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

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

60 De : Pedro Lacerda [pslace...@gmail.com] 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

[PyMOL] Python script with iterate_state and selection command

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

[PyMOL] Write the number of molecules for each state in a file

Hello PyMOLers I have PDB file that contains different frames ( or state or models) extracted from a MD simulation and I would like to select the number the water near (say 3.5 Angstroms) a protein for each state and write the results in the file. For instance like this where resid is a list

[PyMOL] Membrane protein view according to X/Y axis and to Z=0 with Pymol

Hello Pymol users I have a snapshot of a membrane protein embedded in a model of bilayer. And I would like to have a picture of the protein according to X/Y axis and at z=0 It is possible with a script. If yes how ? Thank you Stéphane ___

Re: [PyMOL] colored secondary structure of two chains with different colors [resolved]

phone: +41 44 635 55 62 fax:+41 44 635 57 12 > > Message: 4 > Date: Thu, 6 Jun 2019 10:26:29 + > From: ABEL Stephane > To: "h. adam steinberg" > Cc: "pymol-users@lists.sourceforge.net" > > Subject: Re: [PyMOL] colored secondary st

Re: [PyMOL] PyMOL-users Digest, Vol 157, Issue 6

: honeg...@bioc.uzh.ch phone: +41 44 635 55 62 fax:+41 44 635 57 12 > > Message: 4 > Date: Thu, 6 Jun 2019 10:26:29 + > From: ABEL Stephane > To: "h. adam steinberg" > Cc: "pymol-users@lists.sourceforge.net" > > Subject: Re: [PyMO

Re: [PyMOL] colored secondary structure of two chains with different colors

mail.com] Envoyé : mercredi 5 juin 2019 21:36 À : ABEL Stephane Objet : Re: [PyMOL] colored secondary structure of two chains with different colors If you change your mouse / selection mode to chains, you can then click on one of the monomers and choose a color for it from the (sale) in the right side

[PyMOL] colored secondary structure of two chains with different colors

Hello all I have a pdb structure of gramicidin A dimer (PDB 1MAG) and I would like to color the beta sheets of each monomer with different colors (for instance in red and blue colors) in Figure https://cdn.rcsb.org/images/rutgers/ma/1mag/1mag.pdb-500.jpg How to do this ? Thank you

[PyMOL] how to keep the atom order when convert mol2 file to pdb in pymol

Hello Did you try to use the following command* before to save your pdb file? * set retain_order,[0,1] : http://www.pymolwiki.org/index.php/Retain_order Stephane -- Message: 4 Date: Sat, 13 Aug 2016 00:25:06 +0800 (CST) From: windy Subject:

[PyMOL] Pymol Script to automatize the construction of alkyl chain bonded to a molecule

Hello, I would like to add a long alkyl chain to a molecule with Pymol. I know that i can use the Build---> Fragment ---> Carbon command. However doing this manually is quite painful and error prone, since only one carbone is add, so I am wondering if possible to use a script to automatize

[PyMOL] Problem with loadBfact.py on windows

Stéphane, It looks like a slash/backslash issue between windows and linux: C:\Program Files (x86)\PyMOL_v13\PyMOL/modules\pymol\parser.py Thanks Jed, How to change it, since I can not to modify it with text editor (it seems to be used by another

[PyMOL] Problem with loadBfact.py on windows (ABEL Stephane 175950

I have reinstall the program and removed an old version of Pymol. Now the script works Thanks -- Message: 2 Date: Fri, 10 Jul 2015 12:44:40 + From: ABEL Stephane 175950 stephane.a...@cea.fr Subject: [PyMOL] Problem with loadBfact.py on windows To: pymol-users

[PyMOL] TR : Problem with loadBfact.py on windows - FIXED

De : ABEL Stephane 175950 Envoyé : vendredi 10 juillet 2015 18:39 À : pymol-users@lists.sourceforge.net Objet : Problem with loadBfact.py on windows (ABEL Stephane 175950 I have re installed the program and removed an old version of Pymol and now my

[PyMOL] time bar in a movie done with pymol

Hello Pymol users I want to add a time bar in movie done with pymol. Is it possible with a pymol script ? If not do you know an alternative (except VMD)? Thanks in advance Stéphane --

[PyMOL] Replicate a cubic unit cell in the x, y, z directions

Hi all, I want to know if is possible to replicate a cubic unit cell in the x, y, z directions (as with the graphic representation - periodic command in VMD) with pymol(v1.3)? if yes how I can do that ? Thanks in advance Stephane

[PyMOL] How to install Psico module for pymol with window 7

Hello I have downloaded the Psico module of T. Holder to use the command supercell. I have followed the wiki http://www.pymolwiki.org/index.php/Psico and https://github.com/speleo3/pymol-psico/. I did the followings: 1) Installed the ccbtx and numpy librairies 2) Dowloaded the Psico

[PyMOL] RE : Replicate a cubic unit cell in the x, y, z directions

Hi Jason It is exactly what I want !!! Merci beaucoup Cheers Stephane De : Jason Vertrees [jason.vertr...@schrodinger.com] Date d'envoi : vendredi 10 mai 2013 20:25 À : ABEL Stephane 175950 Objet : Re: [PyMOL] Replicate a cubic unit cell in the x, y

[PyMOL] Showing secondary structure of coarse grained protein

Hello everybody, I have done several MD simulations with the Martini force field of systems that contain a small protein and surfactant with GROMACS. It is possible to show with pymol the secondary structure of the protein with a cartoon representation and the detergent molecules with beads

[PyMOL] RE : Pymol Scripts for Coarse grained for non-protein molecules

Hi Tsjerk, Many thanks for your help, once again ;0 It works and it gives what i want. cool !! Stephane De : Tsjerk Wassenaar [tsje...@gmail.com] Date d'envoi : vendredi 1 mars 2013 13:56 À : ABEL Stephane 175950 Cc: pymol-users@lists.sourceforge.net

[PyMOL] Pymol Scripts for Coarse grained for non-protein molecules

Hi all, I am looking for pymol scripts for showing coarse grained representation of non-protein molecules. I am currently using the sphere representation for each bead, but the bond between two beads are not shown, so it does not nice figures. Can you help me or give some advices Thanks

[PyMOL] Obtain the number of molecule in the first hydration shell of a peptide.

Dear pymol users, I would like to obtain with Pymol (v1.3) the number of urea molecules in the first shell of a peptide. To do this I have defined the object urea as following select UREA, resn URE and used the following cutoff for the first hydration shell: select UREA_firstshell, UREA

Re: [PyMOL] Obtain the number of molecule in the first hydration shell of a peptide.

From: ABEL Stephane 175950 stephane.a...@cea.fr Subject: [PyMOL] Obtain the number of molecule in the first hydration shell of a peptide. To: pymol-users@lists.sourceforge.net pymol-users@lists.sourceforge.net Message-ID: 3e39b768bb199548ab18f7289e7534af02c4d...@exdag0-b0

[PyMOL] Create a dummy atom

Dear all, I have a simple question but i have found no response: i have downloaded a pymol script COM.py from the pymol wiki to obtain the coordinates x, y and z of the center of mass of my protein. Now i would like to create a dummy at these coordinates. How to do that with pymol ? Thank

[PyMOL] Create a dummy atom

Thank you Jason and Troels for your quick response. I have an additional question. Now if i want to pass the COM coordinates x, y and z obtained with the COM script in the pseudoatom pos. For example to use in the script How i can do that ? Thank you again for your response. Stephane

[PyMOL] RE : Write in a file the number of water at a distance from a protein surface

Thank you for your response, i will try your suggestion A bientot Stephane De : Thomas Holder [ad...@thomas-holder.de] de la part de Thomas Holder [spel...@users.sourceforge.net] Date d'envoi : jeudi 22 septembre 2011 11:14 À : ABEL Stephane 175950 Cc