pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] surface representation of the protein-ligand interactions

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

Hi Enrico, 

This is beyond my understanding, try and run this bash script without making the surface transparent (to figure out if the issue comes from the transparency)

Also try the rebuild command before saving the image: https://pymolwiki.org/index.php/Rebuild

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 10/1/22, 11:10 pm, "Enrico Martinez" <jms...@gm...> wrote:

    Thank you very much,Ali!
    just one question: when I do the surface calculations using bash
    script operating with the command lines of the pymol it produces
    correctly pse session with the surfaces. BUT if I save an image using
    png, the surface is totally absent. Here are my commands directly from
    the shell script:

    $pymol -c -d "
    from pymol import cmd
    cmd.load('${results}/${output}_${lig_name}_${receptor}_rep${i}.pdb')
    cmd.show( 'surface', '${output}* and polymer within 15 of ${output}*
    and not polymer' )
    cmd.set( 'transparency', '0.5' )
    cmd.save('${vizu}/${output}_${lig_name}_rep${i}.pse')
    cmd.png('${vizu}/${output}_${lig_name}_rep${i}.png',width=${image},height=${image},dpi=50,ray=0)
    "
    As the result of this workflow,  the surface is present in the PSE
    file but not in the png image. Otherwise when I save png directly from
    the pymol's GUI the surface is well captured on the png as well. What
    should I include in my script ?

    пн, 10 янв. 2022 г. в 12:18, Ali Saad Kusay <aku...@un...>:
    >
    > Hi Enrico,
    >
    > You can carve the protein surface around the ligand, i.e. show only the surface behind the ligand, see this guide: https://protect-au.mimecast.com/s/1Of6CNLJyQU0W9yVofmRSV0?domain=pymol.org
    >
    > You can also try and made the surface more transparent, but this doesn't always give the best results, see: https://protect-au.mimecast.com/s/vdsUCOMKzVTp8wQ53fvOudq?domain=pymolwiki.org, i.e.:
    >
    > set transparency, 0.5
    >
    > It would help to see an image of what you are working with atm
    >
    > 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 10/1/22, 10:10 pm, "Enrico Martinez" <jms...@gm...> wrote:
    >
    >     Dear Pymol users!
    >     Working on the vizualisation of the protein-ligand interactions I
    >     would like to switch from cartoon to the surface representation of the
    >     protein, while still being capable to see the ligand-binding cavity
    >     (as well as non-covalent interactions)
    >
    >     Could you suggest me some combination of the options which could helps
    >     me with such vizualisaiton?
    >     I have alread tried
    >     show surface, all within 5 of my_pdb and not polymer
    >     set surface_smooth_edges, onset surface_smooth_edges, on
    >     where my_pdb and not polymer corresponds to the selection of the ligand
    >
    >     Eventualy this create cool surface representation of the protein and
    >     but completely hides the ligand-binding cavity
    >     Many thanks in advance!
    >     Enrico
    >
    >
    >     _______________________________________________
    >     PyMOL-users mailing list
    >     Archives: https://protect-au.mimecast.com/s/5uDYCP7LAXfKwZVvQF1Df45?domain=mail-archive.com
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    >
    >

Re: [PyMOL] surface representation of the protein-ligand interactions

[Enrico M. <jms...@gm...>]

Thank you very much,Ali!
just one question: when I do the surface calculations using bash
script operating with the command lines of the pymol it produces
correctly pse session with the surfaces. BUT if I save an image using
png, the surface is totally absent. Here are my commands directly from
the shell script:

$pymol -c -d "
from pymol import cmd
cmd.load('${results}/${output}_${lig_name}_${receptor}_rep${i}.pdb')
cmd.show( 'surface', '${output}* and polymer within 15 of ${output}*
and not polymer' )
cmd.set( 'transparency', '0.5' )
cmd.save('${vizu}/${output}_${lig_name}_rep${i}.pse')
cmd.png('${vizu}/${output}_${lig_name}_rep${i}.png',width=${image},height=${image},dpi=50,ray=0)
"
As the result of this workflow,  the surface is present in the PSE
file but not in the png image. Otherwise when I save png directly from
the pymol's GUI the surface is well captured on the png as well. What
should I include in my script ?

пн, 10 янв. 2022 г. в 12:18, Ali Saad Kusay <aku...@un...>:
>
> Hi Enrico,
>
> You can carve the protein surface around the ligand, i.e. show only the surface behind the ligand, see this guide: https://pymol.org/dokuwiki/doku.php?id=figure:carving_surfaces
>
> You can also try and made the surface more transparent, but this doesn't always give the best results, see: https://pymolwiki.org/index.php/Transparency, i.e.:
>
> set transparency, 0.5
>
> It would help to see an image of what you are working with atm
>
> 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 10/1/22, 10:10 pm, "Enrico Martinez" <jms...@gm...> wrote:
>
>     Dear Pymol users!
>     Working on the vizualisation of the protein-ligand interactions I
>     would like to switch from cartoon to the surface representation of the
>     protein, while still being capable to see the ligand-binding cavity
>     (as well as non-covalent interactions)
>
>     Could you suggest me some combination of the options which could helps
>     me with such vizualisaiton?
>     I have alread tried
>     show surface, all within 5 of my_pdb and not polymer
>     set surface_smooth_edges, onset surface_smooth_edges, on
>     where my_pdb and not polymer corresponds to the selection of the ligand
>
>     Eventualy this create cool surface representation of the protein and
>     but completely hides the ligand-binding cavity
>     Many thanks in advance!
>     Enrico
>
>
>     _______________________________________________
>     PyMOL-users mailing list
>     Archives: https://protect-au.mimecast.com/s/cnxDCMwGxOtqr9lJjhwM0N6?domain=mail-archive.com
>     Unsubscribe: https://protect-au.mimecast.com/s/ZXpPCNLJyQU0W9R6oh42rcB?domain=sourceforge.net
>
>

Re: [PyMOL] surface representation of the protein-ligand interactions

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

Hi Enrico, 

You can carve the protein surface around the ligand, i.e. show only the surface behind the ligand, see this guide: https://pymol.org/dokuwiki/doku.php?id=figure:carving_surfaces

You can also try and made the surface more transparent, but this doesn't always give the best results, see: https://pymolwiki.org/index.php/Transparency, i.e.:

set transparency, 0.5

It would help to see an image of what you are working with atm

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 10/1/22, 10:10 pm, "Enrico Martinez" <jms...@gm...> wrote:

    Dear Pymol users!
    Working on the vizualisation of the protein-ligand interactions I
    would like to switch from cartoon to the surface representation of the
    protein, while still being capable to see the ligand-binding cavity
    (as well as non-covalent interactions)

    Could you suggest me some combination of the options which could helps
    me with such vizualisaiton?
    I have alread tried
    show surface, all within 5 of my_pdb and not polymer
    set surface_smooth_edges, onset surface_smooth_edges, on
    where my_pdb and not polymer corresponds to the selection of the ligand

    Eventualy this create cool surface representation of the protein and
    but completely hides the ligand-binding cavity
    Many thanks in advance!
    Enrico


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[PyMOL] surface representation of the protein-ligand interactions

[Enrico M. <jms...@gm...>]

Dear Pymol users!
Working on the vizualisation of the protein-ligand interactions I
would like to switch from cartoon to the surface representation of the
protein, while still being capable to see the ligand-binding cavity
(as well as non-covalent interactions)

Could you suggest me some combination of the options which could helps
me with such vizualisaiton?
I have alread tried
show surface, all within 5 of my_pdb and not polymer
set surface_smooth_edges, onset surface_smooth_edges, on
where my_pdb and not polymer corresponds to the selection of the ligand

Eventualy this create cool surface representation of the protein and
but completely hides the ligand-binding cavity
Many thanks in advance!
Enrico

Re: [PyMOL] how to create multi-model pdb for protein-ligand complex?

[Enrico M. <jms...@gm...>]

try this man!

awk 'NR==FNR {s = s $0 ORS; next} $0 == "ENDMDL" {$0 = s $0} 1'
./receptor.pdb ./docking.pdb >> together.pdb

пт, 7 янв. 2022 г. в 18:10, Saurabh Gayali <sau...@gm...>:

> I guess we need to split the docking poses first and then merge them
> together.
> Hope I come up with a python script or anyone else does.
>
> On Fri, 7 Jan, 2022, 18:47 Enrico Martinez, <jms...@gm...>
> wrote:
>
>> In the case of
>> cmd.save("together.pdb", "all", "0", "pdb")
>> it saves everything in one pdb when the protein is present only in the
>> first model, while I need to obtain its representation in all models
>> Cheers
>> E.
>>
>> пт, 7 янв. 2022 г. в 13:14, Saurabh Gayali <sau...@gm...>:
>>
>>> Have you tried the save command after opening both files?
>>> https://pymol.org/dokuwiki/doku.php?id=command:save
>>> Though not sure how the different poses will merge.
>>> Also looking for a solution for a similar problem.
>>>
>>> ------------------------------
>>>
>>> *Saurabh Gayali* / Post Doctoral Fellow
>>> sau...@gm... / +91 8800412916
>>>
>>> *CSIR-IGIB*
>>> <http://example.com/>New Delhi, India
>>>
>>>
>>> [image: Mailtrack]
>>> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&> Sender
>>> notified by
>>> Mailtrack
>>> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&> 07/01/22,
>>> 05:43:49 pm
>>>
>>> On Fri, Jan 7, 2022 at 3:43 PM Enrico Martinez <jms...@gm...>
>>> wrote:
>>>
>>>> Dear Autodock Users!
>>>> I am dealing with the structural analysis of the protein-ligand
>>>> interactions observed in the protein-ligand docking using VINA.
>>>> Basically operating with the outputs I have two different pdb files:
>>>> 1) for docking receptor (1 protein model) as well as for 2) docking
>>>> sollutions (100 solutions). So I use pymol to open the both filles and
>>>> visualize them
>>>>
>>>> pymol sollutions.pdb receptor.pdb
>>>>
>>>> May you suggest me some pymol command to merge the both in the pymol
>>>> to. create multi-model PDB consisted of the both receptor and ligand
>>>> poses in order then I could perform some structural analysis of this
>>>> combined complex?
>>>> Many thanks in advance
>>>> Enrico
>>>>
>>>>
>>>> _______________________________________________
>>>> 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 create multi-model pdb for protein-ligand complex?

[Enrico M. <jms...@gm...>]

In the case of
cmd.save("together.pdb", "all", "0", "pdb")
it saves everything in one pdb when the protein is present only in the
first model, while I need to obtain its representation in all models
Cheers
E.

пт, 7 янв. 2022 г. в 13:14, Saurabh Gayali <sau...@gm...>:

> Have you tried the save command after opening both files?
> https://pymol.org/dokuwiki/doku.php?id=command:save
> Though not sure how the different poses will merge.
> Also looking for a solution for a similar problem.
>
> ------------------------------
>
> *Saurabh Gayali* / Post Doctoral Fellow
> sau...@gm... / +91 8800412916
>
> *CSIR-IGIB*
> <http://example.com/>New Delhi, India
>
>
> [image: Mailtrack]
> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&> Sender
> notified by
> Mailtrack
> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&> 07/01/22,
> 05:43:49 pm
>
> On Fri, Jan 7, 2022 at 3:43 PM Enrico Martinez <jms...@gm...>
> wrote:
>
>> Dear Autodock Users!
>> I am dealing with the structural analysis of the protein-ligand
>> interactions observed in the protein-ligand docking using VINA.
>> Basically operating with the outputs I have two different pdb files:
>> 1) for docking receptor (1 protein model) as well as for 2) docking
>> sollutions (100 solutions). So I use pymol to open the both filles and
>> visualize them
>>
>> pymol sollutions.pdb receptor.pdb
>>
>> May you suggest me some pymol command to merge the both in the pymol
>> to. create multi-model PDB consisted of the both receptor and ligand
>> poses in order then I could perform some structural analysis of this
>> combined complex?
>> Many thanks in advance
>> Enrico
>>
>>
>> _______________________________________________
>> 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 create multi-model pdb for protein-ligand complex?

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

Have you tried the save command after opening both files?
https://pymol.org/dokuwiki/doku.php?id=command:save
Though not sure how the different poses will merge.
Also looking for a solution for a similar problem.

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

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

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


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On Fri, Jan 7, 2022 at 3:43 PM Enrico Martinez <jms...@gm...>
wrote:

> Dear Autodock Users!
> I am dealing with the structural analysis of the protein-ligand
> interactions observed in the protein-ligand docking using VINA.
> Basically operating with the outputs I have two different pdb files:
> 1) for docking receptor (1 protein model) as well as for 2) docking
> sollutions (100 solutions). So I use pymol to open the both filles and
> visualize them
>
> pymol sollutions.pdb receptor.pdb
>
> May you suggest me some pymol command to merge the both in the pymol
> to. create multi-model PDB consisted of the both receptor and ligand
> poses in order then I could perform some structural analysis of this
> combined complex?
> Many thanks in advance
> Enrico
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>

[PyMOL] how to create multi-model pdb for protein-ligand complex?

[Enrico M. <jms...@gm...>]

Dear Autodock Users!
I am dealing with the structural analysis of the protein-ligand
interactions observed in the protein-ligand docking using VINA.
Basically operating with the outputs I have two different pdb files:
1) for docking receptor (1 protein model) as well as for 2) docking
sollutions (100 solutions). So I use pymol to open the both filles and
visualize them

pymol sollutions.pdb receptor.pdb

May you suggest me some pymol command to merge the both in the pymol
to. create multi-model PDB consisted of the both receptor and ligand
poses in order then I could perform some structural analysis of this
combined complex?
Many thanks in advance
Enrico

[PyMOL] Questions_InterfaceResidues

[arooma m. <aro...@gm...>]

Could you please post it on my behalf

Hi Everyone

I have few basic questions, i would really appreciate if any one could answer

 In interfaceResidue script,

def interfaceResidues(cmpx, cA='c. A', cB='c. B', cutoff=1.0,
selName="interface"):

dASA cutoff is *1.0*.

*How to decide this cutoff value? In a few examples I have noticed it
is 0.75 and 2.5. *

*I wonder if residues of the two chains (A and B)  should be at a
certain distance from each other like 6 or 8 Angstroms?  I think I am
confusing dASA with distance between atoms of the residues.*

my second question is

*Is it possible to get the values dASA of the complex and individual
chains (calculated through the script below) printed into any txt or
excel sheet? *

# get the area of the complete complex
	cmd.get_area(tempC, load_b=1)
	# copy the areas from the loaded b to the q, field.
	cmd.alter(tempC, 'q=b')

	# extract the two chains and calc. the new area
	# note: the q fields are copied to the new objects
	# chA and chB
	cmd.extract(chA, tempC + " and (" + cA + ")")
	cmd.extract(chB, tempC + " and (" + cB + ")")
	cmd.get_area(chA, load_b=1)
	cmd.get_area(chB, load_b=1)

My third question is in PyMol GUI, by using Action--preset--protein
interface, are we executing the same ResidueInterface script . If yes,
then why is there a difference in results?

If No, what is the difference in both these functions

I would really appreciate if you please answer these questions

Thank you

[PyMOL] foggy state just for one of the molecules

[Oganesyan, V. <vah...@as...>]

Hello PyMOLers,

Happy New Year!

Is there a way to show one of the molecules on image in a foggy state irrespective of depth-cue? I want to make an illustration showing how one molecule blocks another for interaction with ligand/receptor.

Thanks in advance.

Vaheh Oganesyan, Ph.D.
[cid:image001.png@01D80228.40A93CD0]
R&D | Biologics Engineering
One Medimmune Way, Gaithersburg, MD 20878
T:  301-398-5851
Vah...@as...<mailto:Oga...@me...>

Re: [PyMOL] Distorted 3-10 helix

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

Have you tried the "DSS" command?
https://pymolwiki.org/index.php/Dss

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

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

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


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On Thu, Dec 16, 2021 at 11:38 PM Bonsor, Daniel (NIH/NCI) [C] via
PyMOL-users <pym...@li...> wrote:

> Dear All,
>
>
>
> My latest structure has several 3-10 helices present, however, a few of
> them in cartoon form shows the starting residue of the helix to be
> distorted/twisted.
>
>
>
> The structure is 2.2Ang and I can clearly see the position of the amide
> bond and the direction of carbonyl, but I cannot stop the twisting of the
> cartoon.
>
>
>
> I have tried altering that residue ss to a loop which “works” (as in the
> problem goes away) but I really wish to show the full helix. I have also
> run DSSPtoPDB and force it not to recognize the 3-10 helices as helices but
> in cartoon form you can see they are helices.
>
>
>
> Do anyone have suggestions or a way to force it to be a helix?
>
> [image: A close up of a toy Description automatically generated with low
> confidence]
>
> Thanks,
>
>
>
> Daniel
>
>
>
>
>
> [image: Text Frederick National Laboratory on a teal background]
>
>
>
> [image: LinkedIn icon]
> <https://www.linkedin.com/company/frederick-national-laboratory-for-cancer-research/>
>  [image: Twitter icon] <https://twitter.com/FredNatLab>  [image: Facebook
> icon] <https://www.facebook.com/FredNatLab>  [image: Instagram icon]
> <https://www.instagram.com/frednatlab/>
>
> *Daniel A Bonsor PhD | Scientist I*
>
> RAS Structural Biology
>
>
>
>
>
> [image: Phone icon]
>
> office: 301-846-5134 / cell: 443-983-2930
>
>
>
> [image: Email icon]
>
> dan...@ni... *[Contractor]*
>
>
>
> [image: Location icon]
>
> Post Office Box B, Frederick, MD 21702
>
>
>
> [image: Link icon]
>
> frederick.cancer.gov
>
>
>
>
>
> The Frederick National Laboratory for Cancer Research is operated by
> Leidos Biomedical Research, Inc. for the National Cancer Institute.
>
> --
>
>
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Re: [PyMOL] Ruge problem visualization of PDBQT file on pymol

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

I hope the "show spheres" command represents the ligands better for you.

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

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

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

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On Wed, Dec 15, 2021 at 11:59 PM EDUARDO JOSÉ AZEVEDO CORREA <
ed...@ep...> wrote:

> Dear friends
> how are you? I hope you are doing well
> I am using autodock vina for virtual screening.. I used the LigPret to
> prepare my ligands into mol2 file, however when MGLTools convert the mol2
> to PDBQT and specially the vina output file in PDBQT has become a very
> anomalous and strange molecule structure.
> This file attached is ZINC100199761 molecule structure in mol2 generated
> from SMILE sequence using LigPrep. After LigPrep I pass it
> through the Avogadro to obtain the best geometry optimization
> Only after that I make the PDBQT conversion using the MGLTools and so the
> molecular docking using vina.
>
> Well did you know what is happening?? Is it a pymol visualization problem
> with pdqbt files?
> Could Anyone could know what the problem is and how to fix it?
> Thanks a lot!!
>
> have a nice end year
>
> Kinds Regards
>
> Eduardo Jose Azevedo Correa
> from Brazil
> --
>
> *Eduardo José Azevedo Corrêa*
>
> Biólogo| Professor e Pesquisador
>
>
> (37)9997-5771
>
> (37)3271-4673
>
> *www.epamig.br <http://www.epamig.br/>*
>
> *EPAMIG Pitangui*
> Rodovia BR - MG352 Km35 Zona Rural
>
> Caixa Postal 43
>
> CEP 35650-000 - Pitangui - MG
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Re: [PyMOL] Structure alignment -- general question

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

Hi George,

You can do pairwise alignments, i.e. align 3 of the structures to one structure.

You can also use the "extra_fit" method (https://pymolwiki.org/index.php/Extra_fit), i.e:

extra_fit name CA, "object", super

Replace object with the structure you want the other 3 to align to, this uses the "super" alignment method but you can also use "align", "cealign", "fit", etc. Depending on what gives the best results. Just a note, this will align all PyMOL objects to your selected object, you can make sub selections as needed.

Cheers,

Ali

Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
The University of Sydney School of Pharmacy | Faculty of Medicine and Health

On 4/1/22, 8:52 pm, "George Tzotzos via PyMOL-users" <pym...@li...> wrote:

    I’m dealing with 4 heterogeneous structures belonging to the same fold. I’d like to compare some conserved structural features and for this purpose it would be useful that the structures are aligned and then visualised in a grid.

    I understand that the align command works for 2 structures only. Is there another way achieve what I described above.

    Looking forward to any suggestions

    Many thanks in advance and all the best for 2022




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Re: [PyMOL] Structure alignment -- general question

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

extra_fit command will work in this scenario.

More information in documentation here:
https://pymolwiki.org/index.php/Extra_fit

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

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

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


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04/01/22,
04:18:41 pm

On Tue, Jan 4, 2022 at 3:18 PM George Tzotzos via PyMOL-users <
pym...@li...> wrote:

> I’m dealing with 4 heterogeneous structures belonging to the same fold.
> I’d like to compare some conserved structural features and for this purpose
> it would be useful that the structures are aligned and then visualised in a
> grid.
>
> I understand that the align command works for 2 structures only. Is there
> another way achieve what I described above.
>
> Looking forward to any suggestions
>
> Many thanks in advance and all the best for 2022
>
>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] Structure alignment -- general question

[George T. <gtz...@me...>]

I’m dealing with 4 heterogeneous structures belonging to the same fold. I’d like to compare some conserved structural features and for this purpose it would be useful that the structures are aligned and then visualised in a grid.

I understand that the align command works for 2 structures only. Is there another way achieve what I described above.

Looking forward to any suggestions

Many thanks in advance and all the best for 2022

[PyMOL] Analysis of protein-ligand interactions

[Enrico M. <jms...@gm...>]

Dear Pymol users!
I am performing analysis of protein-ligand interactions for the ligand
pose established in protein-docking and comparing it with the pattern
observed in the X-ray structure for the same complex.
Is it possible to use some Pymol command in the pymol's command line
to save (in the text log) all of the non-bonded interactions
established between ligand and all of the surrounded groups of the
receptor for two different selections:
(1) between the conformation used for docking and the best docking pose
(2) between the X-ray structure + it's (native) ligand pose

assuming that ((1): two different objects for receptor.pdb and the
ensemble of docking conformations) and ((2): one object consisting of
ligand and receptor together) are loaded in Pymol.
Many thanks in advance!
Cheers
Enrico

[PyMOL] Unable to run pymol from Linux command line

[Max L. <ma...@ya...>]

Hi, 

I installed pymol on Ubuntu 20.04 on WSL (Windows 10) using:

sudo apt-get install -y pymol

However, when I run pymol on the command line, I get this error:

<string>:1: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses
qt.qpa.xcb: could not connect to display
qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found.
This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.
Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, xcb.
Aborted

What should I do to get pymol to work?  

Best regards, 
Max

[PyMOL] Distorted 3-10 helix

[Bonsor, D. (NIH/N. [C] <dan...@ni...>]

Dear All,

My latest structure has several 3-10 helices present, however, a few of them in cartoon form shows the starting residue of the helix to be distorted/twisted.

The structure is 2.2Ang and I can clearly see the position of the amide bond and the direction of carbonyl, but I cannot stop the twisting of the cartoon.

I have tried altering that residue ss to a loop which “works” (as in the problem goes away) but I really wish to show the full helix. I have also run DSSPtoPDB and force it not to recognize the 3-10 helices as helices but in cartoon form you can see they are helices.

Do anyone have suggestions or a way to force it to be a helix?
[A close up of a toy  Description automatically generated with low confidence]
Thanks,

Daniel


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Re: [PyMOL] Can i find a specific sequence in pymol?

[Mirna D. <mir...@uc...>]

Hello,

Can I please unsubscribe from the mail lists?

Best,
Mirna

From: Ambbar Aballay González <amb...@gm...>
Sent: December 15, 2021 12:06 PM
To: Thomas Holder <th...@th...>
Cc: he...@sc...; pymol-users <pym...@li...>
Subject: Re: [PyMOL] Can i find a specific sequence in pymol?

[△EXTERNAL]

Thank you very much.


Ambbar


El mié, 15 dic 2021 a las 16:02, Thomas Holder (<th...@th...<mailto:th...@th...>>) escribió:
Hi Ambbar,

To select sequence "ACDEF", you can do:

select mysele, pepseq ACDEF

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

Cheers,
  Thomas

On Wed, Dec 15, 2021 at 7:54 PM Ambbar Aballay González
<amb...@gm...<mailto:amb...@gm...>> wrote:
>
> Dear friends,
> How can I find and select a specific sequence in pymol, while displaying the PDB?
>
> have a nice day
>
> Kinds Regards
>
> Ambbar Aballay González
> Universidad de Concepción, Chile.
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Can i find a specific sequence in pymol?

[Thomas H. <th...@th...>]

Hi Ambbar,

To select sequence "ACDEF", you can do:

select mysele, pepseq ACDEF

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

Cheers,
  Thomas

On Wed, Dec 15, 2021 at 7:54 PM Ambbar Aballay González
<amb...@gm...> wrote:
>
> Dear friends,
> How can I find and select a specific sequence in pymol, while displaying the PDB?
>
> have a nice day
>
> Kinds Regards
>
> Ambbar Aballay González
> Universidad de Concepción, Chile.
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Can i find a specific sequence in pymol?

[Ambbar A. G. <amb...@gm...>]

Thank you very much.


Ambbar



El mié, 15 dic 2021 a las 16:02, Thomas Holder (<th...@th...>)
escribió:

> Hi Ambbar,
>
> To select sequence "ACDEF", you can do:
>
> select mysele, pepseq ACDEF
>
> See also https://pymolwiki.org/index.php/Selection_Algebra
>
> Cheers,
>   Thomas
>
> On Wed, Dec 15, 2021 at 7:54 PM Ambbar Aballay González
> <amb...@gm...> wrote:
> >
> > Dear friends,
> > How can I find and select a specific sequence in pymol, while displaying
> the PDB?
> >
> > have a nice day
> >
> > Kinds Regards
> >
> > Ambbar Aballay González
> > Universidad de Concepción, Chile.
> >
> > _______________________________________________
> > PyMOL-users mailing list
> > Archives: http://www.mail-archive.com/pym...@li...
> > Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>

[PyMOL] Can i find a specific sequence in pymol?

[Ambbar A. G. <amb...@gm...>]

Dear friends,
How can I find and select a specific sequence in pymol, while displaying
the PDB?

have a nice day

Kinds Regards

Ambbar Aballay González
Universidad de Concepción, Chile.

[PyMOL] Ruge problem visualization of PDBQT file on pymol

[EDUARDO J. A. C. <ed...@ep...>]

Dear friends
how are you? I hope you are doing well
I am using autodock vina for virtual screening.. I used the LigPret to
prepare my ligands into mol2 file, however when MGLTools convert the mol2
to PDBQT and specially the vina output file in PDBQT has become a very
anomalous and strange molecule structure.
This file attached is ZINC100199761 molecule structure in mol2 generated
from SMILE sequence using LigPrep. After LigPrep I pass it
through the Avogadro to obtain the best geometry optimization
Only after that I make the PDBQT conversion using the MGLTools and so the
molecular docking using vina.

Well did you know what is happening?? Is it a pymol visualization problem
with pdqbt files?
Could Anyone could know what the problem is and how to fix it?
Thanks a lot!!

have a nice end year

Kinds Regards

Eduardo Jose Azevedo Correa
from Brazil
-- 

*Eduardo José Azevedo Corrêa*

Biólogo| Professor e Pesquisador


(37)9997-5771

(37)3271-4673

*www.epamig.br <http://www.epamig.br/>*

*EPAMIG Pitangui*
Rodovia BR - MG352 Km35 Zona Rural

Caixa Postal 43

CEP 35650-000 - Pitangui - MG

[PyMOL] Problem Compiling PyMOL in WSL2/Debian Bullseye

[Stephen P. M. <s.m...@sb...>]

I have installed Debian Bullseye on my Windows 10 Laptop using WSL2 and 
have encountered a problem with PyMOL-2.6.a0a.

I compiled the source code using the instructions in the PyMOL Wiki.

Unfortunately, there were errors when I attempted running PyMOL:

Please wait...

Qt not available (pymol.Qt), using GLUT/Tk interface
Traceback (most recent call last):
   File "/home/comp/Apps/PyMOL-2.6.a0a/lib/python/pymol/__init__.py", 
line 73, in <module>
     sys.exit(pymol.launch(args))
   File "/home/comp/Apps/PyMOL-2.6.a0a/lib/python/pymol/__init__.py", 
line 429, in launch
     _cmd.runpymol(None, block_input_hook)
NotImplementedError: compile with --glut

 >>>> END OF COMMAND <<<<

The build commands and build log are attached.

I should mention that I have comp[iled PyMOL quite a few times in 
multiple Linux distros without this particular problem.

A solution will be appreciated.

Thanks in advance.

-- 
Stephen P. Molnar, Ph.D.
www.molecular-modeling.net
614.312.7528 (c)
Skype:  smolnar1

[PyMOL] drawing small organic molecules

[Janos D. <jan...@gm...>]

Dear All,

I am searching for some features in pymol, I hope these are implemented
features:
I would like to:
-add crosses on spheres like:
https://www.cylview.org/ewExternalFiles/CYLview_manual_revC.pdf (page 1.)
or
https://rb.gy/gru47s

-increase the stick diameter for H atoms from commandline like:

Setting: stick_h_scale set to 1.00000. (Settings/ lines and sticks /
hydrogen scale: 1)
-add and remove bonds from commandline
-add dashed bonds from commandline


Many thanks in advance!

Best,

Janos