pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] How to show that one docking is better than another with Pymol visually

[Peter K. <pk...@se...>]

Hello,

Try calculating the solvent accessible surface areas of the docked and 
undocked molecules, including the ligand.  Color atoms whose water 
accessible surfaces are reduced or eliminated by the docking differently 
from the rest of the structures. As an added feature, you might color 
occluded hydrophobic surfaces differently from occluded hydrophilic 
surfaces, but if you do that, use atom hydrophobicity and hydrophilicity 
and not whole amino acid; lysine has four hydrophobic methylene groups 
and one polar group.  All atoms of peptides are polar, etc.

With good wishes,
Peter
-- 
Peter C. Kahn, Ph.D.
Professor of Biochemistry
Department of Biochemistry & Microbiology
Rutgers University
76 Lipman Drive
New Brunswick, NJ 08901

Telephone: 848-932-5618
Telefax:   732-932-8965
Email: pet...@ru...

On 7/19/2021 5:16 PM, Joel Tyndall wrote:
> This is an intriguing question, however I don’t have an answer for you. 
> I would however, turn off the hydrogens as this would make the 
> visualisation easier on the eye. Without knowing the full context of the 
> figure, it is difficult to  interpret further. Text can be the best way 
> here.
> 
> Joel
> 
> *From:*Gundala Viswanath <gun...@gm...>
> *Sent:* Friday, 9 July 2021 1:30 AM
> *To:* pymol-users <pym...@li...>
> *Subject:* [PyMOL] How to show that one docking is better than another 
> with Pymol visually
> 
> Hi
> 
> I have the following docking results.
> 
> |Dock_1|has a better energy score than|Dock_2|. What I want to do is to 
> show with Pymol that|Dock_1|is better visually.
> 
> Here I use a hydrogen bond, highlighted with Yellow (|Dock_1|) and Gray 
> (|Dock_2|). But as you can see, with that I can't show that|Dock_1|is 
> clearly better. That's why I'm looking for a better  alternative than 
> hydrogen bonds.
> 
> G.V.
> 
> 
> 
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
> 

Re: [PyMOL] How to show that one docking is better than another with Pymol visually

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

This is an intriguing question, however I don’t have an answer for you. I would however, turn off the hydrogens as this would make the visualisation easier on the eye. Without knowing the full context of the figure, it is difficult to  interpret further. Text can be the best way here.

Joel

From: Gundala Viswanath <gun...@gm...>
Sent: Friday, 9 July 2021 1:30 AM
To: pymol-users <pym...@li...>
Subject: [PyMOL] How to show that one docking is better than another with Pymol visually


Hi

I have the following docking results.

Dock_1 has a better energy score than Dock_2. What I want to do is to show with Pymol that Dock_1 is better visually.

Here I use a hydrogen bond, highlighted with Yellow (Dock_1) and Gray (Dock_2). But as you can see, with that I can't show that Dock_1 is clearly better. That's why I'm looking for a better  alternative than hydrogen bonds.
[cid:image001.png@01D77D47.FAAEAAE0]

G.V.

[PyMOL] How to show that one docking is better than another with Pymol visually

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

Hi

I have the following docking results.

Dock_1 has a better energy score than Dock_2. What I want to do is to show
with Pymol that Dock_1 is better visually.

Here I use a hydrogen bond, highlighted with Yellow (Dock_1) and Gray (
Dock_2). But as you can see, with that I can't show that Dock_1 is clearly
better. That's why I'm looking for a better  alternative than hydrogen
bonds.
[image: Screen Shot 2021-07-08 at 22.28.45.png]

G.V.

[PyMOL] Help with modelling metalloproteins.

[Duggal, A. <ane...@im...>]

Hello all,

I am an MRes student trying to do some bioinformatics if anyone could help me that would be really appreciated. I have looked to see if my question has been answered and I cannot see the particulars that I am looking for.

I used Phyre2 to model the predicted 3D structure for my protein of interest. Homologues of this protein use Mg2+ which is coordinated to 3 Aspartate residues in the active site. I used both 3DLigandSite and COFACTOR from I-TASSER SUITE to introduce the Mg2+ in my model. However, when looked at it on the site it clearly specified it was the divalent cation but when I opened it on PyMol the formal charge was listed as zero when looking at charge wizard. It also was not co-ordinating as expected with the residues. I tried to manually alter it (PyMOL>alter sele, formal_charge=2) which did not work, I am not sure really why but it never changed.
Another thing was when I was prepping it for docking with autodock vina it noted that the Mg2+ was non-bonded

I also tried to manually edit the PDB file with textedit - writing CONECT bonds to the expected residues based on the homologue and also by specifying the charge (I typed this: HETNAM      MG MAGNESIUM ION
(new line)
FORMUL   2   MG    MG 2+) which was present on the PDB file of the homologue but it did nothing! I am really not sure how to fix this.

If anyone has any insight that would be amazing!
Sorry if this has been answered already!

Thank you very much,
Aneisha

[PyMOL] Exporting structure from PyMOL

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

Hello PyMOL users,

I have a question regarding structure exporting from PyMOL. I have a
peptide that adopts two conformations in gas phase: compact globule and
helical ( see below). I was wondering how to best export these structures
from two different PDB files with the same scale.

[image: image.png]
(compact globular conformation)
[image: image.png]
(helical conformation)

Many thanks,
Neena

Re: [PyMOL] [EXTERNAL] No cartoon view for custom PDB file

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

Thank you so much Kamil and Blaine for the insights, that worked very well!

On Wed, 7 Jul 2021 at 05:04, Mooers, Blaine H.M. (HSC) <
Bla...@ou...> wrote:

> Hi Neena,
>
> Adding to Kamil's explanation, the role of each column for a ATOM record
> in the PDB file is explained here:
> https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM.
>
>
> The PDBeditor.jar program can help you retain the fixed file format of the
> PDB file: http://www.bioinformatics.org/pdbeditor/wiki/.
>
> Best regards,
>
> Blaine
>
> ________________________________________
> From: Kamil Steczkiewicz [kam...@gm...]
> Sent: Wednesday, July 07, 2021 2:29 AM
> To: Neena Susan Eappen
> Cc: Mooers, Blaine H.M.  (HSC); zb...@cu...; pymol-users
> Subject: Re: [PyMOL] [EXTERNAL] No cartoon view for custom PDB file
>
> You got error in column positioning in PDB file - I added two whitespaces
> after ATOM mark. It probably couldn't parse the PDB file properly as the
> PDB file is column-specific format. It works now.
> Chk attached file in PyMOL.
> Kamil
>
>
> wt., 6 lip 2021 o 23:13 Neena Susan Eappen <nee...@gm...
> <mailto:nee...@gm...>> napisał(a):
> Hello PyMOL users,
>
> Please take a look at the two attached PDB files (opt 20 and opt 21); I
> formatted opt21.pdb file to match with that of opt20.pdb for PyMOL to
> recognize the former as a peptide. However, now I can neither see a line
> nor cartoon representation of the opt21 peptide anymore.
> Any insights on what could be wrong in the opt21 PDB file?
>
> Many thanks,
> Neena
>
> On Sat, 3 Jul 2021 at 23:38, Neena Susan Eappen <nee...@gm...
> <mailto:nee...@gm...>> wrote:
> Thank you Blaine and Zuben for your insights and troubleshooting the
> problem! I understood the formatting issue with the current PDB file, will
> do the necessary changes.
>
> Regards,
> Neena
>
> On Sat, 3 Jul 2021 at 09:59, Mooers, Blaine H.M. (HSC) <
> Bla...@ou...<mailto:Bla...@ou...>> wrote:
> Hi Neena,
>
> Thank you for attaching your PDB file.
> That was a good idea.
> It was very helpful for trouble-shooting.
>
> Look inside yourPDB file with a text editor.
> Your pdbPDB file is incomplete in three ways:
>
> 1) The third column of atom types lacks CA (Calpha) atoms.
> PyMOL cannot recognize your coordinates as being from a protein.
> You can use PDBeditor.jar or any good text editor (not MS Word) to edit
> the atom records.
> If you need help selecting a text editor, check out
> https://mooerslab.github.io/pymolsnips/#editors<
> https://urldefense.proofpoint.com/v2/url?u=https-3A__mooerslab.github.io_pymolsnips_-23editors&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=_0_SlrKbnune5f30F7yXXfCZeqLy4On9xiqmMCnp8i8&s=kNiqLqCiIujYjPxmB4ojZgo5FPlLYD2sh_pNAf8a9QI&e=
> >.
>
> 2) Your PDB file lacks  HELIX and SHEET records.
> PyMOL's cartoon function uses these in the default automatic mode.
>
> 3) Your PDB file lacks residue identifiers (resi) and residue names (resn).
> You might still be able to make a cartoon without them, but their absence
> will hinder making selections.
>
> Best regards,
>
> Blaine
>
>
>
>
> Hello PyMOL users,
>
> I performed a geometry optimization of a peptide on gaussview and then
> saved the output log file as a PDB. However, when I open this PDB file
> (attached hereby) in Pymol, I cannot enable the cartoon view of the
> secondary structure; I can only enable the line and stick representation.
>
> Any insight on what might be going wrong?
>
> Many thanks,
> Neena
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...<
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=_0_SlrKbnune5f30F7yXXfCZeqLy4On9xiqmMCnp8i8&s=zOVDhVRXeYBhd3YRxmRvI82_GPmugMqg-4nXdTiwvLM&e=
> >
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe<
> https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=_0_SlrKbnune5f30F7yXXfCZeqLy4On9xiqmMCnp8i8&s=ASKJ73KuITt7Dqx6TGi5LziWphhpFKsW1cP7pRo1KYw&e=
> >
>

Re: [PyMOL] [EXTERNAL] No cartoon view for custom PDB file

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

Hi Neena,
 
Adding to Kamil's explanation, the role of each column for a ATOM record in the PDB file is explained here:  https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM.    

The PDBeditor.jar program can help you retain the fixed file format of the PDB file: http://www.bioinformatics.org/pdbeditor/wiki/.

Best regards,

Blaine

________________________________________
From: Kamil Steczkiewicz [kam...@gm...]
Sent: Wednesday, July 07, 2021 2:29 AM
To: Neena Susan Eappen
Cc: Mooers, Blaine H.M.  (HSC); zb...@cu...; pymol-users
Subject: Re: [PyMOL] [EXTERNAL] No cartoon view for custom PDB file

You got error in column positioning in PDB file - I added two whitespaces after ATOM mark. It probably couldn't parse the PDB file properly as the PDB file is column-specific format. It works now.
Chk attached file in PyMOL.
Kamil


wt., 6 lip 2021 o 23:13 Neena Susan Eappen <nee...@gm...<mailto:nee...@gm...>> napisał(a):
Hello PyMOL users,

Please take a look at the two attached PDB files (opt 20 and opt 21); I formatted opt21.pdb file to match with that of opt20.pdb for PyMOL to recognize the former as a peptide. However, now I can neither see a line nor cartoon representation of the opt21 peptide anymore.
Any insights on what could be wrong in the opt21 PDB file?

Many thanks,
Neena

On Sat, 3 Jul 2021 at 23:38, Neena Susan Eappen <nee...@gm...<mailto:nee...@gm...>> wrote:
Thank you Blaine and Zuben for your insights and troubleshooting the problem! I understood the formatting issue with the current PDB file, will do the necessary changes.

Regards,
Neena

On Sat, 3 Jul 2021 at 09:59, Mooers, Blaine H.M. (HSC) <Bla...@ou...<mailto:Bla...@ou...>> wrote:
Hi Neena,

Thank you for attaching your PDB file.
That was a good idea.
It was very helpful for trouble-shooting.

Look inside yourPDB file with a text editor.
Your pdbPDB file is incomplete in three ways:

1) The third column of atom types lacks CA (Calpha) atoms.
PyMOL cannot recognize your coordinates as being from a protein.
You can use PDBeditor.jar or any good text editor (not MS Word) to edit the atom records.
If you need help selecting a text editor, check out https://mooerslab.github.io/pymolsnips/#editors<https://urldefense.proofpoint.com/v2/url?u=https-3A__mooerslab.github.io_pymolsnips_-23editors&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=_0_SlrKbnune5f30F7yXXfCZeqLy4On9xiqmMCnp8i8&s=kNiqLqCiIujYjPxmB4ojZgo5FPlLYD2sh_pNAf8a9QI&e=>.

2) Your PDB file lacks  HELIX and SHEET records.
PyMOL's cartoon function uses these in the default automatic mode.

3) Your PDB file lacks residue identifiers (resi) and residue names (resn).
You might still be able to make a cartoon without them, but their absence will hinder making selections.

Best regards,

Blaine




Hello PyMOL users,

I performed a geometry optimization of a peptide on gaussview and then saved the output log file as a PDB. However, when I open this PDB file (attached hereby) in Pymol, I cannot enable the cartoon view of the secondary structure; I can only enable the line and stick representation.

Any insight on what might be going wrong?

Many thanks,
Neena
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Re: [PyMOL] [EXTERNAL] No cartoon view for custom PDB file

[Kamil S. <kam...@gm...>]

You got error in column positioning in PDB file - I added two whitespaces
after ATOM mark. It probably couldn't parse the PDB file properly as the
PDB file is column-specific format. It works now.
Chk attached file in PyMOL.
Kamil


wt., 6 lip 2021 o 23:13 Neena Susan Eappen <nee...@gm...>
napisał(a):

> Hello PyMOL users,
>
> Please take a look at the two attached PDB files (opt 20 and opt 21); I
> formatted opt21.pdb file to match with that of opt20.pdb for PyMOL to
> recognize the former as a peptide. However, now I can neither see a line
> nor cartoon representation of the opt21 peptide anymore.
> *Any insights on what could be wrong in the opt21 PDB file?*
>
> Many thanks,
> Neena
>
> On Sat, 3 Jul 2021 at 23:38, Neena Susan Eappen <nee...@gm...>
> wrote:
>
>> Thank you Blaine and Zuben for your insights and troubleshooting the
>> problem! I understood the formatting issue with the current PDB file, will
>> do the necessary changes.
>>
>> Regards,
>> Neena
>>
>> On Sat, 3 Jul 2021 at 09:59, Mooers, Blaine H.M. (HSC) <
>> Bla...@ou...> wrote:
>>
>>> Hi Neena,
>>>
>>> Thank you for attaching your PDB file.
>>> That was a good idea.
>>> It was very helpful for trouble-shooting.
>>>
>>> Look inside yourPDB file with a text editor.
>>> Your pdbPDB file is incomplete in three ways:
>>>
>>> 1) The third column of atom types lacks CA (Calpha) atoms.
>>> PyMOL cannot recognize your coordinates as being from a protein.
>>> You can use PDBeditor.jar or any good text editor (not MS Word) to edit
>>> the atom records.
>>> If you need help selecting a text editor, check out
>>> https://mooerslab.github.io/pymolsnips/#editors.
>>>
>>> 2) Your PDB file lacks  HELIX and SHEET records.
>>> PyMOL's cartoon function uses these in the default automatic mode.
>>>
>>> 3) Your PDB file lacks residue identifiers (resi) and residue names
>>> (resn).
>>> You might still be able to make a cartoon without them, but their
>>> absence will hinder making selections.
>>>
>>> Best regards,
>>>
>>> Blaine
>>>
>>>
>>>
>>>
>>> Hello PyMOL users,
>>>
>>> I performed a geometry optimization of a peptide on gaussview and then
>>> saved the output log file as a PDB. However, when I open this PDB file
>>> (attached hereby) in Pymol, I cannot enable the cartoon view of the
>>> secondary structure; I can only enable the line and stick representation.
>>>
>>> Any insight on what might be going wrong?
>>>
>>> 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

Re: [PyMOL] [EXTERNAL] No cartoon view for custom PDB file

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

Hello PyMOL users,

Please take a look at the two attached PDB files (opt 20 and opt 21); I
formatted opt21.pdb file to match with that of opt20.pdb for PyMOL to
recognize the former as a peptide. However, now I can neither see a line
nor cartoon representation of the opt21 peptide anymore.
*Any insights on what could be wrong in the opt21 PDB file?*

Many thanks,
Neena

On Sat, 3 Jul 2021 at 23:38, Neena Susan Eappen <nee...@gm...>
wrote:

> Thank you Blaine and Zuben for your insights and troubleshooting the
> problem! I understood the formatting issue with the current PDB file, will
> do the necessary changes.
>
> Regards,
> Neena
>
> On Sat, 3 Jul 2021 at 09:59, Mooers, Blaine H.M. (HSC) <
> Bla...@ou...> wrote:
>
>> Hi Neena,
>>
>> Thank you for attaching your PDB file.
>> That was a good idea.
>> It was very helpful for trouble-shooting.
>>
>> Look inside yourPDB file with a text editor.
>> Your pdbPDB file is incomplete in three ways:
>>
>> 1) The third column of atom types lacks CA (Calpha) atoms.
>> PyMOL cannot recognize your coordinates as being from a protein.
>> You can use PDBeditor.jar or any good text editor (not MS Word) to edit
>> the atom records.
>> If you need help selecting a text editor, check out
>> https://mooerslab.github.io/pymolsnips/#editors.
>>
>> 2) Your PDB file lacks  HELIX and SHEET records.
>> PyMOL's cartoon function uses these in the default automatic mode.
>>
>> 3) Your PDB file lacks residue identifiers (resi) and residue names
>> (resn).
>> You might still be able to make a cartoon without them, but their absence
>> will hinder making selections.
>>
>> Best regards,
>>
>> Blaine
>>
>>
>>
>>
>> Hello PyMOL users,
>>
>> I performed a geometry optimization of a peptide on gaussview and then
>> saved the output log file as a PDB. However, when I open this PDB file
>> (attached hereby) in Pymol, I cannot enable the cartoon view of the
>> secondary structure; I can only enable the line and stick representation.
>>
>> Any insight on what might be going wrong?
>>
>> Many thanks,
>> Neena
>>
>

Re: [PyMOL] [EXTERNAL] No cartoon view for custom PDB file

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

Thank you Blaine and Zuben for your insights and troubleshooting the
problem! I understood the formatting issue with the current PDB file, will
do the necessary changes.

Regards,
Neena

On Sat, 3 Jul 2021 at 09:59, Mooers, Blaine H.M. (HSC) <
Bla...@ou...> wrote:

> Hi Neena,
>
> Thank you for attaching your PDB file.
> That was a good idea.
> It was very helpful for trouble-shooting.
>
> Look inside yourPDB file with a text editor.
> Your pdbPDB file is incomplete in three ways:
>
> 1) The third column of atom types lacks CA (Calpha) atoms.
> PyMOL cannot recognize your coordinates as being from a protein.
> You can use PDBeditor.jar or any good text editor (not MS Word) to edit
> the atom records.
> If you need help selecting a text editor, check out
> https://mooerslab.github.io/pymolsnips/#editors.
>
> 2) Your PDB file lacks  HELIX and SHEET records.
> PyMOL's cartoon function uses these in the default automatic mode.
>
> 3) Your PDB file lacks residue identifiers (resi) and residue names (resn).
> You might still be able to make a cartoon without them, but their absence
> will hinder making selections.
>
> Best regards,
>
> Blaine
>
>
>
>
> Hello PyMOL users,
>
> I performed a geometry optimization of a peptide on gaussview and then
> saved the output log file as a PDB. However, when I open this PDB file
> (attached hereby) in Pymol, I cannot enable the cartoon view of the
> secondary structure; I can only enable the line and stick representation.
>
> Any insight on what might be going wrong?
>
> Many thanks,
> Neena
>

Re: [PyMOL] [EXTERNAL] No cartoon view for custom PDB file

[Brown, Z. <zb...@cu...>]

Hi Neena,

It's stored everything as a single object.  Check the display -> sequence and you'll see what I mean.
None of your residues have a number.  I assume Pymol needs discrete residues to display a cartoon.

See an example line--
Yours:
HETATM    1  N           0      -1.172   4.898   0.414                       N

Example:
ATOM      1  O5' U   2   1     197.678 159.150 189.116  1.00 35.29           O

It looks like it is missing chain ID and also residue number.
You could manually fix the PDB.  Have a look at some examples and work out what columns to keep/change.

hope that helps,
Zuben


________________________________
From: Neena Susan Eappen <nee...@gm...>
Sent: Saturday, July 3, 2021 9:26 AM
To: pymol-users <pym...@li...>
Subject: [EXTERNAL] [PyMOL] No cartoon view for custom PDB file

Hello PyMOL users,

I performed a geometry optimization of a peptide on gaussview and then saved the output log file as a PDB. However, when I open this PDB file (attached hereby) in Pymol, I cannot enable the cartoon view of the secondary structure; I can only enable the line and stick representation.

Any insight on what might be going wrong?

Many thanks,
Neena

Re: [PyMOL] [EXTERNAL] No cartoon view for custom PDB file

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

Hi Neena,

Thank you for attaching your PDB file.
That was a good idea.
It was very helpful for trouble-shooting.

Look inside yourPDB file with a text editor.
Your pdbPDB file is incomplete in three ways: 

1) The third column of atom types lacks CA (Calpha) atoms.
PyMOL cannot recognize your coordinates as being from a protein.
You can use PDBeditor.jar or any good text editor (not MS Word) to edit the atom records.
If you need help selecting a text editor, check out https://mooerslab.github.io/pymolsnips/#editors.

2) Your PDB file lacks  HELIX and SHEET records.
PyMOL's cartoon function uses these in the default automatic mode.

3) Your PDB file lacks residue identifiers (resi) and residue names (resn).
You might still be able to make a cartoon without them, but their absence will hinder making selections.

Best regards,

Blaine




Hello PyMOL users,

I performed a geometry optimization of a peptide on gaussview and then saved the output log file as a PDB. However, when I open this PDB file (attached hereby) in Pymol, I cannot enable the cartoon view of the secondary structure; I can only enable the line and stick representation.

Any insight on what might be going wrong?

Many thanks,
Neena

[PyMOL] No cartoon view for custom PDB file

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

Hello PyMOL users,

I performed a geometry optimization of a peptide on gaussview and then
saved the output log file as a PDB. However, when I open this PDB file
(attached hereby) in Pymol, I cannot enable the cartoon view of the
secondary structure; I can only enable the line and stick representation.

Any insight on what might be going wrong?

Many thanks,
Neena

[PyMOL] PyMOL 2.5.1 Released

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

Greetings all,

A maintenance release for 2.5 (as 2.5.1) has been uploaded to
https://pymol.org/. Details of maintenance releases for 2.5 can be found at
the bottom of https://pymol.org/dokuwiki/doku.php?id=media:new25. We will
continue to address feedback and bug reports and expect to have 2.5.2 out
later this month.

I would also like to state a correction from the previous email I sent last
month regarding conda installation for PyMOL 2.5. Our conda packages are
now based on conda-forge. More information about how to install PyMOL via
conda for versions 2.5.0 and later, please refer to:
https://pymol.org/conda/.

Finally, I would like to share an opportunity for educators using PyMOL or
other Schrodinger software:
Schrödinger is proud to be hosting the 2021 Educator’s Day on Wednesday,
July 28th.  This one-day virtual event will highlight the role of
computational tools in the classroom and connect you with educators from
all over the world.
https://www.schrodinger.com/conferences-meetings/2021-schrodinger-educators-day-online

As always, we welcome any feedback and bug reports.

Cheers,
- The PyMOL Team at Schrödinger

-- 

*Jarrett Johnson* | Senior Developer
[image: Schrodinger Logo] <https://www.schrodinger.com/>

Re: [PyMOL] why one atom of the structure is too big in Pymol?

[Kevin J. <kj...@st...>]

The columns of your pdb aren't properly aligned; you have extra spaces
where they shouldn't be. You can fix it in a text editor. See
https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html
for more information.
hth
Kevin


--
Kevin Jude, PhD (he/him/his)
Structural Biology Research Specialist, Garcia Lab
Howard Hughes Medical Institute
Stanford University School of Medicine
Beckman B177, 279 Campus Drive, Stanford CA 94305
Phone: (650) 723-6431

On Fri, Jun 25, 2021 at 7:45 AM Nazi Ebrahimi <naz...@gm...>
wrote:

> Hello,
> Please see the attached. Pymol shows one of the oxygens too big.
>
> Can you help me with this?
>
> Nazi
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] why one atom of the structure is too big in Pymol?

[Nazi E. <naz...@gm...>]

Hello,
Please see the attached. Pymol shows one of the oxygens too big.

Can you help me with this?

Nazi

[PyMOL] pymolrc.pml location

[Michael M. <mic...@gm...>]

Dear all,

 

I have PyMOL (windows, open-source) installed in my windows machine. The
default pymolrc.pml location is "C:\Users\$user\pymolrc.pml". It works well
if I place the pymolrc.pml file there. 

 

Is it possible to change this default location? There is a "Edit pymolrc"
option under "File" tab. However it seems it is just an editor. I could not
find the seting to change this location.

 

Thank you very much!

 

Michael

[PyMOL] How to enable Pymol when give ModuleNotFoundError: No module named '_tkinter' error

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

Hi,
I am using MacOSX Catalina.
I installed Pymol with this command:


brew install brewsci/bio/pymol

However when I called it

 $ pymol

It gave me this error:


7, in <module>
    import _tkinter # If this fails your Python may not be configured for Tk
ModuleNotFoundError: No module named '_tkinter'


How can I resolve this?


My Python version is:
Python 3.8.5 (default, Sep  4 2020, 02:22:02)
[Clang 10.0.0 ] :: Anaconda, Inc. on darwin
Type "help", "copyright", "credits" or "license" for more information.

G.V.

Re: [PyMOL] Programmatically adding hydrogen and remove water to multiple PDB files

[sriram r. <hyp...@gm...>]

Hi Viswanath,
Please find the attach file which might help you,
You have to give the input folder path containing all the pdbs, for example
in terminal input:
"Please provide the input directory:/home/viswanath/pdb "and "Enter the
required files extension .pdb:.pdb" as input,
It will create a new folder "new" which will contain all the pdb files with
water removed and hydrogen added.
I hope that solves your issue.

Best wishes.
S.Sriram
Postdoctoral Research fellow,
Computational Structural Biology Team,
RIKEN Center for Computational Science(R-CCS), Kobe, Japan.

On Thu, Jun 17, 2021 at 6:16 PM Gundala Viswanath <gun...@gm...>
wrote:

> Does Autodocktools provide a command line for batch processing?
>
> G.V.
>
> On Thu, Jun 17, 2021 at 9:24 PM Saurabh Gayali <sau...@gm...>
> wrote:
>
>> You should use autodocktools [ADT] or openbabel for this purpose.
>> Converting PDB to PDBQT.
>>
>> ------------------------------
>>
>> *Saurabh Gayali* / Post Doctoral Fellow
>> sau...@gm... / +91 8800412916
>>
>> *CSIR-IGIB*
>> <http://example.com/>New Delhi, India
>>
>>
>> On Thu, Jun 17, 2021 at 4:01 PM Gundala Viswanath <gun...@gm...>
>> wrote:
>>
>>> Hi
>>>
>>> I'm trying to dock a ligand to several hundred PDB files (receptors). I
>>> thus need to prepare those files like removing water and adding hydrogen.
>>>
>>> I can do that manually using Pymol. But it's too troublesome. Is there a
>>> way to do it programmatically with Pymol command line procedure?
>>>
>>>
>>> Sincerely,
>>>
>>> G.V.
>>> _______________________________________________
>>> PyMOL-users mailing list
>>> Archives: http://www.mail-archive.com/pym...@li...
>>> Unsubscribe:
>>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>>
>> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Programmatically adding hydrogen and remove water to multiple PDB files

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

Does Autodocktools provide a command line for batch processing?

G.V.

On Thu, Jun 17, 2021 at 9:24 PM Saurabh Gayali <sau...@gm...>
wrote:

> You should use autodocktools [ADT] or openbabel for this purpose.
> Converting PDB to PDBQT.
>
> ------------------------------
>
> *Saurabh Gayali* / Post Doctoral Fellow
> sau...@gm... / +91 8800412916
>
> *CSIR-IGIB*
> <http://example.com/>New Delhi, India
>
>
> On Thu, Jun 17, 2021 at 4:01 PM Gundala Viswanath <gun...@gm...>
> wrote:
>
>> Hi
>>
>> I'm trying to dock a ligand to several hundred PDB files (receptors). I
>> thus need to prepare those files like removing water and adding hydrogen.
>>
>> I can do that manually using Pymol. But it's too troublesome. Is there a
>> way to do it programmatically with Pymol command line procedure?
>>
>>
>> Sincerely,
>>
>> G.V.
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>

[PyMOL] Programmatically adding hydrogen and remove water to multiple PDB files

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

Hi

I'm trying to dock a ligand to several hundred PDB files (receptors). I
thus need to prepare those files like removing water and adding hydrogen.

I can do that manually using Pymol. But it's too troublesome. Is there a
way to do it programmatically with Pymol command line procedure?


Sincerely,

G.V.

Re: [PyMOL] Farewell

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

Thank you for the incredible support to the community via this marvelous
tool.
Hope to see more of your wonderful work in future.

Best Regards,

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

*Saurabh Gayali* / Post Doctoral Fellow
sau...@gm... / +91 8800412916

*CSIR-IGIB*
<http://example.com/>New Delhi, India


On Fri, Apr 30, 2021 at 7:47 PM Thomas Holder <tho...@sc...>
wrote:

> Dear PyMOL community -
>
> The time has come for me to hand over my PyMOL development
> responsibilities at Schrödinger. It's been an incredible journey for
> me to get involved with the PyMOL community, to become a PyMOL fellow
> in 2011 and to start working full time for the project in 2012. I'm
> extremely grateful to all the people at Schrödinger who made this
> possible, and of course to all of you - the user community - who've
> shown me every day that my work is meaningful.
>
> PyMOL has a unique place within Schrödinger, and a highly motivated
> and skilled team of developers and scientists stand behind it. They
> have some great plans and I'm excited to watch how they will take
> PyMOL to the next level.
>
> I don't think that my PyMOL journey is over yet. But for the next
> chapter in my career, I'll "just" be a user and a member of the
> community. See you around.
>
> Cheers,
>   Thomas
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Farewell

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

I can only but agree with al of these comments! Thanks for the support and god luck with the future Thomas. 

PyMOL has been my go to software for probably close to 20 years !

Regards

Joel

-----Original Message-----
From: Jason Key <ke...@hk...> 
Sent: Saturday, 1 May 2021 3:15 AM
To: Thomas Holder <tho...@sc...>
Cc: Pymol User list <pym...@li...>
Subject: Re: [PyMOL] Farewell

Hi Everyone,

I'd like to publicly thank Thomas for his contribution to PyMOL over the last decade.

PyMOL is the primary tool the broader scientific community uses to access the results we create as structural biologists.
For many researchers, PyMOL is their first window into macromolecular structures. And, at the very least, journal covers are MUCH nicer because of it.
It is, without doubt, the most popular title in the SBGrid installation. It always has been.

I assure everyone here that creating reliable software that runs on 3 operating systems with an open source model and great user support is no easy task.
Sustaining that effort for nearly 10 years is another feat altogether.

If you'd like to see how far PyMOL has come, here's a webinar we did
(live!) in 2013 here :
https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.youtube.com%2Fwatch%3Fv%3DUHOUFJmj_fM&amp;data=04%7C01%7Cjoel.tyndall%40otago.ac.nz%7C9b08137f4082497b23a108d90bfc06b3%7C0225efc578fe4928b1579ef24809e9ba%7C1%7C0%7C637553999355683603%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&amp;sdata=4ClB06YR4cNyUz3yLYkq7rA5vAO9BjTP9w%2FMbRZC4KE%3D&amp;reserved=0

Best of luck in your next chapter Thomas!

Cheers,
Jason

--
Jason Key, PhD
Project Lead
SBGrid Consortium, Harvard Medical School


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[PyMOL] Merging multiple ligands as separate pdb

[sriram r. <hyp...@gm...>]

Dear Pymol user,
I have a protein and multiple ligand conformations as trajectories, i.e, i
have loaded the protein
using "cmd.load("protein.pdb", "input")"
I have split the ligand into multiple states using the following command
split_states ligand, prefix=sel

now I have multiple objected created from "sel0001-sel0010" for example
I wanted to create merged object as as individual files, like
trj0001-traj0010
l.e,
create trj0001, protein or sel0001
save traj0001.pdb, traj0001
create trj0002, protein or sel0002
save traj0002.pdb, traj0002
...
...

I want to automate file creation using python but I am wrote a script like
the below but it is lengthy and I was not not able to effectively use pymol
commands,"(cmd.createand cmd.save)" and I am stuck, can anyone suggest, if
this can be shortened. My script is as follows, I am new to python
programming, any user input will be helpful.
Thankyou
with regards
Sriram
### script###
python

x=[]
for i in range(1,10):
 x.append(f"trj%04d"%i)


y=[]
for j in range(1,10):
 y.append(f"sel%04d"%j)


z=[]
for i,j in zip(x,y):
 z.append(f"create {i},{j} or input")


A=[]
for k in zip(x):
  A.append("save {}.pdb,{}".format(*k,*k))


f=open('create.pml','w+')
for e in zip(z):
 print(*e,sep="\n",file=f)
f.close()

s=open('save.pml','w+')
for f in zip(A):
  print(*f,sep="\n",file=s)
s.close()
python end

run create.pml
run save.pml
###END###

[PyMOL] generate vacuum electrostatics fails in v. 2.5.0

[Stefan G. <sga...@gm...>]

Hi,

I was trying to generate a vacuum electrostatics map in the new Pymol
version 2.5.0 on Windows and it failed with this error in all PDB
files I tried.

WARNING: unrecognized or incomplete residues are being deleted:

[list of the entire residue range]

Pop-Error: invalid source selection name 'assign_tmp1'

Any advice?

Best,
Stefan