pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] Radius of gyration of a trimer

[Pedro L. <psl...@gm...>]

Correction: gyradius is the name.

Em dom., 5 de jul. de 2020 às 06:42, Pedro Lacerda <psl...@gm...>
escreveu:

> It can be accomplished with the following command (gyration on psico
> library):
>
> https://pymolwiki.org/index.php/Radius_of_gyration
>
>
> Em dom., 5 de jul. de 2020 às 04:15, Dr. Subramanian, Senthil Kumar <
> sen...@hu...> escreveu:
>
>> Hello,
>>
>> I would like to measure radius of gyration for a protein (1JB0). The PDB
>> structure is only a monomer. But, I would like to find the RoG for the
>> trimer. Could any one please help me? Bytheway, I failed massively even to
>> get RoG for monomer and it says 'RoG is not defined'. I would appreciate
>> your time and effort.
>>
>> Thank you.
>>
>> Best regards,
>>
>> Senthil
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>
>
> --
> Pedro Sousa Lacerda
>
> Laboratório de Bioinformática e Modelagem Molecular
> Faculdade de Farmácia / UFBA
>
> @pslacerda
> +55 71 9 9981-1856
> http://lattes.cnpq.br/8338596525330907
>


-- 
Pedro Sousa Lacerda

Laboratório de Bioinformática e Modelagem Molecular
Faculdade de Farmácia / UFBA

@pslacerda
+55 71 9 9981-1856
http://lattes.cnpq.br/8338596525330907

Re: [PyMOL] Radius of gyration of a trimer

[Pedro L. <psl...@gm...>]

It can be accomplished with the following command (gyration on psico
library):

https://pymolwiki.org/index.php/Radius_of_gyration


Em dom., 5 de jul. de 2020 às 04:15, Dr. Subramanian, Senthil Kumar <
sen...@hu...> escreveu:

> Hello,
>
> I would like to measure radius of gyration for a protein (1JB0). The PDB
> structure is only a monomer. But, I would like to find the RoG for the
> trimer. Could any one please help me? Bytheway, I failed massively even to
> get RoG for monomer and it says 'RoG is not defined'. I would appreciate
> your time and effort.
>
> Thank you.
>
> Best regards,
>
> Senthil
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe



-- 
Pedro Sousa Lacerda

Laboratório de Bioinformática e Modelagem Molecular
Faculdade de Farmácia / UFBA

@pslacerda
+55 71 9 9981-1856
http://lattes.cnpq.br/8338596525330907

[PyMOL] Radius of gyration of a trimer

[Dr. S. S. K. <sen...@hu...>]

Hello, 

I would like to measure radius of gyration for a protein (1JB0). The PDB
structure is only a monomer. But, I would like to find the RoG for the
trimer. Could any one please help me? Bytheway, I failed massively even
to get RoG for monomer and it says 'RoG is not defined'. I would
appreciate your time and effort. 

Thank you. 

Best regards, 

Senthil

[PyMOL] cmd.get_fastastr()

[Pedro L. <psl...@gm...>]

Hi,

The get_fastastr function changed. Before it returned the aminoacid
sequence. Now it returns a FASTA  formatted string.

How can I get the old behaviour (ie. get the aminoacid sequence)?

-- 
Pedro Sousa Lacerda

Laboratório de Bioinformática e Modelagem Molecular
Faculdade de Farmácia / UFBA

@pslacerda
+55 71 9 9981-1856
http://lattes.cnpq.br/8338596525330907

Re: [PyMOL] extract monomer from trimer structure

[Tamas H. <bio...@gm...>]

Hi,

I think that:
* You have a couple chains in a monomer.
* You have to know which chains build a monomer.
* Then you create a new object from these chains. E.g. create monomer, 
chain A1 or chain B1 or chain C1 or etc... (here the "or" is an operator 
and it does not indicate that I do not know which chain you need)
* You can likely simplify the selection; I guess that all chains with 
the same digit/number build a monomer, thus you can use a wild char for 
selection:
       create monomer1, chain *1
       create monomer2, chain *2
* Then file, save molecule, and select the "monomer" object for saving

Bests, tamas

On 7/4/20 7:58 AM, Dr. Subramanian, Senthil Kumar wrote:
>
> Hello,
>
> I am new to PyMOL. I would like to work with the monomer structure of 
> PDB id: 5zf0, not the entire structure of how they have shown (two 
> trimers against each other). Is there any way I could extract monomer 
> from trimers structure and save it as a PDB? Your help is very much 
> appreciated.
>
> Thank you.
>
> Kind regards,
>
> Senthil
>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] extract monomer from trimer structure

[Dr. S. S. K. <sen...@hu...>]

Hello, 

I am new to PyMOL. I would like to work with the monomer structure of
PDB id: 5zf0, not the entire structure of how they have shown (two
trimers against each other). Is there any way I could extract monomer
from trimers structure and save it as a PDB? Your help is very much
appreciated. 

Thank you. 

Kind regards, 

Senthil

[PyMOL] Question about multi-sequence edition in PyMOL

[sepehr d. <dej...@gm...>]

Hi,

I have a question regarding adding peptide sequence to the original
sequence in PyMOL. I have an original structure of a nanoparticle
consisting of 420 monomers and I like to add a similar peptide sequence to
each monomer. Is that any easy way to apply a sequence addition/ change to
one monomer and apply it to the. whole structure rather than going and
adding the sequence manually 420 times in PyMOL?

Sincerely,
Sepehr

[PyMOL] Mutagenesis function not working

[<pat...@lo...>]

Hey list,

I have an actin chain that I've attached linkers to (all the linkers are identical but have separate chain IDs), and I'm trying to perform mutagenesis on a specific part of each of the linkers, but whenever I try to do this, PyMOL only allows me to perform mutagenesis on the first linker. I tried going back to earlier versions of the model to see if I could properly use mutagenesis there and it worked, but I can't figure out what is causing the difficulty with my newest model. Does anyone know what's happening?

Thanks,
Patricia

[PyMOL] Which 3D setup for a new installation? (Since 3D Vision is discontinued)

[David K. <kr...@bi...>]

Dear List,


one of our research groups needs a new 3D PyMol setup.
Looking through the wiki 
(https://pymolwiki.org/index.php/Stereo_3D_Display_Options) the most 
prominent way to do 3D seemed through Nvidia's 3D Vision,
but since 3D Vision is discontinued, i struggle a bit to find a good and 
future proof 3D solution.

Can you recommend a 3D Setup?
Should we go VR?

We're planning to use the Commercial PyMol version, not the open source one.


-- 
Mit freundlichen Grüßen / With kind regards

David Krause
IT
Institute of Biochemistry II

Gustav Embden-Zentrum der Biochemie
Goethe University Frankfurt - Medical Faculty

University Hospital - Building 75
Theodor-Stern-Kai 7
60590 Frankfurt am Main
Germany

+49 (0)69 6301 84971 (Phone)
+49 (0)69 6301 84975 (Fax)
kr...@bi...

Re: [PyMOL] [EXTERNAL] Question about python commands in PyMOL

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

Hi Hrutvik,

After run script.py, enter 'load filenane' to run the function.
Your function load() only prints the PyMOL commands that you want to execute.

Add below or above the print lines, add these indented lines.

    cmd.do("load 1u8q.pdb")
    cmd.do("color red, (chain y)" )

You might consider splitting the load and color into two separate functions to make your code easier to read and use.
Functions in Python are suppose to do only one thing.

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419

________________________________________
From: Hrutvik Bhavsar [hru...@gm...]
Sent: Wednesday, July 01, 2020 6:26 PM
To: pym...@li...
Subject: [EXTERNAL] [PyMOL] Question about python commands in PyMOL

Hello,

I'm writing a python script that loads in PDBs then selects certain chains colors them according to a standardized chart. However, I've run into the issue where my when I try running my script in Pymol via the run command it just displays the text on the python script but doesn't actually execute the command. I've pasted a sample script below. Please let me if there's a way to fix this. Thank you for your help.
Sincerely, Hrutvik.


from pymol import cmd, stored

def load( arg1):

    print ("load 1u8q.pdb")
    print ("color red, (chain y)" + "\n")

    return (arg1)

cmd.extend( "load", load );
cmd.extend( "color", color );

Re: [PyMOL] Question about python commands in PyMOL

[Ali K. <ali...@sy...>]

Hi Hrutvik,

The print function doesn’t actually execute the PyMOL commands the “cmd” module does

Change the prints to:
cmd.load(“1u8q.pdb”)
cmd.color(“red”,”chain y”)

For specific instruction on how to use the cmd based functions, visit the PyMOL wiki

Two other things:

  1.  the color function does not need to need to be extended as it is already built into PyMOL
  2.  PyMOL already has a load function which may be overwritten using your new load function, call it something else just to be safe

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
Email: aku...@un...

From: Ali Kusay <aku...@un...>
Date: Thursday, 2 July 2020 at 8:55 pm
To: Ali Kusay <ali...@sy...>
Subject: FW: [PyMOL] Question about python commands in PyMOL


________________________________
From: Hrutvik Bhavsar
Sent: Thursday, 2 July 2020 9:26:23 AM (UTC+10:00) Canberra, Melbourne, Sydney
To: pym...@li...
Subject: [PyMOL] Question about python commands in PyMOL
Hello,

I'm writing a python script that loads in PDBs then selects certain chains colors them according to a standardized chart. However, I've run into the issue where my when I try running my script in Pymol via the run command it just displays the text on the python script but doesn't actually execute the command. I've pasted a sample script below. Please let me if there's a way to fix this. Thank you for your help.
Sincerely, Hrutvik.


from pymol import cmd, stored

def load( arg1):

    print ("load 1u8q.pdb")
    print ("color red, (chain y)" + "\n")

    return (arg1)

cmd.extend( "load", load );
cmd.extend( "color", color );

[PyMOL] Question about python commands in PyMOL

[Hrutvik B. <hru...@gm...>]

Hello,

I'm writing a python script that loads in PDBs then selects certain chains
colors them according to a standardized chart. However, I've run into the
issue where my when I try running my script in Pymol via the run command it
just displays the text on the python script but doesn't actually execute
the command. I've pasted a sample script below. Please let me if there's a
way to fix this. Thank you for your help.
Sincerely, Hrutvik.

from pymol import cmd, stored

def load( arg1):

    print ("load 1u8q.pdb")
    print ("color red, (chain y)" + "\n")

    return (arg1)

cmd.extend( "load", load );
cmd.extend( "color", color );

[PyMOL] translate command after reorienting molecule

[Daniel B. <db...@ia...>]

Hello,

Say that I have two small molecules on top of each other at the origin
[0,0,0].  I move one molecule to [50,50,50] and then I pan around and then
try to move the second molecule to the same location as the first.  If I
"translate [50,50,50], name" the second molecule, it will not end up in the
same position as the first.  The "centerofmass" command stil returns the
same coordinates for the molecules despite the image being moved into a new
position.

How can I resolve this? Is there something I can do with the object
matrix?


Dan

Re: [PyMOL] 13th CCP4/APS Crystallographic School in the US

[Xu, Q. <qx...@an...>]

Dear colleagues,

The 2020 CCP4 School at APS has been cancelled. Due to the pandemic, it is not possible to find a timeslot for the gathering at Argonne for the rest of the year. We are very sorry for the inconvenience.

We want to thank the registrants for their interest in the School. The registration information will be carried over for the next event (Let us know if you are no longer interested).

Hope to see everybody next year! Stay safe!

The CCP4 School at APS Organizers

From: Xu, Qingping
Sent: Wednesday, April 1, 2020 7:18 AM
To: CC...@JI...; phe...@ph...; pym...@li...
Subject: RE: 13th CCP4/APS Crystallographic School in the US


Dear colleagues,



Due to the on-going pandemic, the 2020 CCP4/APS workshop (originally scheduled for June 15-22, 2020) is postponed. We will try to schedule the workshop at a later date. If no suitable date is found, the event will be cancelled. Further notice will be announced in the CCP4 bulletin board.  In the meantime, the registration site remains open. We are sorry for the inconvenience.





The CCP4/APS school organizers


From: Xu, Qingping <qx...@an...<mailto:qx...@an...>>
Sent: Monday, January 6, 2020 12:04 PM
To: CC...@JI...<mailto:CC...@JI...>; phe...@ph...<mailto:phe...@ph...>; pym...@li...<mailto:pym...@li...>
Subject: 13th CCP4/APS Crystallographic School in the US


Dear Colleagues,

We are pleased to announce the 13th annual CCP4/APS crystallographic school “From data collection to structure refinement and beyond” will be held on June 15-22, 2020 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-2020/index.php.

Dates: June 15 through 22, 2020

Location: Advanced Photon Source, Argonne National Laboratory, Argonne (Near Chicago), Illinois, USA

The school comprises two parts: data collection workshop and crystallographic computing workshop. Data collection workshop includes beamline training, data collection on GM/CA@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 trouble-shooting 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 sample program, contact info and other details can be found at the School website.

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 1st, 2020. To apply, visit https://www.ccp4.ac.uk/schools/APS-2020/application.php<https://www.ccp4.ac.uk/schools/APS-2019/application.php>.

Fees: The registration for application is free but there is $500 participation fee for the selected academic students and $950 for industrial researchers. A valid credit card is required for registration, however, it will be charged only for students selected to participate. The students will be responsible for their transportation and lodging. The workshop organizers can assist in making lodging reservations at the Argonne Guest House. The workshop will cover all other expenses (including meals).


We hope to see you at the school.


Charles, Garib and Qingping

Re: [PyMOL] Python script with iterate_state and selection command

[ABEL S. <Ste...@ce...>]

Thank you very much, 

It was very helpful since i did not find similar examples on the web that combine this directives 

Thanks again 

Stéphane
----------------------------------------------------------

Envoyé : mardi 23 juin 2020 09:10
À : ABEL Stephane
Cc : Pedro Lacerda; pymol-users
Objet : Re: [PyMOL] Python script with iterate_state and selection command

Hi Stéphane,

Pedro is correct, you should change the selection like he suggested.

You also need to:
- Make a state specific selection with cmd.select(..., state=i)
- Adjust the loop to start at 1 and not at 0
- Use "stored.resid.append(resv)" as the expression

This should work:

###
from pymol import cmd, stored

objname = "mytraj"

cmd.load("1JNO_GrA_DMPC_NACL_Membrane_TIP3P_SemiIso_rep3_Water_InChannel_0ns.pdb", objname)
cmd.load_traj("1JNO_GrA_DMPC_NACL_Membrane_TIP3P_SemiIso_rep3_Water_InChannel_0_50ns_Every_0.5ns_TRANSLATED.xtc", objname)

nb_states = cmd.count_states(objname)

for i in range(1, nb_states + 1):
    stored.resid = []
    cmd.select("water_channel", "resn SOL within 3.5 of resn CHO", state=i)
    cmd.iterate("water_channel", 'stored.resid.append(resv)')
    print("frame " + str(i) + ":" + str(stored.residues))
###


Hope that helps.

Cheers,
  Thomas


> On Jun 22, 2020, at 4:52 PM, ABEL Stephane <Ste...@ce...> wrote:
>
> Hi Pedro
>
> It does not work, the pymol crashes if I use this selection
>
> Stéphane
>
> ----------------------------------------------------------
> Stéphane Abel, Ph.D.
> CEA Centre de Saclay
> DRF/JOLIOT/I2BC-S/SB2SM/LBMS
> Bat 528, Office 138C
> Gif-sur-Yvette, F-91191 FRANCE
> Phone (portable) : +33 6 49 37 70 60
> ________________________________________
> De : Pedro Lacerda [psl...@gm...]
> Envoyé : lundi 22 juin 2020 16:26
> À : ABEL Stephane
> Cc : pymol-users
> Objet : Re: [PyMOL] Python script with iterate_state and selection command
>
> Hi,
>
> Not sure if I understood your code but maybe you want change Myselection to:
>
> Myselection="resname SOL within 3.5 of resname CHO"
>
> -- Pedro Lacerda
>
> Em seg, 22 de jun de 2020 10:44, ABEL Stephane <Ste...@ce...<mailto:Ste...@ce...>> escreveu:
> Hello all,
>
> I would like to write a basic python script to select residues for each state using the iterate_state and output the results first in pymol console window with the following format
>
> frame 1 : resid ...
> frame 2 : resid ...
> ...
>
> ### my script ##
>
> from pymol import cmd, stored
>
> mytraj=""
> mytraj2=""
>
> ## Load PDB
> cmd.load("1JNO_GrA_DMPC_NACL_Membrane_TIP3P_SemiIso_rep3_Water_InChannel_0ns.pdb"), mytraj
>
> ## Load XTC
> cmd.load_traj("1JNO_GrA_DMPC_NACL_Membrane_TIP3P_SemiIso_rep3_Water_InChannel_0_50ns_Every_0.5ns_TRANSLATED.xtc"), mytraj2
>
> stored.resid = []
>
> Myselection="select water_channel, resname SOL within 3.5 of resname CHO"
>
> nb_states=cmd.count_states(mytraj2)    ---> Contains 102 states
> print(mytraj2, nb_states)
>
> state=1
> for i in range (nb_states) :
>        print(i)
>        cmd.iterate_state (i, (Myselection), 'resid.append(resv)')   ----> Should to ireate for all the states
>        print("frame " + str(i) + ":" + str(stored.residues))   ---> Print the results of the Myselection command in the console
>
> ###
>
> But the first problem I have is the syntax of the iterate_state. I obtain the  following error
> "Selector-Error: Invalid selection name "select".
> ( select water_channel, resname SOL within 3.5 of resname CHO )<--"
>
> When I put this selection command directly in Pymol, it works and i can obtain the desired waters that was near 3.5 A of the CHO over all the states . So What is the correct syntax for the selection with "iterate_state" ? And how to output the results again for each state in the screen .
>
> Thanks in advance for your help
>
> Stéphane
>
>
> _______________________________________________
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> Archives: http://www.mail-archive.com/pym...@li...
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>
>
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--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

[PyMOL] Question: How can I analyze the binding strength/energy between a small molecule and DNA using Pymol?

[Alexander R. <ale...@gm...>]

Dear PyMOL maillist people:
I am new to mail lists. Please excuse any breaks of convention.
I suspect that a small molecule I am working with may have some DNA binding
property due to its triphenylphosphonium group. I would like to assess this
using Pymol. How could I do this? I do not have much background in
programming or how to use Pymol commands in general.

Re: [PyMOL] Install license file from CLI

[Antonio S. <ase...@uc...>]

Hi, Thomas. Yeah, solution no. 1 worked! Thank you very much indeed.

Kind regards,
Antonio

-- 

"Este mensaje es privado y confidencial y se dirige exclusivamente a su 
destinatario. Si usted recibe este mensaje por error, no debe revelar, 
distribuir o copiar este e-mail. Por favor, comuníquelo al remitente y 
borre el mensaje y los archivos adjuntos de su sistema. No hay renuncia a 
la confidencialidad ni a ningún privilegio a causa de una transmisión 
errónea o por mal funcionamiento". 


"This message is private and 
confidential and it is intended exclusively for the addressee. If your 
receive this message by mistake, you should not disseminate, distribute or 
copy this e-mail. Please inform the sender and delete the message and 
attachments from your system. No confidentiality or any privilege regarding 
the information is waived or lost by any mistransmission or malfunction".



No me imprimas si no es necesario.Don't print me unless it's necessary.

Re: [PyMOL] transparent electron density silhouette

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

Hi Dan and Thomas,

### Had to send message again due to size restriction, now image can be found a link ###

Perhaps this will do the trick,

Show the protein as surface and cartoon then set the surface to almost invisible:
set transparency, 0.99

Then set the surface transparency to be angle dependent (done through menu, can't find command for it):
Setting > Transparency > Angle-dependent

I have rendered an image of what it looks like, can certainly play around with the surface settings to further clean up the image: https://photos.app.goo.gl/7CGZY1Zyrihjw4D96

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
Email: aku...@un...

https://photos.app.goo.gl/7CGZY1Zyrihjw4D96


On 23/6/20, 5:28 pm, "Thomas Holder" <tho...@sc...> wrote:

    Hi Dan,

    I think in PyMOL you can only do this in two steps and compose the two images, e.g. with ImageMagick.

    # white background
    bg white

    # step 1
    as surface
    set ray_trace_mode, 2
    png surface.png, ray=1

    # step 2
    hide surface
    show cartoon
    set cartoon_cylindrical_helices
    set ray_trace_mode, 1
    png cartoon.png, ray=1

    # If you have ImageMagick installed
    system composite surface.png cartoon.png combined.png
    load combined.png

    Cheers,
      Thomas


    > On Jun 19, 2020, at 4:04 AM, Daniel P Farrell <da...@uw...> wrote:
    > 
    > Hello,
    > I'm working with some cryo-EM density and I'm trying to get my isosurface or volume (whichever's easier) to display transparent except for the curves and turns of the density.
    > similar to this (done in chimeraX) https://protect-au.mimecast.com/s/qAmgCD1vlpTgWg47HWiw6v?domain=imgur.com
    > 
    > Does anyone know if this is possible?
    > 
    > thanks
    > ~Dan
    > _______________________________________________
    > PyMOL-users mailing list
    > Archives: https://protect-au.mimecast.com/s/KUWLCE8wmrtRzREwHw5Pkx?domain=mail-archive.com
    > Unsubscribe: https://protect-au.mimecast.com/s/OaZCCGv0oyCjPjvrTpweYH?domain=sourceforge.net

    --
    Thomas Holder
    PyMOL Principal Developer
    Schrödinger, Inc.



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Re: [PyMOL] transparent electron density silhouette

[Thomas H. <tho...@sc...>]

Hi Dan,

I think in PyMOL you can only do this in two steps and compose the two images, e.g. with ImageMagick.

# white background
bg white

# step 1
as surface
set ray_trace_mode, 2
png surface.png, ray=1

# step 2
hide surface
show cartoon
set cartoon_cylindrical_helices
set ray_trace_mode, 1
png cartoon.png, ray=1

# If you have ImageMagick installed
system composite surface.png cartoon.png combined.png
load combined.png

Cheers,
  Thomas


> On Jun 19, 2020, at 4:04 AM, Daniel P Farrell <da...@uw...> wrote:
> 
> Hello,
> I'm working with some cryo-EM density and I'm trying to get my isosurface or volume (whichever's easier) to display transparent except for the curves and turns of the density.
> similar to this (done in chimeraX) https://imgur.com/a/lZuG8gD
> 
> Does anyone know if this is possible?
> 
> thanks
> ~Dan
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] Python script with iterate_state and selection command

[Thomas H. <tho...@sc...>]

Hi Stéphane,

Pedro is correct, you should change the selection like he suggested.

You also need to:
- Make a state specific selection with cmd.select(..., state=i)
- Adjust the loop to start at 1 and not at 0
- Use "stored.resid.append(resv)" as the expression

This should work:

###
from pymol import cmd, stored

objname = "mytraj"

cmd.load("1JNO_GrA_DMPC_NACL_Membrane_TIP3P_SemiIso_rep3_Water_InChannel_0ns.pdb", objname)
cmd.load_traj("1JNO_GrA_DMPC_NACL_Membrane_TIP3P_SemiIso_rep3_Water_InChannel_0_50ns_Every_0.5ns_TRANSLATED.xtc", objname)

nb_states = cmd.count_states(objname)

for i in range(1, nb_states + 1):
    stored.resid = []
    cmd.select("water_channel", "resn SOL within 3.5 of resn CHO", state=i)
    cmd.iterate("water_channel", 'stored.resid.append(resv)')
    print("frame " + str(i) + ":" + str(stored.residues))
###


Hope that helps.

Cheers,
  Thomas


> On Jun 22, 2020, at 4:52 PM, ABEL Stephane <Ste...@ce...> wrote:
> 
> Hi Pedro 
> 
> It does not work, the pymol crashes if I use this selection
> 
> Stéphane
> 
> ----------------------------------------------------------
> Stéphane Abel, Ph.D.
> CEA Centre de Saclay
> DRF/JOLIOT/I2BC-S/SB2SM/LBMS
> Bat 528, Office 138C
> Gif-sur-Yvette, F-91191 FRANCE
> Phone (portable) : +33 6 49 37 70 60
> ________________________________________
> De : Pedro Lacerda [psl...@gm...]
> Envoyé : lundi 22 juin 2020 16:26
> À : ABEL Stephane
> Cc : pymol-users
> Objet : Re: [PyMOL] Python script with iterate_state and selection command
> 
> Hi,
> 
> Not sure if I understood your code but maybe you want change Myselection to:
> 
> Myselection="resname SOL within 3.5 of resname CHO"
> 
> -- Pedro Lacerda
> 
> Em seg, 22 de jun de 2020 10:44, ABEL Stephane <Ste...@ce...<mailto:Ste...@ce...>> escreveu:
> Hello all,
> 
> I would like to write a basic python script to select residues for each state using the iterate_state and output the results first in pymol console window with the following format
> 
> frame 1 : resid ...
> frame 2 : resid ...
> ...
> 
> ### my script ##
> 
> from pymol import cmd, stored
> 
> mytraj=""
> mytraj2=""
> 
> ## Load PDB
> cmd.load("1JNO_GrA_DMPC_NACL_Membrane_TIP3P_SemiIso_rep3_Water_InChannel_0ns.pdb"), mytraj
> 
> ## Load XTC
> cmd.load_traj("1JNO_GrA_DMPC_NACL_Membrane_TIP3P_SemiIso_rep3_Water_InChannel_0_50ns_Every_0.5ns_TRANSLATED.xtc"), mytraj2
> 
> stored.resid = []
> 
> Myselection="select water_channel, resname SOL within 3.5 of resname CHO"
> 
> nb_states=cmd.count_states(mytraj2)    ---> Contains 102 states
> print(mytraj2, nb_states)
> 
> state=1
> for i in range (nb_states) :
>        print(i)
>        cmd.iterate_state (i, (Myselection), 'resid.append(resv)')   ----> Should to ireate for all the states
>        print("frame " + str(i) + ":" + str(stored.residues))   ---> Print the results of the Myselection command in the console
> 
> ###
> 
> But the first problem I have is the syntax of the iterate_state. I obtain the  following error
> "Selector-Error: Invalid selection name "select".
> ( select water_channel, resname SOL within 3.5 of resname CHO )<--"
> 
> When I put this selection command directly in Pymol, it works and i can obtain the desired waters that was near 3.5 A of the CHO over all the states . So What is the correct syntax for the selection with "iterate_state" ? And how to output the results again for each state in the screen .
> 
> Thanks in advance for your help
> 
> Stéphane
> 
> 
> _______________________________________________
> 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

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] Python script with iterate_state and selection command

[ABEL S. <Ste...@ce...>]

Hi Pedro 

It does not work, the pymol crashes if I use this selection

Stéphane

----------------------------------------------------------
Stéphane Abel, Ph.D.
CEA Centre de Saclay
DRF/JOLIOT/I2BC-S/SB2SM/LBMS
Bat 528, Office 138C
Gif-sur-Yvette, F-91191 FRANCE
Phone (portable) : +33 6 49 37 70 60
________________________________________
De : Pedro Lacerda [psl...@gm...]
Envoyé : lundi 22 juin 2020 16:26
À : ABEL Stephane
Cc : pymol-users
Objet : Re: [PyMOL] Python script with iterate_state and selection command

Hi,

Not sure if I understood your code but maybe you want change Myselection to:

Myselection="resname SOL within 3.5 of resname CHO"

-- Pedro Lacerda

Em seg, 22 de jun de 2020 10:44, ABEL Stephane <Ste...@ce...<mailto:Ste...@ce...>> escreveu:
Hello all,

I would like to write a basic python script to select residues for each state using the iterate_state and output the results first in pymol console window with the following format

frame 1 : resid ...
frame 2 : resid ...
...

### my script ##

from pymol import cmd, stored

mytraj=""
mytraj2=""

## Load PDB
cmd.load("1JNO_GrA_DMPC_NACL_Membrane_TIP3P_SemiIso_rep3_Water_InChannel_0ns.pdb"), mytraj

## Load XTC
cmd.load_traj("1JNO_GrA_DMPC_NACL_Membrane_TIP3P_SemiIso_rep3_Water_InChannel_0_50ns_Every_0.5ns_TRANSLATED.xtc"), mytraj2

stored.resid = []

Myselection="select water_channel, resname SOL within 3.5 of resname CHO"

nb_states=cmd.count_states(mytraj2)    ---> Contains 102 states
print(mytraj2, nb_states)

state=1
for i in range (nb_states) :
        print(i)
        cmd.iterate_state (i, (Myselection), 'resid.append(resv)')   ----> Should to ireate for all the states
        print("frame " + str(i) + ":" + str(stored.residues))   ---> Print the results of the Myselection command in the console

###

But the first problem I have is the syntax of the iterate_state. I obtain the  following error
"Selector-Error: Invalid selection name "select".
( select water_channel, resname SOL within 3.5 of resname CHO )<--"

When I put this selection command directly in Pymol, it works and i can obtain the desired waters that was near 3.5 A of the CHO over all the states . So What is the correct syntax for the selection with "iterate_state" ? And how to output the results again for each state in the screen .

Thanks in advance for your help

Stéphane


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Archives: http://www.mail-archive.com/pym...@li...
Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Python script with iterate_state and selection command

[Pedro L. <psl...@gm...>]

Hi,

Not sure if I understood your code but maybe you want change Myselection to:

Myselection="resname SOL within 3.5 of resname CHO"

-- Pedro Lacerda

Em seg, 22 de jun de 2020 10:44, ABEL Stephane <Ste...@ce...>
escreveu:

> Hello all,
>
> I would like to write a basic python script to select residues for each
> state using the iterate_state and output the results first in pymol console
> window with the following format
>
> frame 1 : resid ...
> frame 2 : resid ...
> ...
>
> ### my script ##
>
> from pymol import cmd, stored
>
> mytraj=""
> mytraj2=""
>
> ## Load PDB
> cmd.load("1JNO_GrA_DMPC_NACL_Membrane_TIP3P_SemiIso_rep3_Water_InChannel_0ns.pdb"),
> mytraj
>
> ## Load XTC
> cmd.load_traj("1JNO_GrA_DMPC_NACL_Membrane_TIP3P_SemiIso_rep3_Water_InChannel_0_50ns_Every_0.5ns_TRANSLATED.xtc"),
> mytraj2
>
> stored.resid = []
>
> Myselection="select water_channel, resname SOL within 3.5 of resname CHO"
>
> nb_states=cmd.count_states(mytraj2)    ---> Contains 102 states
> print(mytraj2, nb_states)
>
> state=1
> for i in range (nb_states) :
>         print(i)
>         cmd.iterate_state (i, (Myselection), 'resid.append(resv)')   ---->
> Should to ireate for all the states
>         print("frame " + str(i) + ":" + str(stored.residues))   ---> Print
> the results of the Myselection command in the console
>
> ###
>
> But the first problem I have is the syntax of the iterate_state. I obtain
> the  following error
> "Selector-Error: Invalid selection name "select".
> ( select water_channel, resname SOL within 3.5 of resname CHO )<--"
>
> When I put this selection command directly in Pymol, it works and i can
> obtain the desired waters that was near 3.5 A of the CHO over all the
> states . So What is the correct syntax for the selection with
> "iterate_state" ? And how to output the results again for each state in the
> screen .
>
> Thanks in advance for your help
>
> Stéphane
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>

[PyMOL] Python script with iterate_state and selection command

[ABEL S. <Ste...@ce...>]

Hello all, 

I would like to write a basic python script to select residues for each state using the iterate_state and output the results first in pymol console window with the following format 

frame 1 : resid ...
frame 2 : resid ... 
...

### my script ## 

from pymol import cmd, stored

mytraj=""
mytraj2=""

## Load PDB 
cmd.load("1JNO_GrA_DMPC_NACL_Membrane_TIP3P_SemiIso_rep3_Water_InChannel_0ns.pdb"), mytraj

## Load XTC
cmd.load_traj("1JNO_GrA_DMPC_NACL_Membrane_TIP3P_SemiIso_rep3_Water_InChannel_0_50ns_Every_0.5ns_TRANSLATED.xtc"), mytraj2

stored.resid = []

Myselection="select water_channel, resname SOL within 3.5 of resname CHO"

nb_states=cmd.count_states(mytraj2)    ---> Contains 102 states
print(mytraj2, nb_states)

state=1
for i in range (nb_states) :
	print(i)
	cmd.iterate_state (i, (Myselection), 'resid.append(resv)')   ----> Should to ireate for all the states
	print("frame " + str(i) + ":" + str(stored.residues))   ---> Print the results of the Myselection command in the console

### 

But the first problem I have is the syntax of the iterate_state. I obtain the  following error 
"Selector-Error: Invalid selection name "select".
( select water_channel, resname SOL within 3.5 of resname CHO )<--"

When I put this selection command directly in Pymol, it works and i can obtain the desired waters that was near 3.5 A of the CHO over all the states . So What is the correct syntax for the selection with "iterate_state" ? And how to output the results again for each state in the screen .  

Thanks in advance for your help

Stéphane 

Re: [PyMOL] Install license file from CLI

[Thomas H. <tho...@sc...>]

Hi Antonio,

Thanks for the diagnostics data.

> I'm working with a virtual environment.

Ah, that's the crux. I assume you've used something like `python3 -m venv --system-site-packages`. That happens to be not compatible with how PyMOL finds $PYMOL_PATH, it uses `sys.prefix` for that which now points to your virtual environment.

Here some options which should all solve the issue:

1) Place the license file at $HOME/.pymol/license.lic

2) Export PYMOL_PATH=/home/my_user/pymol/share/pymol before importing the `pymol` module (can be done with `os.environ['PYMOL_PATH'] = ...` from your Python script). This option I would avoid if possible, better not to hard-code any paths in your script.

3) Use conda environments instead of venv. That's my preferred solution.

. $HOME/pymol/bin/activate
conda create -p $HOME/envs/dqn_pymol2 schrodinger::pymol
conda activate $HOME/envs/dqn_pymol2


Cheers,
  Thomas

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] Install license file from CLI

[Antonio S. <ase...@uc...>]

This is the diagnostics log. Please keep reading at the end of the log:

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

PyMOL(TM) 2.3.4 - Incentive Product
 Copyright (C) Schrodinger, LLC

 This Executable Build integrates and extends Open-Source PyMOL.
 Detected 40 CPU cores.  Enabled multithreaded rendering.
PyMOL>diagnostics
PyMOL 2.3.4
build date: Wed Nov  6 20:04:05 2019 -0100
git sha: b5302154d05cd6c9f0ed78394d1ca2dcf91ebf8f
conda build: py37h75f9260_0 file:///tmp/miniconda/conda-bld/linux-64

License Information:
No License File - For Evaluation Only (0 days remaining)
License Files:
(no license file found)

Operating System:
Linux-4.4.0-178-generic-x86_64-with-debian-stretch-sid
#208-Ubuntu SMP Sun Apr 5 23:45:10 UTC 2020

OpenGL Driver:
(none)
(none)
(none)
PyQt5 5.6 (Qt 5.6.2)

Python:
3.7.5 (default, Oct 25 2019, 15:51:11)
[GCC 7.3.0]
prefix=/home/my_user/pymol
executable=/home/my_user/pymol/bin/python
filesystemencoding=utf-8

Startup Scripts:
(no pymolrc file found)

Qt, Python and PyMOL Environment Variables:
LANG=es_ES.UTF-8
PYMOL_DATA=/home/my_user/pymol/share/pymol/data
PYMOL_LICENSE_FILE=
PYMOL_PATH=/home/my_user/pymol/share/pymol
PYTHONEXECUTABLE=/home/my_user/pymol/bin/python
PYTHONPATH=/home/my_user/envs/dqn_docking/RDKit:/home/my_user/envs/dqn_docking/lib:/home/my_user/envs/dqn_docking/local/lib:/home/my_user/envs/dqn_docking/bin/python:/home/my_user/miniconda3/bin/python
PYTHONSTARTUP=/home/my_user/.startup.py
QT_API=PyQt5
QT_QPA_PLATFORMTHEME=appmenu-qt5
QT_XKB_CONFIG_ROOT=/home/my_user/pymol/lib

PATH:
/home/my_user/pymol/bin:/home/my_user/envs/dqn_pymol/bin:/usr/local/MGLTools
-1.5.6/bin:/home/my_user/miniconda3/bin:/home/my_user/projects/baselines/bas
elines/deepq/mgltools/bin:/home/my_user/bin:/home/my_user/.local/bin:/usr/lo
cal/MGLTools-1.5.6/bin:/home/my_user/miniconda3/bin/conda:/home/my_user/proj
ects/baselines/baselines/deepq/mgltools/bin:/usr/local/sbin:/usr/local/bin:/us
r/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/usr/lib/jvm/jdk-11.0.5
/bin:/snap/bin:/usr/local/cuda/bin:/usr/local/cuda/bin

Diagnostics collected on Fri Jun 19 18:33:16 2020 -0100

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

So, no license file was found. My PyMol is installed in $HOME/pymol/. So, I
moved the license file to $HOME/pymol/share/pymol/license.lic . Then I ran
the diagnostics again:

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

PyMOL(TM) 2.3.4 - Incentive Product
 Copyright (C) Schrodinger, LLC

 This Executable Build integrates and extends Open-Source PyMOL.
 Detected 40 CPU cores.  Enabled multithreaded rendering.
PyMOL>diagnostics
PyMOL 2.3.4
build date: Wed Nov  6 20:04:05 2019 -0100
git sha: b5302154d05cd6c9f0ed78394d1ca2dcf91ebf8f
conda build: py37h75f9260_0 file:///tmp/miniconda/conda-bld/linux-64

License Information:
PyMOL for educational use only
Expiry date: 01-jan-2021
License Files:
/home/my_user/pymol/share/pymol/license.lic

Operating System:
Linux-4.4.0-178-generic-x86_64-with-debian-stretch-sid
#208-Ubuntu SMP Sun Apr 5 23:45:10 UTC 2020

OpenGL Driver:(none)(none)(none)
PyQt5 5.6 (Qt 5.6.2)

Python:
3.7.5 (default, Oct 25 2019, 15:51:11)
[GCC 7.3.0]
prefix=/home/my_user/pymol
executable=/home/my_user/pymol/bin/python
filesystemencoding=utf-8

Startup Scripts:
(no pymolrc file found)

Qt, Python and PyMOL Environment Variables:
LANG=es_ES.UTF-8
PYMOL_DATA=/home/my_user/pymol/share/pymol/data
PYMOL_LICENSE_FILE=/home/my_user/pymol/share/pymol/license.lic
PYMOL_PATH=/home/my_user/pymol/share/pymol
PYTHONEXECUTABLE=/home/my_user/pymol/bin/python
PYTHONPATH=/home/my_user/envs/dqn_docking/RDKit:/home/my_user/envs/dqn_docking/lib:/home/my_user/envs/dqn_docking/local/lib:/home/my_user/envs/dqn_docking/bin/python:/home/my_user/miniconda3/bin/python
PYTHONSTARTUP=/home/my_user/.startup.py
QT_API=PyQt5
QT_QPA_PLATFORMTHEME=appmenu-qt5
QT_XKB_CONFIG_ROOT=/home/my_user/pymol/lib

PATH:
/home/my_user/pymol/bin:/home/my_user/envs/dqn_pymol/bin:/usr/local/MGLTools
-1.5.6/bin:/home/my_user/miniconda3/bin:/home/my_user/projects/baselines/bas
elines/deepq/mgltools/bin:/home/my_user/bin:/home/my_user/.local/bin:/usr/lo
cal/MGLTools-1.5.6/bin:/home/my_user/miniconda3/bin/conda:/home/my_user/proj
ects/baselines/baselines/deepq/mgltools/bin:/usr/local/sbin:/usr/local/bin:/us
r/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/usr/lib/jvm/jdk-11.0.5
/bin:/snap/bin:/usr/local/cuda/bin:/usr/local/cuda/bin

Diagnostics collected on Fri Jun 19 18:46:42 2020 -0100

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

Now the license file is recognized. So, apparently this problem should be
solved. But unfortunately the warning message persists. It should be noted
that I'm calling pymol through the Python's API. I'm working with a virtual
environment. I wonder if the problem is related to this fact?? Thanks for
your help, Thomas. I really appreciate it.

Kind regards,


El vie., 19 jun. 2020 a las 14:02, Thomas Holder (<
tho...@sc...>) escribió:

> That's unexpected. Can you send the output of the following command?
>
> pymol -cd diagnostics
>
> This will report the exact installation location, and also if a license
> file was found.
>
>
> > On Jun 19, 2020, at 10:33 AM, Antonio Serrano <ase...@uc...>
> wrote:
> >
> > I changed the name of the license file as you said, but the warning
> message keeps popping:
> >
> > <current_pos.png>
> >
> >
> >
> >
> >
> >
> > El jue., 18 jun. 2020 a las 20:16, Thomas Holder (<
> tho...@sc...>) escribió:
> > Hi Antonio,
> >
> > Rename the file to "license.lic".
> >
> > Cheers,
> >   Thomas
> >
> > > On Jun 18, 2020, at 6:08 PM, Antonio Serrano <ase...@uc...>
> wrote:
> > >
> > > Hi Thomas. Thanks for your quick response. I installed Miniconda, so I
> put the license file (pymol-edu-license.lic) in the following path:
> $HOME/miniconda3/share/pymol/ . But a warning text stating "No License File
> - For evaluation Only (0 days remaining)" still appears when rendering PNG
> files with PyMol. Any suggestions?
> > >
> > > El jue., 18 jun. 2020 a las 12:44, Thomas Holder (<
> tho...@sc...>) escribió:
> > > Hi Antonio,
> > >
> > > Did you install PyMOL into $HOME/anaconda3 ? If you installed into a
> different location, then that path to the license file will differ of
> course. Basically, path-to-pymol-dir/share/pymol/license.lic is the path.
> > >
> > > Cheers,
> > >   Thomas
> > >
> > > > On Jun 17, 2020, at 2:15 PM, Antonio Serrano <ase...@uc...>
> wrote:
> > > >
> > > > Hi:
> > > >
> > > > I'm working with PyMol installed on a remote server, so I don't have
> access to the GUI. I already have an educational license. According to your
> FAQ at https://pymol.org/2/support.html?, the license file should be
> placed in $HOME/anaconda3/share/pymol/license.lic on a Linux computer. I
> already did it but PyMol isn't still activated. Any idea on how to
> completely install the license file using only the Command Line Interface?
> Many thx.
> > > >
> > > > BR,
> > > > Antonio Serrano
> >
> > --
> > Thomas Holder
> > PyMOL Principal Developer
> > Schrödinger, Inc.
> >
> >
> >
> > --
> > Antonio Serrano
> > Predoctoral researcher - Contratado predoctoral
> >
> > UCAM Universidad Católica de Murcia
> > Phone:  +34 968 278 821
> > Email:    ase...@uc...
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>

-- 
Antonio Serrano
Predoctoral researcher - Contratado predoctoral

*UCAM Universidad Católica de Murcia*

Phone:  +34 968 278 821
Email:    ase...@uc... <//ase...@uc...>

<https://scholar.google.es/citations?user=ZEJJCuUAAAAJ&hl=en&authuser=1>
<https://orcid.org/0000-0002-8121-5032>
<https://www.researchgate.net/profile/Antonio_Serrano9?ev=hdr_xprf>

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