pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] conversion of the small molecules from sdf to mol2

[Chris S. <sw...@ma...>]

Hi,

You could try --append in openbabel to add the ID_STRUCTURE to the title of the molecule sdf?

https://openbabel.org/docs/dev/Command-line_tools/babel.html#append-property-values-to-the-title <https://openbabel.org/docs/dev/Command-line_tools/babel.html#append-property-values-to-the-title>

Chris

> On 14 Jan 2022, at 12:03, pym...@li... wrote:
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> Today's Topics:
> 
>   1. conversion of the small molecules from sdf to mol2
>      (Enrico Martinez)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Thu, 13 Jan 2022 16:23:53 +0100
> From: Enrico Martinez <jms...@gm...>
> To: pymol-users <pym...@li...>
> Subject: [PyMOL] conversion of the small molecules from sdf to mol2
> Message-ID:
> 	<CAA...@ma...>
> Content-Type: text/plain; charset="UTF-8"
> 
> Dear Pymol users, dear Friends!
> 
> I have a question regarding file conversion of the small organic
> molecules, which is not directly related to pymol but I believe that I
> may use it for the solution.
> 
> I am dealing with the conversion of SDF file (2d formulas) to mol2
> format (3d coordinates)
> Usually I use it in one line command with babel
> obabel --gen3d -isdf ligands.sdf -omol2 > ligands.mol2
> 
> It creates a multi-model mol2 file, that I may open in pymol and split
> the molecules manually using split_states command:
> pymol ligands.mol2
> cmd.split_states('ligands', 'prefix=conf')
> This creates several separate objects conf0001, conf0002 etc that I
> may save as the individual mol2.
> Alternatively I may obtain individual mol2 filles for each model of the SDF:
> obabel ./ligands.sdf -O ./babel/conf.mol2 --gen3d -m
> which creates separate files conf1.mol2 , conf2.mol2 .. confN.mol2
> that I may load in pymol in one command from terminal
> pymol ./babel/conf*.mol2
> 
> The problem that the name of the initial model stored in the initial sdf, as:
> <ID_STRUCTURE>
> name_of_the_ligand
> 
> always lost during conversion from sdf to mol2 (regardless of the way
> of the conversion). So the mol2 files always lack their initials
> defined from sdf :-)
> 
> Could you suggest some trick to associate the name of the model (From
> initial sdf) to the corresponding object loaded in pymol or
> alternatively keep them during the conversion?
> Many thanks in advance!
> Enrico
> 
> 
> 
> ------------------------------
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[PyMOL] conversion of the small molecules from sdf to mol2

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

Dear Pymol users, dear Friends!

I have a question regarding file conversion of the small organic
molecules, which is not directly related to pymol but I believe that I
may use it for the solution.

I am dealing with the conversion of SDF file (2d formulas) to mol2
format (3d coordinates)
Usually I use it in one line command with babel
obabel --gen3d -isdf ligands.sdf -omol2 > ligands.mol2

It creates a multi-model mol2 file, that I may open in pymol and split
the molecules manually using split_states command:
pymol ligands.mol2
cmd.split_states('ligands', 'prefix=conf')
This creates several separate objects conf0001, conf0002 etc that I
may save as the individual mol2.
Alternatively I may obtain individual mol2 filles for each model of the SDF:
obabel ./ligands.sdf -O ./babel/conf.mol2 --gen3d -m
which creates separate files conf1.mol2 , conf2.mol2 .. confN.mol2
that I may load in pymol in one command from terminal
pymol ./babel/conf*.mol2

The problem that the name of the initial model stored in the initial sdf, as:
 <ID_STRUCTURE>
name_of_the_ligand

always lost during conversion from sdf to mol2 (regardless of the way
of the conversion). So the mol2 files always lack their initials
defined from sdf :-)

Could you suggest some trick to associate the name of the model (From
initial sdf) to the corresponding object loaded in pymol or
alternatively keep them during the conversion?
Many thanks in advance!
Enrico

Re: [PyMOL] Set label for visible amino acids

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

Dear Vijay,
thank you very much, it works very good. Magic! :-)
Cheers,
Enrico

ср, 12 янв. 2022 г. в 13:53, Dr. Vijay Masand <vij...@gm...>:
>
> Dear Enrico
> Use the following command:
> label n. CA & all within 5 of organic, "%s%s" % (resn,resi)
> The above command will label all CA atoms within 5 angstrom from Organic molecule with residue number and name.
> I have collected a good number of commands for showing ligand-protein complexes.
>
> With Warm Regards
> Dr. Vijay H. Masand
> Department of Chemistry,
> Vidya Bharati College, Amravati, 444 602
> Maharashtra, India.
> Phone number- +91-9403312628
> https://sites.google.com/site/vijaymasand/
>
>
>
> On Wed, Jan 12, 2022 at 5:55 PM Enrico Martinez <jms...@gm...> wrote:
>>
>> exactly we may do it in the context meny for the particular selection
>> (we do not need to select a particular residues, so ..)
>> but may we create the same label using label command as well ??
>> cmd.label('sele', 'resn')
>> I think something should be used instead of 'resn'. there is also
>> option 'resi' which shows only the number of the amino acid. So I need
>> to combine "resn" and "resi"
>> :-)
>>
>> вт, 11 янв. 2022 г. в 21:27, Oganesyan, Vaheh <vah...@as...>:
>> >
>> > For label like ‘R87’ I manually do “label /s309/B/H/ARG`87/CA, ‘R87’”
>> >
>> >
>> >
>> > Vaheh
>> >
>> >
>> >
>> > From: Enrico Martinez <jms...@gm...>
>> > Sent: Tuesday, January 11, 2022 12:34 PM
>> > To: pymol-users <pym...@li...>
>> > Subject: [PyMOL] Set label for visible amino acids
>> >
>> >
>> >
>> > Dear Pymol users!
>> > Here is the chain of the pymol commands that I am using to label the
>> > visible amino-acids shown as lines in the current pymol session.
>> > cmd.select('name CA and rep lines')
>> > cmd.label('sele', 'resn')
>> > cmd.set('label_font_id', '14')
>> > cmd.set('label_color', 'indigo')
>> > cmd.set('label_position', '3,0,0')
>> > It produces nice labeling according to the amino acid name (example
>> > Tyr). How it would be possible to indicate additionally the number of
>> > the amino acid like Tyr-119 or simply using one letter code + the
>> > number?
>> > 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
>>
>>
>> _______________________________________________
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Re: [PyMOL] Set label for visible amino acids

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

Hi Enrico, 

This is actually quite simple, see the PyMOL wiki: https://pymolwiki.org/index.php/Aa_codes

Paste this python dictionary  into PyMOL:
one_letter ={'VAL':'V', 'ILE':'I', 'LEU':'L', 'GLU':'E', 'GLN':'Q', \
'ASP':'D', 'ASN':'N', 'HIS':'H', 'TRP':'W', 'PHE':'F', 'TYR':'Y',    \
'ARG':'R', 'LYS':'K', 'SER':'S', 'THR':'T', 'MET':'M', 'ALA':'A',    \
'GLY':'G', 'PRO':'P', 'CYS':'C'}

The one letter codes can be accessed with one_letter[resn]

To do something like Y-119:

label sele, '{}-{}'.format(one_letter[resn], resi) # front end command
cmd.label('sele', "'{}-{}'.format(one_letter[resn], resi)") # backend command

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 12/1/22, 11:26 pm, "Enrico Martinez" <jms...@gm...> wrote:

    exactly we may do it in the context meny for the particular selection
    (we do not need to select a particular residues, so ..)
    but may we create the same label using label command as well ??
    cmd.label('sele', 'resn')
    I think something should be used instead of 'resn'. there is also
    option 'resi' which shows only the number of the amino acid. So I need
    to combine "resn" and "resi"
    :-)

    вт, 11 янв. 2022 г. в 21:27, Oganesyan, Vaheh <vah...@as...>:
    >
    > For label like ‘R87’ I manually do “label /s309/B/H/ARG`87/CA, ‘R87’”
    >
    >
    >
    > Vaheh
    >
    >
    >
    > From: Enrico Martinez <jms...@gm...>
    > Sent: Tuesday, January 11, 2022 12:34 PM
    > To: pymol-users <pym...@li...>
    > Subject: [PyMOL] Set label for visible amino acids
    >
    >
    >
    > Dear Pymol users!
    > Here is the chain of the pymol commands that I am using to label the
    > visible amino-acids shown as lines in the current pymol session.
    > cmd.select('name CA and rep lines')
    > cmd.label('sele', 'resn')
    > cmd.set('label_font_id', '14')
    > cmd.set('label_color', 'indigo')
    > cmd.set('label_position', '3,0,0')
    > It produces nice labeling according to the amino acid name (example
    > Tyr). How it would be possible to indicate additionally the number of
    > the amino acid like Tyr-119 or simply using one letter code + the
    > number?
    > Many thanks in advance
    > Enrico
    >
    >
    > _______________________________________________
    > PyMOL-users mailing list
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    > Unsubscribe: https://protect-au.mimecast.com/s/Kl0ACk81N9tOENmZDfVicB0?domain=sourceforge.net


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Re: [PyMOL] Set label for visible amino acids

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

exactly we may do it in the context meny for the particular selection
(we do not need to select a particular residues, so ..)
but may we create the same label using label command as well ??
cmd.label('sele', 'resn')
I think something should be used instead of 'resn'. there is also
option 'resi' which shows only the number of the amino acid. So I need
to combine "resn" and "resi"
:-)

вт, 11 янв. 2022 г. в 21:27, Oganesyan, Vaheh <vah...@as...>:
>
> For label like ‘R87’ I manually do “label /s309/B/H/ARG`87/CA, ‘R87’”
>
>
>
> Vaheh
>
>
>
> From: Enrico Martinez <jms...@gm...>
> Sent: Tuesday, January 11, 2022 12:34 PM
> To: pymol-users <pym...@li...>
> Subject: [PyMOL] Set label for visible amino acids
>
>
>
> Dear Pymol users!
> Here is the chain of the pymol commands that I am using to label the
> visible amino-acids shown as lines in the current pymol session.
> cmd.select('name CA and rep lines')
> cmd.label('sele', 'resn')
> cmd.set('label_font_id', '14')
> cmd.set('label_color', 'indigo')
> cmd.set('label_position', '3,0,0')
> It produces nice labeling according to the amino acid name (example
> Tyr). How it would be possible to indicate additionally the number of
> the amino acid like Tyr-119 or simply using one letter code + the
> number?
> 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] Visualisation of protein-ligand interactions using cmd

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

I've just found the list of the presets:
https://pymolwiki.org/index.php/Preset
so a new question is still about preset.ligand_cartoon.

It works well, but shows me too much information. Is it possible to
limit the set of the identified residues e.g. to indicating only the
residues involved in the hydrogen bonds/ salt bridges?
Thank you in advance!
Enrico

вт, 11 янв. 2022 г. в 18:10, Enrico Martinez <jms...@gm...>:
>
> Thank you very much Jared!
> Could you tell me if you have  some cool present for the surface
> representations ?
>
> For example I am using the following script to visualize the surface
> of the protein around the ligand binding site:
> cmd.show('surface', 'polymer within 15 of complex* and not polymer')
> cmd.set('surface_color','marine','polymer')
> cmd.set('transparency', '0.4')
> cmd.hide('cartoon', 'all')
> cmd.png('image.png',width=${image},height=${image},dpi=50,ray=1)
>
> It produces a good looking image but the surface looks monotone. How
> could I improve its representation using some preset??
> Cheers,
> Enrico
>
> вт, 11 янв. 2022 г. в 15:58, Jared Sampson <jar...@co...>:
> >
> > Hi Enrico -
> >
> > If you want to reproduce GUI actions programmatically, you can see what happens under the hood for most things by opening a log file:
> >
> >     log_open log.pml
> >
> > then perform the desired action and the Python API version of the corresponding command will be written to the log file.  For example, for the ligand sites > cartoon action menu item, this would be:
> >
> >     preset.ligand_cartoon("myobject",_self=cmd)
> >
> > If you want to use this in a script I think you'll also have to do:
> >
> >     from pymol import preset
> >
> > Hope that helps.
> >
> > Cheers,
> > Jared
> >
> >
> > On Tue, Jan 11, 2022 at 5:21 AM Enrico Martinez <jms...@gm...> wrote:
> >>
> >> Dear Pymol Users!
> >> Is it possible to visualize protein-ligand interactions (which
> >> normally is achieved in GUI via a - > present -> ligand sites
> >> using some combination of the pymol commands, which could be scripted
> >> using cmd. syntax ?
> >> I've found this explanation
> >> https://pymolwiki.org/index.php/Displaying_Biochemical_Properties#Hydrogen_bonds_and_Polar_Contacts
> >> but did not understand quite well how it works.
> >> I would be grateful for the example of the commands which show the
> >> polar contacts (I am mostly interested in hydrogen bonds) in my pymol
> >> session without calling each time the GUI menu.
> >> 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] Set label for visible amino acids

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

Dear Pymol users!
Here is the chain of the pymol commands that I am using to label the
visible amino-acids shown as lines in the current pymol session.
cmd.select('name CA and rep lines')
cmd.label('sele', 'resn')
cmd.set('label_font_id', '14')
cmd.set('label_color', 'indigo')
cmd.set('label_position', '3,0,0')
It produces nice labeling according to the amino acid name (example
Tyr). How it would be possible to indicate additionally the number of
the amino acid like Tyr-119 or simply using one letter code + the
number?
Many thanks in advance
Enrico

Re: [PyMOL] Visualisation of protein-ligand interactions using cmd

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

Thank you very much Jared!
Could you tell me if you have  some cool present for the surface
representations ?

For example I am using the following script to visualize the surface
of the protein around the ligand binding site:
cmd.show('surface', 'polymer within 15 of complex* and not polymer')
cmd.set('surface_color','marine','polymer')
cmd.set('transparency', '0.4')
cmd.hide('cartoon', 'all')
cmd.png('image.png',width=${image},height=${image},dpi=50,ray=1)

It produces a good looking image but the surface looks monotone. How
could I improve its representation using some preset??
Cheers,
Enrico

вт, 11 янв. 2022 г. в 15:58, Jared Sampson <jar...@co...>:
>
> Hi Enrico -
>
> If you want to reproduce GUI actions programmatically, you can see what happens under the hood for most things by opening a log file:
>
>     log_open log.pml
>
> then perform the desired action and the Python API version of the corresponding command will be written to the log file.  For example, for the ligand sites > cartoon action menu item, this would be:
>
>     preset.ligand_cartoon("myobject",_self=cmd)
>
> If you want to use this in a script I think you'll also have to do:
>
>     from pymol import preset
>
> Hope that helps.
>
> Cheers,
> Jared
>
>
> On Tue, Jan 11, 2022 at 5:21 AM Enrico Martinez <jms...@gm...> wrote:
>>
>> Dear Pymol Users!
>> Is it possible to visualize protein-ligand interactions (which
>> normally is achieved in GUI via a - > present -> ligand sites
>> using some combination of the pymol commands, which could be scripted
>> using cmd. syntax ?
>> I've found this explanation
>> https://pymolwiki.org/index.php/Displaying_Biochemical_Properties#Hydrogen_bonds_and_Polar_Contacts
>> but did not understand quite well how it works.
>> I would be grateful for the example of the commands which show the
>> polar contacts (I am mostly interested in hydrogen bonds) in my pymol
>> session without calling each time the GUI menu.
>> 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] Visualisation of protein-ligand interactions using cmd

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

Dear Pymol Users!
Is it possible to visualize protein-ligand interactions (which
normally is achieved in GUI via a - > present -> ligand sites
using some combination of the pymol commands, which could be scripted
using cmd. syntax ?
I've found this explanation
https://pymolwiki.org/index.php/Displaying_Biochemical_Properties#Hydrogen_bonds_and_Polar_Contacts
but did not understand quite well how it works.
I would be grateful for the example of the commands which show the
polar contacts (I am mostly interested in hydrogen bonds) in my pymol
session without calling each time the GUI menu.
Many thanks in advance!
Enrico

[PyMOL] visualisation of ligand conformations predicted in Docking

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

Dear Pymol Users!
I am working on the visualization of the ligand binding poses
predicted by protein-ligand docking. Having 88 solutions I split these
states into different states and then set transparency=0.8 to each of
them, in order to visualize them as the "cloud" of the conformational
space of the ligand predicted in docking. I also selected the best
docking pose (always the first model) and colored it in Red without
the transparency. The problem is that, during the visualization, on
the  png graph, the best docking pose looks to be on the second plane
compared to others (transparent) poses. How could I always move this
model on the first plane compared to other aligned ligand poses?
P.S. I tried to enclose the PNG to my message but it seems that it
could not pass the moderator filter ..

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

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

Right, thank you, Blaine!
It works very well now! Actually there was a problem in the selection
from my part so..
I will play with the surfaces a little bit and then will update this
topic with my questions :-)
Cheers,
Enrico

пн, 10 янв. 2022 г. в 16:25, Mooers, Blaine H.M. (HSC)
<Bla...@ou...>:
>
> Hi Enrico,
>
> You do not need the first line of your script.
>
> This one-liner worked for me in the terminal.
>
> pymol -c -d "cmd.fetch('3nd3');cmd.show('surface');cmd.set('transparency','0.5');cmd.save('surf.pse');cmd.png('surf.png')"
>
> You might test reversing the order of the cmd.png() and cmd.save() commands.
>
> 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: Ali Saad Kusay via PyMOL-users [pym...@li...]
> Sent: Monday, January 10, 2022 8:48 AM
> To: Enrico Martinez
> Cc: pymol-users
> Subject: [EXTERNAL] Re: [PyMOL] surface representation of the protein-ligand interactions
>
> 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://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_Rebuild&d=DwIGaQ&c=qKdtBuuu6dQK9MsRUVJ2DPXW6oayO8fu4TfEHS8sGNk&r=rxarJ7aLyHGI62pje1gd6hPxYn9Xv-2lWNWh_1Owonw&m=LJPkRnhTZf8Utg8JOTi736pL_UGe7aSsJfSdAISU1O6habH3BmWqqUuvTrUfXWMh&s=QM8ZtM6vxjrnYB0Cs6BSV-M8WweuPuuTS1xLMGYQdKU&e=
>
> 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://urldefense.proofpoint.com/v2/url?u=https-3A__protect-2Dau.mimecast.com_s_1Of6CNLJyQU0W9yVofmRSV0-3Fdomain-3Dpymol.org&d=DwIGaQ&c=qKdtBuuu6dQK9MsRUVJ2DPXW6oayO8fu4TfEHS8sGNk&r=rxarJ7aLyHGI62pje1gd6hPxYn9Xv-2lWNWh_1Owonw&m=LJPkRnhTZf8Utg8JOTi736pL_UGe7aSsJfSdAISU1O6habH3BmWqqUuvTrUfXWMh&s=eU60ct3XrRn6e7JdG6JrHLyikGkuUbzJY35JQFXvTv8&e=
>     >
>     > You can also try and made the surface more transparent, but this doesn't always give the best results, see: https://urldefense.proofpoint.com/v2/url?u=https-3A__protect-2Dau.mimecast.com_s_vdsUCOMKzVTp8wQ53fvOudq-3Fdomain-3Dpymolwiki.org&d=DwIGaQ&c=qKdtBuuu6dQK9MsRUVJ2DPXW6oayO8fu4TfEHS8sGNk&r=rxarJ7aLyHGI62pje1gd6hPxYn9Xv-2lWNWh_1Owonw&m=LJPkRnhTZf8Utg8JOTi736pL_UGe7aSsJfSdAISU1O6habH3BmWqqUuvTrUfXWMh&s=pOFWGOP750OszaW7BCL8qGLr_VvBCCumHmvodMSYBeo&e= , 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://urldefense.proofpoint.com/v2/url?u=https-3A__protect-2Dau.mimecast.com_s_5uDYCP7LAXfKwZVvQF1Df45-3Fdomain-3Dmail-2Darchive.com&d=DwIGaQ&c=qKdtBuuu6dQK9MsRUVJ2DPXW6oayO8fu4TfEHS8sGNk&r=rxarJ7aLyHGI62pje1gd6hPxYn9Xv-2lWNWh_1Owonw&m=LJPkRnhTZf8Utg8JOTi736pL_UGe7aSsJfSdAISU1O6habH3BmWqqUuvTrUfXWMh&s=f6UjxY4QYDP77HQZ2CqSwjcwA_HDNuyv4cn6nskHIq0&e=
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>     >
>     >
>
>
>
> _______________________________________________
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Re: [PyMOL] surface representation of the protein-ligand interactions

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

Hi Enrico, 

You do not need the first line of your script.

This one-liner worked for me in the terminal.

pymol -c -d "cmd.fetch('3nd3');cmd.show('surface');cmd.set('transparency','0.5');cmd.save('surf.pse');cmd.png('surf.png')"

You might test reversing the order of the cmd.png() and cmd.save() commands.

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: Ali Saad Kusay via PyMOL-users [pym...@li...]
Sent: Monday, January 10, 2022 8:48 AM
To: Enrico Martinez
Cc: pymol-users
Subject: [EXTERNAL] Re: [PyMOL] surface representation of the protein-ligand interactions

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://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_Rebuild&d=DwIGaQ&c=qKdtBuuu6dQK9MsRUVJ2DPXW6oayO8fu4TfEHS8sGNk&r=rxarJ7aLyHGI62pje1gd6hPxYn9Xv-2lWNWh_1Owonw&m=LJPkRnhTZf8Utg8JOTi736pL_UGe7aSsJfSdAISU1O6habH3BmWqqUuvTrUfXWMh&s=QM8ZtM6vxjrnYB0Cs6BSV-M8WweuPuuTS1xLMGYQdKU&e=

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://urldefense.proofpoint.com/v2/url?u=https-3A__protect-2Dau.mimecast.com_s_1Of6CNLJyQU0W9yVofmRSV0-3Fdomain-3Dpymol.org&d=DwIGaQ&c=qKdtBuuu6dQK9MsRUVJ2DPXW6oayO8fu4TfEHS8sGNk&r=rxarJ7aLyHGI62pje1gd6hPxYn9Xv-2lWNWh_1Owonw&m=LJPkRnhTZf8Utg8JOTi736pL_UGe7aSsJfSdAISU1O6habH3BmWqqUuvTrUfXWMh&s=eU60ct3XrRn6e7JdG6JrHLyikGkuUbzJY35JQFXvTv8&e=
    >
    > You can also try and made the surface more transparent, but this doesn't always give the best results, see: https://urldefense.proofpoint.com/v2/url?u=https-3A__protect-2Dau.mimecast.com_s_vdsUCOMKzVTp8wQ53fvOudq-3Fdomain-3Dpymolwiki.org&d=DwIGaQ&c=qKdtBuuu6dQK9MsRUVJ2DPXW6oayO8fu4TfEHS8sGNk&r=rxarJ7aLyHGI62pje1gd6hPxYn9Xv-2lWNWh_1Owonw&m=LJPkRnhTZf8Utg8JOTi736pL_UGe7aSsJfSdAISU1O6habH3BmWqqUuvTrUfXWMh&s=pOFWGOP750OszaW7BCL8qGLr_VvBCCumHmvodMSYBeo&e= , 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://urldefense.proofpoint.com/v2/url?u=https-3A__protect-2Dau.mimecast.com_s_5uDYCP7LAXfKwZVvQF1Df45-3Fdomain-3Dmail-2Darchive.com&d=DwIGaQ&c=qKdtBuuu6dQK9MsRUVJ2DPXW6oayO8fu4TfEHS8sGNk&r=rxarJ7aLyHGI62pje1gd6hPxYn9Xv-2lWNWh_1Owonw&m=LJPkRnhTZf8Utg8JOTi736pL_UGe7aSsJfSdAISU1O6habH3BmWqqUuvTrUfXWMh&s=f6UjxY4QYDP77HQZ2CqSwjcwA_HDNuyv4cn6nskHIq0&e=
    >     Unsubscribe: https://urldefense.proofpoint.com/v2/url?u=https-3A__protect-2Dau.mimecast.com_s_Q3GJCQnMBZfkQ9ZB7FkIfVr-3Fdomain-3Dsourceforge.net&d=DwIGaQ&c=qKdtBuuu6dQK9MsRUVJ2DPXW6oayO8fu4TfEHS8sGNk&r=rxarJ7aLyHGI62pje1gd6hPxYn9Xv-2lWNWh_1Owonw&m=LJPkRnhTZf8Utg8JOTi736pL_UGe7aSsJfSdAISU1O6habH3BmWqqUuvTrUfXWMh&s=lxdjMlSEnLEry730CbGSXWOU9HvpC8iBFjlmcWohToU&e=
    >
    >



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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
    >     Unsubscribe: https://protect-au.mimecast.com/s/Q3GJCQnMBZfkQ9ZB7FkIfVr?domain=sourceforge.net
    >
    >

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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    Archives: https://protect-au.mimecast.com/s/cnxDCMwGxOtqr9lJjhwM0N6?domain=mail-archive.com
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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
>>>
>>>
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>>> notified by
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>>> 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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04:38:43 pm

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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04:31:07 pm

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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