Re: [PyMOL] ModuleNotFoundError: No module named 'pymol._cmd'

I settled for a fresh start, i.e. recompiling PyMol. This solved the issue. > -Original Message- > From: Markus Heller > Sent: Wednesday, November 27, 2019 4:01 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] ModuleNotFoundError: No module named '

[PyMOL] ModuleNotFoundError: No module named 'pymol._cmd'

Hi, This is just an attempt to see if my issue has popped up before. I have compiled open source Pymol 2.4, which I used for a few months now. Today, the following error prevents launching Pymol: $ pymol Traceback (most recent call last): File "/home/mheller/pymol-2.4/lib/python/pymol/__ini

Re: [PyMOL] Compiling open source pymol 2.4

Agreed, Thomas. Thanks for your help! > -Original Message- > From: Thomas Holder > Sent: Tuesday, March 12, 2019 12:14 PM > To: Markus Heller > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] Compiling open source pymol 2.4 > > Hi Markus, > &g

[PyMOL] Compiling open source pymol 2.4

Hi all, I'm having trouble compiling open source Pymol 2.4. If I compile with python 2.7, the compilation finishes without errors or warnings, but when I start Pymol, I don't see the menu bar at the top of the window, and I don't see any errors. If, on the other hand, I compile with python 3,

[PyMOL] Hbond to backbone cartoon

Hi all, what's the best way to show a hydrogen bond to a backbone atom in the following scenario: Protein shown as cartoon, ligand as sticks, binding site residues (within 5A of ligand) shown as lines, and sidechain help is on. If the ligand forms a hydrogen bond with a backbone atom, the dash

Re: [PyMOL] Display metal coordination

Hi Thomas, Ya, something like that would work. Thank you very much! Markus > -Original Message- > From: Thomas Holder > Sent: Wednesday, August 29, 2018 1:33 AM > To: Joel Tyndall ; Markus Heller > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [Py

[PyMOL] Display metal coordination

Hi all, Is there a way to display the coordination of a metal, e.g. Zn2+ or Mg2+, that doesn't require manual selection of atoms and showing of bonds? I wasn't able to find anything online ... Thanks Markus -- Markus Heller, Ph.D. Senior Scientist, Medicinal Chemistry Direct: 60

Re: [PyMOL] Calculate RMSD between ligands from a crystal structure and from a docking

Not knowing what your molecule looks like, could it be automorphism? > -Original Message- > From: Baptiste Legrand > Sent: Wednesday, July 25, 2018 9:17 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Calculate RMSD between ligands from a crystal structure and > from a docki

Re: [PyMOL] Add to existing selection

Of course! Works like a charm. Thanks Jarrett! From: Jarrett Johnson Sent: Monday, July 23, 2018 11:43 AM To: Markus Heller Cc: Pymol User list Subject: Re: [PyMOL] Add to existing selection Hello Markus, Selection algebra (https://pymolwiki.org/index.php/Selection_Algebra) may be able to

[PyMOL] Add to existing selection

Hi, How can I add a residue to an existing selection? Example: I'm comparing the binding sites of two superposed protein structures, and show the side chains with a certain distance to the ligand. Sometimes the side chain of one protein falls just outside that distance, and thus isn't shown,

[PyMOL] APBS plug in

C:\Users\mheller\AppData\Local\Temp\pymol-generated-PE0.dx' exist? -- Markus Heller, Ph.D. Senior Scientist, NMR CDRD - The Centre for Drug Research and Development 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC  V6T 1Z3 | Main: (604) 827-1147 Direct: (604) 827-1122 | F: (604) 827

Re: [PyMOL] Clip surface only

, 2015 1:49 PM To: H. Adam Steinberg Cc: Markus Heller; pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Clip surface only Hey :) If you want to do it using only Pymol in just a few minutes, try this: set auto_zoom, 0 scale=1.0 import numpy M=numpy.array(cmd.get_view()).reshape(6,3

[PyMOL] Clip surface only

Hello all, I'm trying to show a ligand in a binding site, and I'd like to selectively clip the surface only.  I haven't found anything on the web, only that it was not possible a few years ago. Surely this has changed? Thanks and Cheers Markus -- Markus Heller, Ph.D. NMR

Re: [PyMOL] h_add breaks surface?

Would if I could. How do I sign up for the PyMOLWiki? THanks Markus -Original Message- From: Thomas Holder [mailto:thomas.hol...@schrodinger.com] Sent: Thursday, October 16, 2014 1:48 PM To: Markus Heller Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] h_add breaks surface

Re: [PyMOL] Show all residues forming H-bonds

k but I'll need to refine it ;-) Cheers Markus From: Sampson, Jared [mailto:jared.samp...@nyumc.org] Sent: Thursday, October 16, 2014 6:36 AM To: Markus Heller Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Show all residues forming H-bonds Hi Markus -  First, you need

Re: [PyMOL] h_add breaks surface?

er 16, 2014 10:44 AM To: Markus Heller Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] h_add breaks surface? Hi Markus, > # hide non-polar hydrogens > hide (h. and (e. c extend 1)) This will hide all representations -- including surface -- for non-polar hydrogens. I guess what you

Re: [PyMOL] h_add breaks surface?

Wednesday, October 15, 2014 4:18 PM To: Markus Heller Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] h_add breaks surface? Hi Markus, I can't reproduce this. Do you have an example? Thanks, Thomas On 15 Oct 2014, at 18:32, Markus Heller wrote: > Hi all, > >

[PyMOL] h_add breaks surface?

ticed that, or does this occur just for me? Thanks Markus -- Markus Heller, Ph.D. NMR Scientist CDRD - The Centre for Drug Research and Development 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC  V6T 1Z3 | Main: (604) 827-1147 Direct: (604) 827-1122 | F: (604) 827-1299 | E: mhel...@cdrd.ca | www.cd

Re: [PyMOL] Show all residues forming H-bonds

Jared, I'm a newbie to pythom/PyMOL; how do I get this to work in a pml script? A pointer to an example script would be enough . Thanks Markus From: Sampson, Jared [mailto:jared.samp...@nyumc.org] Sent: Friday, October 10, 2014 4:17 PM To: Markus Heller Cc: pymol-users@lists.sourceforg

Re: [PyMOL] Show all residues forming H-bonds

Jared, You da man!! Sounds exactly like what i'm looking for!! Unfortunately i won't be able to try until Tuesday :/ Thanks and cheers Markus -- Markus Heller, Ph.D. Scientist, NMR CDRD -- The Centre for Drug Research and Development 2405 Wesbrook Mall, Fourth Floor Vancouver, B

Re: [PyMOL] Show all residues forming H-bonds

7;s clearer now what I'm after ... Cheers M From: Sampson, Jared [mailto:jared.samp...@nyumc.org] Sent: Friday, October 10, 2014 3:33 PM To: Markus Heller Subject: Re: [PyMOL] Show all residues forming H-bonds Hi Markus - Under the GUI "action" menu A > find > polar contacts

[PyMOL] Show all residues forming H-bonds

Hello list, subject says it all. The 2 options I came across search the www are: http://sourceforge.net/p/pymol/mailman/message/7562444/http://sourceforge.net/p/pymol/mailman/message/7562444/ and DistancesRH (http://www.pymolwiki.org/index.php/DistancesRH)http://www.pymolwiki.org/index.php/Dis

Re: [PyMOL] CONECT table

ber their three-letter codes of the top of my head. Engin On 10/7/14 2:43 PM, Markus Heller wrote: D'uh. Thanks for pointing this out. Follow-up question: I want to show my glycosylated protein as cartoon, with the glycosides *and* the side chains they're attached to shown in sticks.

Re: [PyMOL] CONECT table

Thanks for the info about the Pymol wiki page on Selection algebra. I looked at it before, but I must have never gotten the proper syntax ☹ From: Andreas Warnecke [mailto:4ndreas.warne...@gmail.com] Sent: Tuesday, October 07, 2014 4:26 PM To: Markus Heller Cc: David Hall; pymol-users

Re: [PyMOL] CONECT table

ks and Cheers Markus -Original Message- From: David Hall [mailto:li...@cowsandmilk.net] Sent: Monday, October 06, 2014 4:40 PM To: Markus Heller Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] CONECT table http://www.pymolwiki.org/index.php/Connect_mode -David > On Oct 6, 2014, at

[PyMOL] CONECT table

Hello, How can I get PYMOL to use the CONECT table from a PDB file? My protein is glycosylated, and I'd like to properly and automatically display the glycosides including their linkage to the protein. Thanks and Cheers Markus -- Markus Heller, Ph.D. NMR Scientist CDRD - The Centre for

[PyMOL] Select residues involved in H-bonds

residues involved into a selection for easier visualization? I did find a post related to this, but this pointed to yet another post which could not be accessed anymore (http://sourceforge.net/p/pymol/mailman/message/7562444/). Thanks and Cheers Markus -- Markus Heller, Ph.D. NMR Scientist CDRD

[PyMOL] Show DNA/RNA phosphate backbone

DNA/RNA (phosphate backbone) and a protein.  Any hints would be highly appreciated . Thanks and Cheers Markus -- Markus Heller, Ph.D. NMR Scientist CDRD - The Centre for Drug Research and Development 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC  V6T 1Z3 | Main: (604) 827-1147 Direct: (604

Re: [PyMOL] cartoon_transparency issue

nsparency issue On 25/08/14 18:42, Markus Heller wrote: > Hello, > > Attached is a crop of a figure create with the latest PyMOL under Windoze 7 > 64 bit. When setting cartoon_transparency, I get a gray band on the > cartoons. Where does this come from, and how do I get rid

[PyMOL] cartoon_transparency issue

) # color ROIs color atomic color yellow, (name C* and roi) # show H-bonds between sidechains and assign to slots dist Hbo-sc, resi 37, resi 41, mode = 2 # hide alls labels hide labels # color all dashes green set dash_color, green # deselect all to avoid little pink squares deselect -- Mar

[PyMOL] Hbonds in grid mode

out making them an object which gets displayed in its own panel? Thanks again and Cheers! Markus -- Markus Heller, Ph.D. NMR Scientist CDRD - The Centre for Drug Research and Development 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC  V6T 1Z3 | Main: (604) 827-1147 Direct: (604) 827-1122 | F:

[PyMOL] Coloring of helices

d little pink squares deselect -- Markus Heller, Ph.D. NMR Scientist CDRD - The Centre for Drug Research and Development 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC  V6T 1Z3 | Main: (604) 827-1147 Direct: (604) 827-1122 | F: (604) 827-1299 | E: mhel...@cdrd.ca | www.cdrd.ca Follow us:

Re: [PyMOL] Special word to select ligand?

ligand, I would go with byres (organic and symbol X) On 8/19/14 11:32 PM, Markus Heller wrote: > Hi, > > I'm wondering if the following exists: a special word to select the ligand. > The expression "organic" will select all organic molecules *including* buffer > and

[PyMOL] Special word to select ligand?

ay has somebody done this already? ;-)) to select the organic molecule with the largest mass or highest number of heavy atoms? Chances are this would select th eligand. Thanks and Cheers Markus -- Markus Heller, Ph.D. NMR Scientist CDRD - The Centre for Drug Research and Development 2405 W

Re: [PyMOL] Show cation-pi/pi-pi interactions

cript-repo/blob/master/modules/ADT/AutoDockTools/InteractionDetector.py), and I'm wondering if this could be adapted to work with neat PyMOL. Unfortunately, I don't speak python :( Cheers Markus From: Sampson, Jared [mailto:jared.samp...@nyumc.org] Sent: Wednesday, August 13, 2014 3:07

[PyMOL] Show cation-pi/pi-pi interactions

s? Thanks and Cheers Markus -- Markus Heller, Ph.D. NMR Scientist CDRD - The Centre for Drug Research and Development 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC  V6T 1Z3 | Main: (604) 827-1147 Direct: (604) 827-1122 | F: (604) 827-1299 | E: mhel...@cdrd.ca | www.cdrd.ca Follow us: