pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] distance-based selection of the side-chains

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

Dear Pymol Users!
I am working on the visualization of the protein-ligand contacts
identified using
preset.ligand_cartoon('pdb',_self=cmd)
Since the command also displays some residues, which are not involved
in the interactions (with the radicals located too far away) with the
ligand, I need to filter the displayed side-chains focusing only on
the important interactions. I am using a distance-based criterion for
the selection of the residues which I am going to hide.

this is what I've already tried:

# display visible side chains as the sticks
cmd.select('rep lines and visible and sidechain')
cmd.show('sticks', 'sele')
# select all visible sticks of the sidechains far away from the ligand
cmd.select('sidechain & (rep sticks & visible beyond 4 of not polymer)')
cmd.hide('everything', 'sele')

the problem is that the "select" command with such syntax, always
selects the ATOMS, but not the whole side-chains. Is it possible to
hide the whole side-chain using such syntax as well as it's displayed
label?
Many thanks in advance!
Enrico

[PyMOL] Virtual Annual CCP4/APS Crystallographic School (2022) in the US

[Qingping Xu <qx...@an...>]

Dear Colleagues,

We are pleased to announce the virtual annual CCP4/APS crystallographic 
school “From data collection to structure refinement and beyond” will be 
held on June 13-24, 2022 at the Advanced Photon Source (APS), Argonne 
National Laboratory (ANL), near Chicago, Illinois, USA. All details can 
be found at the school website: 
http://www.ccp4.ac.uk/schools/APS-2022/index.php.

Dates: June 6 (Bioinformatics & setup) and June 13 through 24, 2022 
(with a weekend break on June 18 and 19th)

Location: Virtual/Remote

The school comprises two parts: remote data collection workshop and 
virtual crystallographic computing workshop. Data collection workshop 
includes beamline training, data collection on GM/CA at APS beamlines 
23ID-D and 23ID-B equipped with Pilatus3 6M and Eiger 16M detectors 
respectively, and data processing. For data collection, only the 
participants’ crystals will be used. Crystallographic computation 
workshop will feature many modern crystallographic software packages 
taught by authors and other experts. The daily schedule will be 
organized in three sections – lectures, tutorials, and hands-on 
(interactive troubleshooting of the technical difficulties the 
participants face in their projects). We have had considerable success 
resolving these problems in past years, attested by resulting 
publications (see 
http://www.ccp4.ac.uk/schools/APS-school/publications.php). A draft of 
the program, contact info and other details can be found at the School 
website. Note that for the virtual school, an additional day (June 6th, 
2022) was scheduled to prepare for the main event, with lectures on 
generating AlphaFold models to use in later part of the school.

Applicants: Graduate students, postdoctoral researchers and early-career 
faculty, along with commercial/industrial researchers are encouraged to 
apply. Only about 20 applicants will be selected for participation. 
Participants of the workshop are strongly encouraged to bring their own 
problem data sets or crystals so the problems can be addressed during 
data collection and/or computation workshops.

Application: Application deadline is April 15th, 2022. To apply, visit 
https://www.ccp4.ac.uk/schools/APS-2022/application.php.

Fees: There is no fee for attending the virtual school for the chosen 
applicants.

We hope to see you at the school.

Charles, Andrey, Garib and Qingping

Re: [PyMOL] How to label atom at proper positions?

[<sun...@al...>]

Hello Professor, 

That's great. Finally, is it possible to show mutation information in the labels, like "T389S", "R201E", etc.? 

Best
------------------------------------------------------------------
From:Halil İbrahim Özdemir <ozd...@gm...>
Send Time:2022年1月19日(星期三) 14:05
To:孙业平 <sun...@al...>
Subject:Re: [PyMOL] How to label atom at proper positions?

You can modify the previous script like this,

# ONE LETTER CODES
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'}

# Select all C-Alpha atoms and set the object name as "CAs"
select CAs, n. CA

# Give Label Them as (Residue Name+Residue Number)
label CAs, "%s%s" % (one_letter[resn],resi)

# Set Label Positions for object "CAs"
set label_position, (3,2,1), CAs

Regards,

sunyeping <sun...@al...>, 19 Oca 2022 Çar, 06:43 tarihinde şunu yazdı:
Dear Professor Halil İbrahim Özdemir,

Thank you for your help. The labels shown now are fomatted as "(THR339)", "(SER308)", etc.
I wonder how to show them as single-letter codes plus the numbers without the parentheses, like "T339", "S308".
Thank you again.

Best,
------------------------------------------------------------------
From:Halil İbrahim Özdemir <ozd...@gm...>
Send Time:2022年1月18日(星期二) 18:50
To:孙业平 <sun...@al...>
Subject:Re: [PyMOL] How to label atom at proper positions?

Hi  Sunyeping,

You can easily apply the following script from PyMOL terminal. Have a nice days.

# Select all C-Alpha atoms and set the object name as "CAs"
select CAs, n. CA

# Give Label Them as (Residue Name+Residue Number)
label CAs, "(%s%s)" % (resn, resi)

# Set Label Positions for object "CAs"
set label_position, (3,2,1), CAs

Regards,



sunyeping via PyMOL-users <pym...@li...>, 18 Oca 2022 Sal, 13:14 tarihinde şunu yazdı:
Dear pymol users,

I select a series of CA atoms in a structure in pymol and show them as sphere in pymol and want to label them. If using the label menu at the up-right conner of pymol, the labels shown overlaps with spheres and can not be seen. So I wish to show the labels at a bit distance from the seleccted atoms. Is there a method to do that? I will appreciate to any help! 

Best regards
 _______________________________________________
 PyMOL-users mailing list
 Archives: http://www.mail-archive.com/pym...@li...
 Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] Two different kinds of GUI's

[Martin U. <mar...@st...>]

Dear PyMol users,

I encountered a strange behavior of PyMol on Windows 10. I installed 
PyMol two times and get two different graphical user interfaces.

I already wrote a GitHub issue report, but didn't revive an answer yet, 
so I thought I ask this question here. The full problem is described in 
the issue report (with images): 
https://github.com/schrodinger/pymol-open-source/issues/216.

I would appreciate an answer.

Greetings from Germany

-- Martin

Re: [PyMOL] problem with ray of PNG using pymol in non-gui mode

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

yep, it is not possible actually to switch off the Ray using no-gui mode in
pymol ( i've just read another topic on this case). BTW I found that the
problem of the disappearing of carton is mor related to the transparency,
since it had already been set for the surface as well. In the case when I
set it both for cartoon and surface, the cartoon diagram is lost :-)
here is my script:
cmd.set('transparency_mode','1')
cmd.set('transparency', '0.7', '${output}* and polymer')
cmd.set('cartoon_transparency', '0.3', '${output}* and polymer')

пт, 21 янв. 2022 г. в 05:40, Saurabh Gayali <sau...@gm...>:

> Have you tried setting ray_trace_mode?
> Info here: https://pymolwiki.org/index.php/Ray
>
> ------------------------------
>
> *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&> 21/01/22,
> 10:10:28 am
>
> On Thu, Jan 20, 2022 at 11:02 PM Enrico Martinez <jms...@gm...>
> wrote:
>
>> Dear Pymol Users!
>> I've faced the problem of saving a PNG image without ray using the png
>> command in non-gui mode. First if I do it in pymol gui
>> #cmd.png('test.png',width=800,height=800,ray=0)
>> .. it produces fine image (without ray)
>>
>> However if I execute the same command inside of my bash sript:
>>
>> $pymol -c -d "
>> from pymol import cmd
>> from pymol import preset
>> cmd.load('my_pdb.pdb')
>> cmd.show('surface', 'my_pdb and polymer')
>> cmd.set('surface_color', 'default', 'my_pdb and polymer')
>> cmd.set('transparency', '0.8', 'my_pdb and polymer')
>> cmd.save('${vizu}/${output}_${lig_name}_rep${i}.pse')
>>
>> cmd.png('${vizu}/${output}_${lig_name}_interact_rep${i}.png',width=${image},height=${image},ray=0)
>> "
>>
>> Eventually It produces the correct pymol session but on the PNG image
>> I do not see any cartoon representation (only transparent surface) of
>> my protein. I did some tests and found that using non-gui mode (like
>> in the script shown above) pymol always sets the ray flag to ray=1
>> even if it is disabled in my script. Is there any way to disable ray
>> (ray=0) in my script besides setting it in the cmd.png?
>> 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] problem with ray of PNG using pymol in non-gui mode

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

Have you tried setting ray_trace_mode?
Info here: https://pymolwiki.org/index.php/Ray

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

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

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


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Sender
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21/01/22,
10:10:28 am

On Thu, Jan 20, 2022 at 11:02 PM Enrico Martinez <jms...@gm...>
wrote:

> Dear Pymol Users!
> I've faced the problem of saving a PNG image without ray using the png
> command in non-gui mode. First if I do it in pymol gui
> #cmd.png('test.png',width=800,height=800,ray=0)
> .. it produces fine image (without ray)
>
> However if I execute the same command inside of my bash sript:
>
> $pymol -c -d "
> from pymol import cmd
> from pymol import preset
> cmd.load('my_pdb.pdb')
> cmd.show('surface', 'my_pdb and polymer')
> cmd.set('surface_color', 'default', 'my_pdb and polymer')
> cmd.set('transparency', '0.8', 'my_pdb and polymer')
> cmd.save('${vizu}/${output}_${lig_name}_rep${i}.pse')
>
> cmd.png('${vizu}/${output}_${lig_name}_interact_rep${i}.png',width=${image},height=${image},ray=0)
> "
>
> Eventually It produces the correct pymol session but on the PNG image
> I do not see any cartoon representation (only transparent surface) of
> my protein. I did some tests and found that using non-gui mode (like
> in the script shown above) pymol always sets the ray flag to ray=1
> even if it is disabled in my script. Is there any way to disable ray
> (ray=0) in my script besides setting it in the cmd.png?
> 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] problem with ray of PNG using pymol in non-gui mode

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

Dear Pymol Users!
I've faced the problem of saving a PNG image without ray using the png
command in non-gui mode. First if I do it in pymol gui
#cmd.png('test.png',width=800,height=800,ray=0)
.. it produces fine image (without ray)

However if I execute the same command inside of my bash sript:

$pymol -c -d "
from pymol import cmd
from pymol import preset
cmd.load('my_pdb.pdb')
cmd.show('surface', 'my_pdb and polymer')
cmd.set('surface_color', 'default', 'my_pdb and polymer')
cmd.set('transparency', '0.8', 'my_pdb and polymer')
cmd.save('${vizu}/${output}_${lig_name}_rep${i}.pse')
cmd.png('${vizu}/${output}_${lig_name}_interact_rep${i}.png',width=${image},height=${image},ray=0)
"

Eventually It produces the correct pymol session but on the PNG image
I do not see any cartoon representation (only transparent surface) of
my protein. I did some tests and found that using non-gui mode (like
in the script shown above) pymol always sets the ray flag to ray=1
even if it is disabled in my script. Is there any way to disable ray
(ray=0) in my script besides setting it in the cmd.png?
Many thanks in advance!
Enrico

[PyMOL] ball-and-stick representatation of the ligand and non-polar contacts

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

I am using the combination of two presets to visualise protein-ligand
interactions:

1) to visualise protein-ligand contacts
preset.ligand_cartoon('${output}*',_self=cmd)

2) and then to change the representation of the ligand:
preset.ball_and_stick(selection='my_system and not polymer', mode=1)

Unfortunately after the execution of the second command I do not see
anymore dashed yellow lines for non-polar contacts between protein and
ligand
Is there any quick command, which may return it for a multi-model file
and better to change the color of the dotted line from yellow
(default) to another color (blue)?
Thank you in advance!
Enrico

[PyMOL] How may I color surface using spectral palette ?

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

Dear All,
I am working on the visualization of the transparent surface in my
model. For the moment I found only one possibility for non-monotone
coloring palette of the surface, using
cmd.set('surface_color', 'default')
How may I color the surface using some spectrum (e.g. from orange to
yellow) or alternatively according to the electrostatic properties of
the amino-acids?
Thank you in advance
Enrico

Re: [PyMOL] How to label atom at proper positions?

[sunyeping <sun...@al...>]

Dear Professor Halil İbrahim Özdemir,

Thank you for your help. The labels shown now are fomatted as "(THR339)", "(SER308)", etc.
I wonder how to show them as single-letter codes plus the numbers without the parentheses, like "T339", "S308".
Thank you again.

Best,
------------------------------------------------------------------
From:Halil İbrahim Özdemir <ozd...@gm...>
Send Time:2022年1月18日(星期二) 18:50
To:孙业平 <sun...@al...>
Subject:Re: [PyMOL] How to label atom at proper positions?

Hi  Sunyeping,

You can easily apply the following script from PyMOL terminal. Have a nice days.

# Select all C-Alpha atoms and set the object name as "CAs"
select CAs, n. CA

# Give Label Them as (Residue Name+Residue Number)
label CAs, "(%s%s)" % (resn, resi)

# Set Label Positions for object "CAs"
set label_position, (3,2,1), CAs

Regards,



sunyeping via PyMOL-users <pym...@li...>, 18 Oca 2022 Sal, 13:14 tarihinde şunu yazdı:
Dear pymol users,

I select a series of CA atoms in a structure in pymol and show them as sphere in pymol and want to label them. If using the label menu at the up-right conner of pymol, the labels shown overlaps with spheres and can not be seen. So I wish to show the labels at a bit distance from the seleccted atoms. Is there a method to do that? I will appreciate to any help! 

Best regards
 _______________________________________________
 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 label atom at proper positions?

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

Hi sunyeping,

Try this:

     set label_position, [0, 0, 5]

The 5 here moves the label 5 Å closer to the viewer along the viewport Z
axis.  See also: https://pymolwiki.org/index.php/Label_position

Hope that helps.

Cheers,
Jared

On Tue, Jan 18, 2022 at 5:15 AM sunyeping via PyMOL-users <
pym...@li...> wrote:

> Dear pymol users,
>
> I select a series of CA atoms in a structure in pymol and show them as
> sphere in pymol and want to label them. If using the label menu at the
> up-right conner of pymol, the labels shown overlaps with spheres and can
> not be seen. So I wish to show the labels at a bit distance from the
> seleccted atoms. Is there a method to do that? I will appreciate to any
> help!
>
> Best regards
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] 1. How to label atom at proper positions? (sunyeping)

[ahoneg <hon...@bi...>]

You can shift the label position relative to the atom position using the “set label_position” command, or, in edit mode, ctrl-shift-left_click to move the labels in the z-direction.
See https://pymolwiki.org/index.php/Label for details

Annemarie Honegger

> 
> Message: 1
> Date: Tue, 18 Jan 2022 17:57:46 +0800
> From: "sunyeping" <sun...@al...>
> To: "pymol-users" <pym...@li...>
> Subject: [PyMOL] How to label atom at proper positions?
> Message-ID:
> 	<fe9...@al...>
> Content-Type: text/plain; charset="utf-8"
> 
> Dear pymol users,
> 
> I select a series of CA atoms in a structure in pymol and show them as sphere in pymol and want to label them. If using the label menu at the up-right conner of pymol, the labels shown overlaps with spheres and can not be seen. So I wish to show the labels at a bit distance from the seleccted atoms. Is there a method to do that? I will appreciate to any help! 
> 
> Best regards
> 

[PyMOL] How to label atom at proper positions?

[sunyeping <sun...@al...>]

Dear pymol users,

I select a series of CA atoms in a structure in pymol and show them as sphere in pymol and want to label them. If using the label menu at the up-right conner of pymol, the labels shown overlaps with spheres and can not be seen. So I wish to show the labels at a bit distance from the seleccted atoms. Is there a method to do that? I will appreciate to any help! 

Best regards
 

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:
> 
> Send PyMOL-users mailing list submissions to
> 	pym...@li...
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> 	https://lists.sourceforge.net/lists/listinfo/pymol-users
> or, via email, send a message with subject or body 'help' to
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> 
> You can reach the person managing the list at
> 	pym...@li...
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of PyMOL-users digest..."
> 
> 
> 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:
> 	<CAALQopyYfQGuLwsde74=sTB...@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
> 
> 
> 
> ------------------------------
> 
> 
> 
> ------------------------------
> 
> Subject: Digest Footer
> 
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
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> ------------------------------
> 
> End of PyMOL-users Digest, Vol 188, Issue 11
> ********************************************

[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
>>
>>
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

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
    > Archives: https://protect-au.mimecast.com/s/JP1lCjZ1N7inr9pkzFWa1_a?domain=mail-archive.com
    > 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
    >
    >
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