdb --frame-pair=last -o=model1-ref-last.pdb
>>>>
>>>> x3dna-dssr fiber --seq=GG --rna-ds -o=conn.pdb
>>>> x3dna-dssr tasks -i=conn.pdb --frame-pair=first --remove-pair
>>>> -o=ref-conn.pdb
>>>>
>>>> x3dna-dssr tasks --merge-file='model1-ref-last.pdb ref-conn.pdb'
>>>> -o=temp1.pdb
>>>>
>>>> x3dna-dssr tasks -i=temp1.pdb --frame-pair=last --remove-pair
>>>> -o=temp2.pdb
>>>> x3dna-dssr tasks -i=model.pdb --frame-pair=first -o=model1-ref-first.pdb
>>>>
>>>> x3dna-dssr tasks --merge-file='temp2.pdb model1-ref-first.pdb'
>>>> -o=duplicate-model.pdb
>>>> ```
>>>>
>>>> It takes seconds to run. Moreover, by replacing `--seq=GG` with
>>>> `--seq=GA10G` for example, one can easily get a linker with 10 adenines.
>>>> The 'GG` is just a space-holder, and can be replaced with any other bases.
>>>> The linker sequence could be any bases: eg. A5T3G6, AAATTGG, etc. Users who
>>>> want to know more about DSSR can watch the overview video
>>>> http://docs.x3dna.org/dssr-overview/ (20m).
>>>>
>>>>
>>>>> PyMOL does not generate the cartoon representation for the backbones
>>>>> of your duplicate helix.
>>>>> Do you know why?
>>>>>
>>>>
>>>> I noticed the phenomenon but I really do not know why. I used 'as
>>>> lines' in PyMOL to verify the duplicated model.
>>>>
>>>> Best regards,
>>>>
>>>> Xiang-Jun
>>>>
>>>> Best regards,
>>>>>
>>>>> Blaine
>>>>>
>>>>> Blaine Mooers, Ph.D.
>>>>> Associate Professor
>>>>> Department of Biochemistry and Molecular Biology, College of Medicine
>>>>> Director of the Laboratory of Biomolecular Structure and Function
>>>>> Academic Director, Biomolecular Structure Core, COBRE in Structural
>>>>> Biology
>>>>> Full Member, Cancer Biology Program, Stephenson Cancer Center
>>>>> University of Oklahoma Health Sciences Center
>>>>>
>>>>> Mailing Address:
>>>>> 975 NE 10th Street, BRC 466
>>>>> Oklahoma City, OK 73104-5419
>>>>> Office: 405-271-8300 Lab: 405-271-8312
>>>>>
>>>> _______________________________________________
>>>> PyMOL-users mailing list
>>>> Archives: http://www.mail-archive.com/pym...@li...
>>>> Unsubscribe:
>>>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>>>
>>>

Re: [PyMOL] [EXTERNAL] create a 26 bp RNA from a 13 bp system

[amirhossein t. <tag...@gm...>]

Hi Xiang-Jun,

Sorry to bother. I meant if I can do the same thing you have done with DSSR
pro with free version of x3dna-dssr, as I am getting some error messages:

x3dna-dssr -i=model.pdb --frame-pair=last -o=model1-ref-last.pdb
Processing file 'model.pdb'
total number of nucleotides: 26
[e] no matched residue for option --frame

Thanks for your help.

Best,
Amir


On Fri, Nov 12, 2021 at 11:00 AM Xiang-Jun Lu <3d...@gm...> wrote:

> Hi Amir,
>
> Please have a look at the announcement "No more grant funding for
> 3DNA/DSSR" (
> http://forum.x3dna.org/site-announcements/no-more-grant-funding-for-3dnadssr/)
> on the 3DNA Forum. DSSR results are reproduced, period.
>
> Best wishes,
>
> Xiang-Jun
>
> --
> Xiang-Jun Lu (Ph.D.)
> Email: xia...@x3...
> Web: http://x3dna.org/
> Forum: http://forum.x3dna.org/
>
>
> On Fri, Nov 12, 2021 at 10:51 AM amirhossein taghavi <
> tag...@gm...> wrote:
>
>> Hello Dr. Xiang-Jun Lu,
>>
>> Thanks a lot for your help. The model you have duplicated is exactly what
>> I am looking for (checked it with VMD). Unfortunately I do not have access
>> to DSSR-Pro. Is there any way that I can reproduce your procedure with
>> x3dna-dssr?
>> I need to create different numbers of duplicates (2,4,6,5,8) for
>> different systems and this will be very helpful.
>>
>> Thanks in advance.
>>
>> Best regards,
>> Amir
>>
>> On Fri, Nov 12, 2021 at 10:33 AM Xiang-Jun Lu <3d...@gm...> wrote:
>>
>>> Dear Blaine,
>>>
>>> On Fri, Nov 12, 2021 at 10:14 AM Mooers, Blaine H.M. (HSC) <
>>> Bla...@ou...> wrote:
>>>
>>>> Hi Xiang-Jun Lu,
>>>>
>>>> Thanks for proving me wrong. Congratulations on your duplicated model!
>>>> Please share the commands that you used with DSSR to generate the
>>>> duplicated helix.
>>>>
>>>
>>> The duplicated model was generated with following DSSR Pro commands:
>>>
>>> ```
>>> x3dna-dssr tasks -i=model.pdb --frame-pair=last -o=model1-ref-last.pdb
>>>
>>> x3dna-dssr fiber --seq=GG --rna-ds -o=conn.pdb
>>> x3dna-dssr tasks -i=conn.pdb --frame-pair=first --remove-pair
>>> -o=ref-conn.pdb
>>>
>>> x3dna-dssr tasks --merge-file='model1-ref-last.pdb ref-conn.pdb'
>>> -o=temp1.pdb
>>>
>>> x3dna-dssr tasks -i=temp1.pdb --frame-pair=last --remove-pair
>>> -o=temp2.pdb
>>> x3dna-dssr tasks -i=model.pdb --frame-pair=first -o=model1-ref-first.pdb
>>>
>>> x3dna-dssr tasks --merge-file='temp2.pdb model1-ref-first.pdb'
>>> -o=duplicate-model.pdb
>>> ```
>>>
>>> It takes seconds to run. Moreover, by replacing `--seq=GG` with
>>> `--seq=GA10G` for example, one can easily get a linker with 10 adenines.
>>> The 'GG` is just a space-holder, and can be replaced with any other bases.
>>> The linker sequence could be any bases: eg. A5T3G6, AAATTGG, etc. Users who
>>> want to know more about DSSR can watch the overview video
>>> http://docs.x3dna.org/dssr-overview/ (20m).
>>>
>>>
>>>> PyMOL does not generate the cartoon representation for the backbones of
>>>> your duplicate helix.
>>>> Do you know why?
>>>>
>>>
>>> I noticed the phenomenon but I really do not know why. I used 'as lines'
>>> in PyMOL to verify the duplicated model.
>>>
>>> Best regards,
>>>
>>> Xiang-Jun
>>>
>>> Best regards,
>>>>
>>>> Blaine
>>>>
>>>> Blaine Mooers, Ph.D.
>>>> Associate Professor
>>>> Department of Biochemistry and Molecular Biology, College of Medicine
>>>> Director of the Laboratory of Biomolecular Structure and Function
>>>> Academic Director, Biomolecular Structure Core, COBRE in Structural
>>>> Biology
>>>> Full Member, Cancer Biology Program, Stephenson Cancer Center
>>>> University of Oklahoma Health Sciences Center
>>>>
>>>> Mailing Address:
>>>> 975 NE 10th Street, BRC 466
>>>> Oklahoma City, OK 73104-5419
>>>> Office: 405-271-8300 Lab: 405-271-8312
>>>>
>>> _______________________________________________
>>> PyMOL-users mailing list
>>> Archives: http://www.mail-archive.com/pym...@li...
>>> Unsubscribe:
>>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>>
>>

Re: [PyMOL] [EXTERNAL] create a 26 bp RNA from a 13 bp system

[Xiang-Jun Lu <3d...@gm...>]

Hi Amir,

Please have a look at the announcement "No more grant funding for
3DNA/DSSR" (
http://forum.x3dna.org/site-announcements/no-more-grant-funding-for-3dnadssr/)
on the 3DNA Forum. DSSR results are reproduced, period.

Best wishes,

Xiang-Jun

--
Xiang-Jun Lu (Ph.D.)
Email: xia...@x3...
Web: http://x3dna.org/
Forum: http://forum.x3dna.org/


On Fri, Nov 12, 2021 at 10:51 AM amirhossein taghavi <
tag...@gm...> wrote:

> Hello Dr. Xiang-Jun Lu,
>
> Thanks a lot for your help. The model you have duplicated is exactly what
> I am looking for (checked it with VMD). Unfortunately I do not have access
> to DSSR-Pro. Is there any way that I can reproduce your procedure with
> x3dna-dssr?
> I need to create different numbers of duplicates (2,4,6,5,8) for different
> systems and this will be very helpful.
>
> Thanks in advance.
>
> Best regards,
> Amir
>
> On Fri, Nov 12, 2021 at 10:33 AM Xiang-Jun Lu <3d...@gm...> wrote:
>
>> Dear Blaine,
>>
>> On Fri, Nov 12, 2021 at 10:14 AM Mooers, Blaine H.M. (HSC) <
>> Bla...@ou...> wrote:
>>
>>> Hi Xiang-Jun Lu,
>>>
>>> Thanks for proving me wrong. Congratulations on your duplicated model!
>>> Please share the commands that you used with DSSR to generate the
>>> duplicated helix.
>>>
>>
>> The duplicated model was generated with following DSSR Pro commands:
>>
>> ```
>> x3dna-dssr tasks -i=model.pdb --frame-pair=last -o=model1-ref-last.pdb
>>
>> x3dna-dssr fiber --seq=GG --rna-ds -o=conn.pdb
>> x3dna-dssr tasks -i=conn.pdb --frame-pair=first --remove-pair
>> -o=ref-conn.pdb
>>
>> x3dna-dssr tasks --merge-file='model1-ref-last.pdb ref-conn.pdb'
>> -o=temp1.pdb
>>
>> x3dna-dssr tasks -i=temp1.pdb --frame-pair=last --remove-pair -o=temp2.pdb
>> x3dna-dssr tasks -i=model.pdb --frame-pair=first -o=model1-ref-first.pdb
>>
>> x3dna-dssr tasks --merge-file='temp2.pdb model1-ref-first.pdb'
>> -o=duplicate-model.pdb
>> ```
>>
>> It takes seconds to run. Moreover, by replacing `--seq=GG` with
>> `--seq=GA10G` for example, one can easily get a linker with 10 adenines.
>> The 'GG` is just a space-holder, and can be replaced with any other bases.
>> The linker sequence could be any bases: eg. A5T3G6, AAATTGG, etc. Users who
>> want to know more about DSSR can watch the overview video
>> http://docs.x3dna.org/dssr-overview/ (20m).
>>
>>
>>> PyMOL does not generate the cartoon representation for the backbones of
>>> your duplicate helix.
>>> Do you know why?
>>>
>>
>> I noticed the phenomenon but I really do not know why. I used 'as lines'
>> in PyMOL to verify the duplicated model.
>>
>> Best regards,
>>
>> Xiang-Jun
>>
>> Best regards,
>>>
>>> Blaine
>>>
>>> Blaine Mooers, Ph.D.
>>> Associate Professor
>>> Department of Biochemistry and Molecular Biology, College of Medicine
>>> Director of the Laboratory of Biomolecular Structure and Function
>>> Academic Director, Biomolecular Structure Core, COBRE in Structural
>>> Biology
>>> Full Member, Cancer Biology Program, Stephenson Cancer Center
>>> University of Oklahoma Health Sciences Center
>>>
>>> Mailing Address:
>>> 975 NE 10th Street, BRC 466
>>> Oklahoma City, OK 73104-5419
>>> Office: 405-271-8300 Lab: 405-271-8312
>>>
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>

Re: [PyMOL] [EXTERNAL] create a 26 bp RNA from a 13 bp system

[amirhossein t. <tag...@gm...>]

Hello Dr. Xiang-Jun Lu,

Thanks a lot for your help. The model you have duplicated is exactly what I
am looking for (checked it with VMD). Unfortunately I do not have access to
DSSR-Pro. Is there any way that I can reproduce your procedure with
x3dna-dssr?
I need to create different numbers of duplicates (2,4,6,5,8) for different
systems and this will be very helpful.

Thanks in advance.

Best regards,
Amir

On Fri, Nov 12, 2021 at 10:33 AM Xiang-Jun Lu <3d...@gm...> wrote:

> Dear Blaine,
>
> On Fri, Nov 12, 2021 at 10:14 AM Mooers, Blaine H.M. (HSC) <
> Bla...@ou...> wrote:
>
>> Hi Xiang-Jun Lu,
>>
>> Thanks for proving me wrong. Congratulations on your duplicated model!
>> Please share the commands that you used with DSSR to generate the
>> duplicated helix.
>>
>
> The duplicated model was generated with following DSSR Pro commands:
>
> ```
> x3dna-dssr tasks -i=model.pdb --frame-pair=last -o=model1-ref-last.pdb
>
> x3dna-dssr fiber --seq=GG --rna-ds -o=conn.pdb
> x3dna-dssr tasks -i=conn.pdb --frame-pair=first --remove-pair
> -o=ref-conn.pdb
>
> x3dna-dssr tasks --merge-file='model1-ref-last.pdb ref-conn.pdb'
> -o=temp1.pdb
>
> x3dna-dssr tasks -i=temp1.pdb --frame-pair=last --remove-pair -o=temp2.pdb
> x3dna-dssr tasks -i=model.pdb --frame-pair=first -o=model1-ref-first.pdb
>
> x3dna-dssr tasks --merge-file='temp2.pdb model1-ref-first.pdb'
> -o=duplicate-model.pdb
> ```
>
> It takes seconds to run. Moreover, by replacing `--seq=GG` with
> `--seq=GA10G` for example, one can easily get a linker with 10 adenines.
> The 'GG` is just a space-holder, and can be replaced with any other bases.
> The linker sequence could be any bases: eg. A5T3G6, AAATTGG, etc. Users who
> want to know more about DSSR can watch the overview video
> http://docs.x3dna.org/dssr-overview/ (20m).
>
>
>> PyMOL does not generate the cartoon representation for the backbones of
>> your duplicate helix.
>> Do you know why?
>>
>
> I noticed the phenomenon but I really do not know why. I used 'as lines'
> in PyMOL to verify the duplicated model.
>
> Best regards,
>
> Xiang-Jun
>
> Best regards,
>>
>> Blaine
>>
>> Blaine Mooers, Ph.D.
>> Associate Professor
>> Department of Biochemistry and Molecular Biology, College of Medicine
>> Director of the Laboratory of Biomolecular Structure and Function
>> Academic Director, Biomolecular Structure Core, COBRE in Structural
>> Biology
>> Full Member, Cancer Biology Program, Stephenson Cancer Center
>> University of Oklahoma Health Sciences Center
>>
>> Mailing Address:
>> 975 NE 10th Street, BRC 466
>> Oklahoma City, OK 73104-5419
>> Office: 405-271-8300 Lab: 405-271-8312
>>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] [EXTERNAL] create a 26 bp RNA from a 13 bp system

[Xiang-Jun Lu <3d...@gm...>]

Dear Blaine,

On Fri, Nov 12, 2021 at 10:14 AM Mooers, Blaine H.M. (HSC) <
Bla...@ou...> wrote:

> Hi Xiang-Jun Lu,
>
> Thanks for proving me wrong. Congratulations on your duplicated model!
> Please share the commands that you used with DSSR to generate the
> duplicated helix.
>

The duplicated model was generated with following DSSR Pro commands:

```
x3dna-dssr tasks -i=model.pdb --frame-pair=last -o=model1-ref-last.pdb

x3dna-dssr fiber --seq=GG --rna-ds -o=conn.pdb
x3dna-dssr tasks -i=conn.pdb --frame-pair=first --remove-pair
-o=ref-conn.pdb

x3dna-dssr tasks --merge-file='model1-ref-last.pdb ref-conn.pdb'
-o=temp1.pdb

x3dna-dssr tasks -i=temp1.pdb --frame-pair=last --remove-pair -o=temp2.pdb
x3dna-dssr tasks -i=model.pdb --frame-pair=first -o=model1-ref-first.pdb

x3dna-dssr tasks --merge-file='temp2.pdb model1-ref-first.pdb'
-o=duplicate-model.pdb
```

It takes seconds to run. Moreover, by replacing `--seq=GG` with
`--seq=GA10G` for example, one can easily get a linker with 10 adenines.
The 'GG` is just a space-holder, and can be replaced with any other bases.
The linker sequence could be any bases: eg. A5T3G6, AAATTGG, etc. Users who
want to know more about DSSR can watch the overview video
http://docs.x3dna.org/dssr-overview/ (20m).


> PyMOL does not generate the cartoon representation for the backbones of
> your duplicate helix.
> Do you know why?
>

I noticed the phenomenon but I really do not know why. I used 'as lines' in
PyMOL to verify the duplicated model.

Best regards,

Xiang-Jun

Best regards,
>
> Blaine
>
> Blaine Mooers, Ph.D.
> Associate Professor
> Department of Biochemistry and Molecular Biology, College of Medicine
> Director of the Laboratory of Biomolecular Structure and Function
> Academic Director, Biomolecular Structure Core, COBRE in Structural Biology
> Full Member, Cancer Biology Program, Stephenson Cancer Center
> University of Oklahoma Health Sciences Center
>
> Mailing Address:
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
> Office: 405-271-8300 Lab: 405-271-8312
>

Re: [PyMOL] [EXTERNAL] create a 26 bp RNA from a 13 bp system

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

Hi Xiang-Jun Lu,

Thanks for proving me wrong. Congratulations on your duplicated model!
Please share the commands that you used with DSSR to generate the duplicated helix.

PyMOL does not generate the cartoon representation for the backbones of your duplicate helix. 
Do you know why?

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology, College of Medicine
Director of the Laboratory of Biomolecular Structure and Function
Academic Director, Biomolecular Structure Core, COBRE in Structural Biology
Full Member, Cancer Biology Program, Stephenson Cancer Center
University of Oklahoma Health Sciences Center

Mailing Address:
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
Office: 405-271-8300 Lab: 405-271-8312

Websites:
Faculty page: https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd
BSC-OKC (LBSF): https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function
COBRE in Structural Biology: https://www.ou.edu/structuralbiology
________________________________________
From: Xiang-Jun Lu [3d...@gm...]
Sent: Friday, November 12, 2021 8:05 AM
To: pym...@li...
Subject: Re: [PyMOL] [EXTERNAL] create a 26 bp RNA from a 13 bp system

Message: 1
Date: Thu, 11 Nov 2021 01:21:47 +0000
From: "Mooers, Blaine H.M.  (HSC)" <Bla...@ou...<mailto:Bla...@ou...>>
To: amirhossein taghavi <tag...@gm...<mailto:tag...@gm...>>,
        "pym...@li...<mailto:pym...@li...>"
        <pym...@li...<mailto:pym...@li...>>
Subject: Re: [PyMOL] [EXTERNAL]  create a 26 bp RNA from a 13 bp
        system
Message-ID:
        <87D...@CO...<mailto:87D...@CO...>>
Content-Type: text/plain; charset="us-ascii"

Hi Amir,

No, not automatically. Your RNA is very distorted from
the standard A-form. I doubt any modeling program
can accurately extend such a distorted helix. Maybe
someone else will prove me wrong.


DSSR was used to create the attached 26-base-pair (bp) long RNA by duplicating the initial 13-bp model. I'm not sure whether this is the outcome Amir was hoping for.

Best regards,

Xiang-Jun

--
Xiang-Jun Lu (Ph.D.)
Email: xia...@x3...<mailto:xia...@x3...>
Web: http://x3dna.org/<https://urldefense.proofpoint.com/v2/url?u=http-3A__x3dna.org_&d=DwMFaQ&c=qKdtBuuu6dQK9MsRUVJ2DPXW6oayO8fu4TfEHS8sGNk&r=rxarJ7aLyHGI62pje1gd6hPxYn9Xv-2lWNWh_1Owonw&m=SezBp4UL1C-pr1f35s70RAkgFpWQaaVnI3ISWKOA7wkFTZWpjoYN2QWKHvmvgwa4&s=SCbMW3JwZkTKAxEfPB8w5TtSItCw4MMTIOr8sxCVEIE&e=>
Forum: http://forum.x3dna.org/<https://urldefense.proofpoint.com/v2/url?u=http-3A__forum.x3dna.org_&d=DwMFaQ&c=qKdtBuuu6dQK9MsRUVJ2DPXW6oayO8fu4TfEHS8sGNk&r=rxarJ7aLyHGI62pje1gd6hPxYn9Xv-2lWNWh_1Owonw&m=SezBp4UL1C-pr1f35s70RAkgFpWQaaVnI3ISWKOA7wkFTZWpjoYN2QWKHvmvgwa4&s=R5l09hlMu8Qv8Uw7eKpaBtB-k1s-E1xX0jqFJ9b_oDg&e=>

 Your RNA does not have the expected
doughnut cross-section of the A-form when
viewed down the helical axis.

Your model has triclinic unit cell dimensions on the first line of the coordinate file.
Is it from a crystal structure? If it is, it might be stacked
end-on-end in the crystal lattice. You could generate its
symmetry mate and save its coordinates.
However, the cryst card in your file is corrupted, and
PyMOL cannot use it to generate symmetry mates.

You can align the terminal base pairs manually through a
series of commands. If you try by dragging one copy
relative to another, you will wind up pulling out all of your
hair. The commands and patience will keep you out  of the mad house.

load model_.pdb
orient
# align along the x-axis
copy model2, model_
translate [38,0,0], model2
rotate x, -45, model2

Issue a series of subsequent translate, rotate, and orient commands as needed.
Use smaller increments like 1 or 2 angstroms and 5 or 10 degrees.
The angle between the terminal base pairs should be about 33 degrees.
With patience, you can do this in less than an hour.

However, I am not sure how relevant the duplicated structure will be given
the distortions in model_.pdb.

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology, College of Medicine
Director of the Laboratory of Biomolecular Structure and Function
Academic Director, Biomolecular Structure Core, COBRE in Structural Biology
Full Member, Cancer Biology Program, Stephenson Cancer Center
University of Oklahoma Health Sciences Center

Mailing Address:
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
Office: 405-271-8300 Lab: 405-271-8312

Websites:
Faculty page: https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd
BSC-OKC<https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phdBSC-OKC> (LBSF): https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function
COBRE in Structural Biology: https://www.ou.edu/structuralbiology
________________________________________
From: amirhossein taghavi [tag...@gm...<mailto:tag...@gm...>]
Sent: Wednesday, November 10, 2021 5:03 PM
To: pym...@li...<mailto:pym...@li...>
Subject: [EXTERNAL] [PyMOL] create a 26 bp RNA from a 13 bp system

Hello,

I have an RNA duplex with 13 base-pairs (attached). Is it possible to duplicate this system and then fuse the two molecules to create a 26 base-pair long system using the pymol.

Thanks in advance.

Cheers,
Amir



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

Message: 2
Date: Wed, 10 Nov 2021 21:44:21 -0500
From: amirhossein taghavi <tag...@gm...<mailto:tag...@gm...>>
To: "Mooers, Blaine H.M. (HSC)" <Bla...@ou...<mailto:Bla...@ou...>>
Cc: "pym...@li...<mailto:pym...@li...>"
        <pym...@li...<mailto:pym...@li...>>
Subject: Re: [PyMOL] [EXTERNAL]  create a 26 bp RNA from a 13 bp
        system
Message-ID:
        <CAP...@ma...<mailto:gK6...@ma...>>
Content-Type: text/plain; charset="utf-8"

Hello Prof. Blaine,

Thanks a lot for the detailed explanation. The model is out of MD
simulations with the box information.
I will try the workflow you suggested.
I very much appreciate your help.

Best regards,
Amir

Re: [PyMOL] [EXTERNAL] create a 26 bp RNA from a 13 bp system

[Xiang-Jun Lu <3d...@gm...>]

> Message: 1
> Date: Thu, 11 Nov 2021 01:21:47 +0000
> From: "Mooers, Blaine H.M.  (HSC)" <Bla...@ou...>
> To: amirhossein taghavi <tag...@gm...>,
>         "pym...@li..."
>         <pym...@li...>
> Subject: Re: [PyMOL] [EXTERNAL]  create a 26 bp RNA from a 13 bp
>         system
> Message-ID:
>         <
> 87D...@CO...>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi Amir,
>
> No, not automatically. Your RNA is very distorted from
> the standard A-form. I doubt any modeling program
> can accurately extend such a distorted helix. Maybe
> someone else will prove me wrong.
>
>
DSSR was used to create the attached 26-base-pair (bp) long RNA by
duplicating the initial 13-bp model. I'm not sure whether this is the
outcome Amir was hoping for.

Best regards,

Xiang-Jun

--
Xiang-Jun Lu (Ph.D.)
Email: xia...@x3...
Web: http://x3dna.org/
Forum: http://forum.x3dna.org/

 Your RNA does not have the expected
> doughnut cross-section of the A-form when
> viewed down the helical axis.
>
> Your model has triclinic unit cell dimensions on the first line of the
> coordinate file.
> Is it from a crystal structure? If it is, it might be stacked
> end-on-end in the crystal lattice. You could generate its
> symmetry mate and save its coordinates.
> However, the cryst card in your file is corrupted, and
> PyMOL cannot use it to generate symmetry mates.
>
> You can align the terminal base pairs manually through a
> series of commands. If you try by dragging one copy
> relative to another, you will wind up pulling out all of your
> hair. The commands and patience will keep you out  of the mad house.
>
> load model_.pdb
> orient
> # align along the x-axis
> copy model2, model_
> translate [38,0,0], model2
> rotate x, -45, model2
>
> Issue a series of subsequent translate, rotate, and orient commands as
> needed.
> Use smaller increments like 1 or 2 angstroms and 5 or 10 degrees.
> The angle between the terminal base pairs should be about 33 degrees.
> With patience, you can do this in less than an hour.
>
> However, I am not sure how relevant the duplicated structure will be given
> the distortions in model_.pdb.
>
> Best regards,
>
> Blaine
>
> Blaine Mooers, Ph.D.
> Associate Professor
> Department of Biochemistry and Molecular Biology, College of Medicine
> Director of the Laboratory of Biomolecular Structure and Function
> Academic Director, Biomolecular Structure Core, COBRE in Structural Biology
> Full Member, Cancer Biology Program, Stephenson Cancer Center
> University of Oklahoma Health Sciences Center
>
> Mailing Address:
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
> Office: 405-271-8300 Lab: 405-271-8312
>
> Websites:
> Faculty page:
> https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd
> BSC-OKC
> <https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phdBSC-OKC>
> (LBSF):
> https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function
> COBRE in Structural Biology: https://www.ou.edu/structuralbiology
> ________________________________________
> From: amirhossein taghavi [tag...@gm...]
> Sent: Wednesday, November 10, 2021 5:03 PM
> To: pym...@li...
> Subject: [EXTERNAL] [PyMOL] create a 26 bp RNA from a 13 bp system
>
> Hello,
>
> I have an RNA duplex with 13 base-pairs (attached). Is it possible to
> duplicate this system and then fuse the two molecules to create a 26
> base-pair long system using the pymol.
>
> Thanks in advance.
>
> Cheers,
> Amir
>
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 10 Nov 2021 21:44:21 -0500
> From: amirhossein taghavi <tag...@gm...>
> To: "Mooers, Blaine H.M. (HSC)" <Bla...@ou...>
> Cc: "pym...@li..."
>         <pym...@li...>
> Subject: Re: [PyMOL] [EXTERNAL]  create a 26 bp RNA from a 13 bp
>         system
> Message-ID:
>         <CAP4-oUjYJ-PbCdeoBsOJ3=cnEje_7vwhTWGVitxd=
> gK6...@ma...>
> Content-Type: text/plain; charset="utf-8"
>
> Hello Prof. Blaine,
>
> Thanks a lot for the detailed explanation. The model is out of MD
> simulations with the box information.
> I will try the workflow you suggested.
> I very much appreciate your help.
>
> Best regards,
> Amir
>
>
>

Re: [PyMOL] [EXTERNAL] How to set spectrum color by default in Pymol

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

I second G.V.'s question. It touches upon a problem that I have been having.

The cartoon representation is shown when the 
structure is loaded from disk or fetched from the PDB.

The default cartoon representation overrides the settings in my pymolrc file.
I have the following in my .pymolrc file. I do not have a /.pymolrc-settings.py file or
any other .pymolrc* files.

hide cartoon
show sticks

I still get the cartoon representation when I fetch a structure or load a structure.

The user should be able to control how the structure appears when it is first loaded.

This behavior started occurring with PyMOL 2.

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology, College of Medicine
Director of the Laboratory of Biomolecular Structure and Function
Academic Director, Biomolecular Structure Core, COBRE in Structural Biology
Full Member, Cancer Biology Program, Stephenson Cancer Center
University of Oklahoma Health Sciences Center

Mailing Address:
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
Office: 405-271-8300 Lab: 405-271-8312

Websites:
Faculty page: https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd
BSC-OKC (LBSF): https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function
COBRE in Structural Biology: https://www.ou.edu/structuralbiology
________________________________________
From: Gundala Viswanath [gun...@gm...]
Sent: Thursday, November 11, 2021 11:39 PM
To: pymol-users
Subject: [EXTERNAL] [PyMOL] How to set spectrum color by default in Pymol

Hi,

Is there a way to do that?
I tried putting this line in .pymolrc, but it doesn't work.

spectrum b, red_yellow_green_cyan_blue, minimum=50, maximum=90

I attached the example PDB file, where the B-factor column is used for the coloring.
An this is the image:

[Screen Shot 2021-11-12 at 14.38.06.png]

G.V/

[PyMOL] How to set spectrum color by default in Pymol

[Gundala V. <gun...@gm...>]

Hi,

Is there a way to do that?
I tried putting this line in *.pymolrc*, but it doesn't work.

spectrum b, red_yellow_green_cyan_blue, minimum=50, maximum=90

I attached the example PDB file, where the B-factor column is used for the
coloring.
An this is the image:

[image: Screen Shot 2021-11-12 at 14.38.06.png]

G.V/

Re: [PyMOL] [EXTERNAL] create a 26 bp RNA from a 13 bp system

[amirhossein t. <tag...@gm...>]

Hello Prof. Blaine,

Thanks a lot for the detailed explanation. The model is out of MD
simulations with the box information.
I will try the workflow you suggested.
I very much appreciate your help.

Best regards,
Amir

On Wed, Nov 10, 2021 at 8:21 PM Mooers, Blaine H.M. (HSC) <
Bla...@ou...> wrote:

> Hi Amir,
>
> No, not automatically. Your RNA is very distorted from
> the standard A-form. I doubt any modeling program
> can accurately extend such a distorted helix. Maybe
> someone else will prove me wrong.
>
> Your RNA does not have the expected
> doughnut cross-section of the A-form when
> viewed down the helical axis.
>
> Your model has triclinic unit cell dimensions on the first line of the
> coordinate file.
> Is it from a crystal structure? If it is, it might be stacked
> end-on-end in the crystal lattice. You could generate its
> symmetry mate and save its coordinates.
> However, the cryst card in your file is corrupted, and
> PyMOL cannot use it to generate symmetry mates.
>
> You can align the terminal base pairs manually through a
> series of commands. If you try by dragging one copy
> relative to another, you will wind up pulling out all of your
> hair. The commands and patience will keep you out  of the mad house.
>
> load model_.pdb
> orient
> # align along the x-axis
> copy model2, model_
> translate [38,0,0], model2
> rotate x, -45, model2
>
> Issue a series of subsequent translate, rotate, and orient commands as
> needed.
> Use smaller increments like 1 or 2 angstroms and 5 or 10 degrees.
> The angle between the terminal base pairs should be about 33 degrees.
> With patience, you can do this in less than an hour.
>
> However, I am not sure how relevant the duplicated structure will be given
> the distortions in model_.pdb.
>
> Best regards,
>
> Blaine
>
> Blaine Mooers, Ph.D.
> Associate Professor
> Department of Biochemistry and Molecular Biology, College of Medicine
> Director of the Laboratory of Biomolecular Structure and Function
> Academic Director, Biomolecular Structure Core, COBRE in Structural Biology
> Full Member, Cancer Biology Program, Stephenson Cancer Center
> University of Oklahoma Health Sciences Center
>
> Mailing Address:
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
> Office: 405-271-8300 Lab: 405-271-8312
>
> Websites:
> Faculty page:
> https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd
> BSC-OKC
> <https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phdBSC-OKC>
> (LBSF):
> https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function
> COBRE in Structural Biology: https://www.ou.edu/structuralbiology
> ________________________________________
> From: amirhossein taghavi [tag...@gm...]
> Sent: Wednesday, November 10, 2021 5:03 PM
> To: pym...@li...
> Subject: [EXTERNAL] [PyMOL] create a 26 bp RNA from a 13 bp system
>
> Hello,
>
> I have an RNA duplex with 13 base-pairs (attached). Is it possible to
> duplicate this system and then fuse the two molecules to create a 26
> base-pair long system using the pymol.
>
> Thanks in advance.
>
> Cheers,
> Amir
>

Re: [PyMOL] [EXTERNAL] create a 26 bp RNA from a 13 bp system

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

Hi Amir,

No, not automatically. Your RNA is very distorted from 
the standard A-form. I doubt any modeling program 
can accurately extend such a distorted helix. Maybe
someone else will prove me wrong.

Your RNA does not have the expected
doughnut cross-section of the A-form when 
viewed down the helical axis. 

Your model has triclinic unit cell dimensions on the first line of the coordinate file.
Is it from a crystal structure? If it is, it might be stacked 
end-on-end in the crystal lattice. You could generate its
symmetry mate and save its coordinates. 
However, the cryst card in your file is corrupted, and 
PyMOL cannot use it to generate symmetry mates.

You can align the terminal base pairs manually through a
series of commands. If you try by dragging one copy 
relative to another, you will wind up pulling out all of your
hair. The commands and patience will keep you out  of the mad house.

load model_.pdb
orient
# align along the x-axis
copy model2, model_
translate [38,0,0], model2
rotate x, -45, model2

Issue a series of subsequent translate, rotate, and orient commands as needed.
Use smaller increments like 1 or 2 angstroms and 5 or 10 degrees.
The angle between the terminal base pairs should be about 33 degrees.
With patience, you can do this in less than an hour. 

However, I am not sure how relevant the duplicated structure will be given
the distortions in model_.pdb.

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology, College of Medicine
Director of the Laboratory of Biomolecular Structure and Function
Academic Director, Biomolecular Structure Core, COBRE in Structural Biology
Full Member, Cancer Biology Program, Stephenson Cancer Center
University of Oklahoma Health Sciences Center

Mailing Address:
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
Office: 405-271-8300 Lab: 405-271-8312

Websites:
Faculty page: https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd
BSC-OKC (LBSF): https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function
COBRE in Structural Biology: https://www.ou.edu/structuralbiology
________________________________________
From: amirhossein taghavi [tag...@gm...]
Sent: Wednesday, November 10, 2021 5:03 PM
To: pym...@li...
Subject: [EXTERNAL] [PyMOL] create a 26 bp RNA from a 13 bp system

Hello,

I have an RNA duplex with 13 base-pairs (attached). Is it possible to duplicate this system and then fuse the two molecules to create a 26 base-pair long system using the pymol.

Thanks in advance.

Cheers,
Amir

[PyMOL] create a 26 bp RNA from a 13 bp system

[amirhossein t. <tag...@gm...>]

Hello,

I have an RNA duplex with 13 base-pairs (attached). Is it possible to
duplicate this system and then fuse the two molecules to create a 26
base-pair long system using the pymol.

Thanks in advance.

Cheers,
Amir

Re: [PyMOL] Getting angle between z axis and a molecules principal axis

[Jared S. <jar...@co...>]

Hi Yogesh -

You may be able to do something similar to the antibody elbow angle script
on the PyMOL Wiki (and PyMOL-scripts GitHub repo) using rotation matrices
aligning various subunits to determine the principal axis. Or if you
already have a way of calculating the principal axis, you can use Christoph
Gohlke’s transformations.py module (which is used by the elbow angle
script) to calculate the angle.

I’m away from my computer at the moment but those two scripts should be
fairly easily found using your favorite search engine.

Hope that helps.

Cheers,
Jared

On Tue, Nov 9, 2021 at 8:03 AM Yogesh Sharma <yog...@gm...> wrote:

> Hi I want to get angle between a molecules principal axis and systems z
> axis iteratively over 100ns trajectory. I am new to pymol. Can someone help
> me with scripting it out? Thank you for your time.
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] Getting angle between z axis and a molecules principal axis

[Yogesh S. <yog...@gm...>]

Hi I want to get angle between a molecules principal axis and systems z
axis iteratively over 100ns trajectory. I am new to pymol. Can someone help
me with scripting it out? Thank you for your time.

Re: [PyMOL] About contacting the PYMOL-creators

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

Hello,

General questions about PyMOL and its features could be answered here by
the community as well. Alternatively we have kept track of such community
requests of new features on our open-source issue tracker (
https://github.com/schrodinger/pymol-open-source/issues ).

Best,
Jarrett J.

On Thu, Nov 4, 2021 at 4:31 AM superpowered via PyMOL-users <
pym...@li...> wrote:

> Hello,
> I wonder is there a way to contact the makers of Pymol for general
> question or to request certain program features?
>
> Regards,
> K. Zeghida.
>
> _______________________________________________
> 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
[image: Schrodinger Logo] <https://www.schrodinger.com/>

[PyMOL] About contacting the PYMOL-creators

[superpowered <sup...@pr...>]

Hello,
I wonder is there a way to contact the makers of Pymol for general question or to request certain program features?

Regards,
K. Zeghida.