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._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/__init__.py", line 64, in > > import pymol > File "/home/mheller/pymol-2.4/lib/python/pymol/__init__.py", line 564, in > > import pymol._cmd > ModuleNotFoundError: No module named 'pymol._cmd' > > > `/usr/local/Pymol-2.4/lib/python/Pymol` contains `cmd.py` and `_cmd.cpython- > 36m-x86_64-linux-gnu.so` > > I'm baffled as to why Pymol fails to open, as I'm not aware of any changes > made > to my python setup or related. > > I'd be very grateful for a slight nudge in the right direction ... > > Thanks > Markus > > > > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol- > users/unsubscribe ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[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/__init__.py", line 64, in import pymol File "/home/mheller/pymol-2.4/lib/python/pymol/__init__.py", line 564, in import pymol._cmd ModuleNotFoundError: No module named 'pymol._cmd' `/usr/local/Pymol-2.4/lib/python/Pymol` contains `cmd.py` and `_cmd.cpython-36m-x86_64-linux-gnu.so` I'm baffled as to why Pymol fails to open, as I'm not aware of any changes made to my python setup or related. I'd be very grateful for a slight nudge in the right direction ... Thanks Markus ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
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,
>
> I recommend to use Python 3. The PyMOLWiki has updated versions of those
> two failing scripts:
>
> https://pymolwiki.org/index.php/Pairwise_distances
> https://pymolwiki.org/index.php/Polarpairs
>
> I don't know why there would be no menu bar with Python 2.7. But if Python 3
> works for you, I think there is no need to figure that out.
>
> Cheers,
> Thomas
>
> > On Mar 12, 2019, at 7:34 PM, Markus Heller wrote:
> >
> > 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 starts and I see the
> > menu
> bar, but I get warnings in the Pymol console that are related to a version
> conflict
> of python 3 used for compilation and python 2 used in some scripts, e.g. the
> ones shown below.
> >
> > What's the python version to use for compiling, and how do I best proceed?
> >
> > Thanks
> > Markus
> >
> > This is part of the output shown in the Pymol console on startup:
> >
> > PyMOL>run /home/mheller/.pymol/show_bumps.py
> > PyMOL>run /home/mheller/.pymol/pairwisedistances.py
> > Traceback (most recent call last):
> > File "/home/mheller/pymol-2.4/lib/python/pymol/parsing.py", line 483, in
> > run
> >run_(path, ns_pymol, ns_pymol)
> > File "/home/mheller/pymol-2.4/lib/python/pymol/parsing.py", line 532, in
> run_file
> >execfile(file,global_ns,local_ns)
> > File "/home/mheller/pymol-2.4/lib/python/pymol/parsing.py", line 526, in
> execfile
> >co = compile(pi.file_read(filename), filename, 'exec') File
> > "/home/mheller/.pymol/pairwisedistances.py", line 13
> >print ""
> > ^
> > SyntaxError: Missing parentheses in call to 'print'. Did you mean print("")?
> > PyMOL>run /home/mheller/.pymol/supercell.py run
> > PyMOL>/home/mheller/.pymol/get_raw_distances.py
> > PyMOL>run /home/mheller/.pymol/polarpairs.py
> > Traceback (most recent call last):
> > File "/home/mheller/pymol-2.4/lib/python/pymol/parsing.py", line 483, in
> > run
> >run_(path, ns_pymol, ns_pymol)
> > File "/home/mheller/pymol-2.4/lib/python/pymol/parsing.py", line 532, in
> run_file
> >execfile(file,global_ns,local_ns)
> > File "/home/mheller/pymol-2.4/lib/python/pymol/parsing.py", line 526, in
> execfile
> >co = compile(pi.file_read(filename), filename, 'exec') File
> > "/home/mheller/.pymol/polarpairs.py", line 39
> >print 'Settings: cutoff=%.1fangstrom angle=%.1fdegree' % (cutoff, angle)
> > ^
> > SyntaxError: invalid syntax
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
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[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 starts and I see the menu
bar, but I get warnings in the Pymol console that are related to a version
conflict of python 3 used for compilation and python 2 used in some scripts,
e.g. the ones shown below.
What's the python version to use for compiling, and how do I best proceed?
Thanks
Markus
This is part of the output shown in the Pymol console on startup:
PyMOL>run /home/mheller/.pymol/show_bumps.py
PyMOL>run /home/mheller/.pymol/pairwisedistances.py
Traceback (most recent call last):
File "/home/mheller/pymol-2.4/lib/python/pymol/parsing.py", line 483, in run
run_(path, ns_pymol, ns_pymol)
File "/home/mheller/pymol-2.4/lib/python/pymol/parsing.py", line 532, in
run_file
execfile(file,global_ns,local_ns)
File "/home/mheller/pymol-2.4/lib/python/pymol/parsing.py", line 526, in
execfile
co = compile(pi.file_read(filename), filename, 'exec')
File "/home/mheller/.pymol/pairwisedistances.py", line 13
print ""
^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print("")?
PyMOL>run /home/mheller/.pymol/supercell.py
PyMOL>run /home/mheller/.pymol/get_raw_distances.py
PyMOL>run /home/mheller/.pymol/polarpairs.py
Traceback (most recent call last):
File "/home/mheller/pymol-2.4/lib/python/pymol/parsing.py", line 483, in run
run_(path, ns_pymol, ns_pymol)
File "/home/mheller/pymol-2.4/lib/python/pymol/parsing.py", line 532, in
run_file
execfile(file,global_ns,local_ns)
File "/home/mheller/pymol-2.4/lib/python/pymol/parsing.py", line 526, in
execfile
co = compile(pi.file_read(filename), filename, 'exec')
File "/home/mheller/.pymol/polarpairs.py", line 39
print 'Settings: cutoff=%.1fangstrom angle=%.1fdegree' % (cutoff, angle)
^
SyntaxError: invalid syntax
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[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 dashes don't touch the cartoon, but leave a gap. What's the recommended solution (or workaround) to avoid this gap? Thanks Markus -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
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: [PyMOL] Display metal coordination > > Hi Markus and Joel, > > Would something like this address your needs? > > # show metal contacts > distance metalcoordination, metals, (donors acceptors), 3.5, label=0 # show > metals as semi-transparent spheres show spheres, metals set > sphere_transparency, .5 # show the metal neighbors as lines show lines, byres > (all within 3.5 of metals) > > The "metals" selector was added in PyMOL 1.6.1. > > Cheers, > Thomas > > > On Aug 24, 2018, at 1:29 AM, Joel Tyndall wrote: > > > > Hi Markus, > > > > I am not aware of this function in pymol but would be interested in one > > being > developed. > > > > J > > > > -Original Message- > > From: Markus Heller > > Sent: Friday, 24 August 2018 6:28 AM > > To: pymol-users@lists.sourceforge.net > > Subject: [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 > > -- > Thomas Holder > PyMOL Principal Developer > Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[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: 604.827.1122 Main: 604.827.1147 2405 Wesbrook Mall, 4th Floor, Vancouver, BC V6T 1Z3 CDRD.CA | Twitter: @C_D_R_D | YouTube: CDRD | LinkedIn: CDRD This email and any attachments thereto may contain confidential material for the sole use of the intended recipient. Any review, copying, or distribution of this email (or any attachments thereto) by others is strictly prohibited. If you are not the intended recipient, please contact the sender immediately and permanently delete the original and any copies of this email and any attachments thereto. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
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 docking > > Dear all, > > I tried to calculate a rmsd value between ligands from a crystal structure and > after docking. The two molecules share similar nomenclatures and are really > well superimposed. I think that the RMSD should be < 1 A. I used the following > lines: > > alter all,segi="" > alter all,chain ="" > rms /ligand_crystal*, /ligand_docking* > > It works but I obtained an abnormal high RMSD value of 6.146 A. When I use the > pair_fit function, pymol completely return one molecule and also write > "ExecutiveRMS: RMS = 6.146 (51 to 51 atoms)". I should have missed > something... > > thanks for the help, > All the Best. > > Baptiste > > > > -- > Check out the vibrant tech community on one of the world's most engaging tech > sites, Slashdot.org! http://sdm.link/slashdot > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
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 help you here. Try doing: "select site, site or res 666" Jarrett J. On Mon, Jul 23, 2018 at 2:02 PM, Markus Heller mailto:mhel...@cdrd.ca>> wrote: 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, which looks odd. In essence what I'd like to be able to do is this: select site, (byres all within 6 of ligand) and polymer add_to_sel site, resi=666 Is this possible somehow? Thanks Markus -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net<mailto:PyMOL-users@lists.sourceforge.net>) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jarrett Johnson, Schrödinger -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[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, which looks odd. In essence what I'd like to be able to do is this: select site, (byres all within 6 of ligand) and polymer add_to_sel site, resi=666 Is this possible somehow? Thanks Markus -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] APBS plug in
Hello all, I'm running incentive pymol 1.7.4 on Windoze 7 64bit professional. The APBS plugin fails with; below is the output. Temp file locations are standard: Temp PQR: C:\Users\mheller\AppData\Local\Temp\pymol-generated.pqr Temp PDB: C:\Users\mheller\AppData\Local\Temp\pymol-generated.pdb Temp DX: C:\Users\mheller\AppData\Local\Temp\pymol-generated.dx APBS input: C:\Users\mheller\AppData\Local\Temp\pymol-generated.in I'm confused that's it's searching for C:\Users\mheller\AppData\Local\Temp\pymol-generated-PE0.dx ... Any ideas what's going? Thanks Markus Erasing contents of C:\Users\mheller\AppData\Local\Temp\pymol-generated.pdb in order to generate new PDB file -- PDB2PQR - a Python-based structural conversion utility -- Please cite your use of PDB2PQR as: Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Research 32 W665-W667 (2004). APBS's psize.py was used to calculated grid dimensions Estimated memory usage 2658.73432159 MB out of maximum allowed 1500.0 Maximum memory usage exceeded. Old grid dimensions were [193, 321, 225] Fine grid points rounded down from [159, 265, 185] New grid dimensions are [129, 257, 161] APBS Tools: coarse grid: (127.315,236.083,151.276) APBS Tools: fine grid: (94.891,158.872,108.986) APBS Tools: center: (5.999,31.917,23.462) APBS Tools: fine grid points (129,257,161) Getting APBS input Erasing contents of C:\Users\mheller\AppData\Local\Temp\pymol-generated.in in order to write new input file Erasing contents of C:\Users\mheller\AppData\Local\Temp\pymol-generated.pdb in order to generate new PDB file -- PDB2PQR - a Python-based structural conversion utility -- Please cite your use of PDB2PQR as: Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Research 32 W665-W667 (2004). Could not find C:\Users\mheller\AppData\Local\Temp\pymol-generated.dx so searching for C:\Users\mheller\AppData\Local\Temp\pymol-generated-PE0.dx ObjectMapLoadDXFile-Error: Unable to open file! ObjectMapLoadDXFile: Does '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) 827-1299 | E: mhel...@cdrd.ca | www.cdrd.ca Follow us: This email and any files transmitted with it are confidential and intended solely for the addressee. If you are not the named addressee you should not disseminate, distribute, copy, or alter this email. -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Clip surface only
Thanks to both of you, guys.
I settled on something far more trivial, sparked by the hide everything command
in Tsjerk’s suggestion ☺ Involves a tiny bit of manual labor but works for me.
Cheers and Thanks!
Markus
From: Tsjerk Wassenaar [mailto:tsje...@gmail.com]
Sent: Wednesday, January 21, 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)
cmd.pseudoatom("dummy",pos=list(M[4,:]-scale*numpy.dot(M[:3,:3],M[3,:])))
hide everything, (not ligand) within 150 of dummy
Adjust the scale to get a more curved or more planar clip.
Hope it helps,
Tsjerk
On Wed, Jan 21, 2015 at 10:21 PM, H. Adam Steinberg
mailto:h.adam.steinb...@gmail.com>> wrote:
if you have access to Gimp or photoshop and want to do this in just a few
minutes… clip and render the surface how you want it, then without moving
anything, unclip and render just the ligand. In any bitmap editing program
layer the ligand image over the clipped surface image and merge the two into
one image.
> On Jan 21, 2015, at 2:57 PM, Markus Heller
> mailto:mhel...@cdrd.ca>> wrote:
>
> 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 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<mailto:mhel...@cdrd.ca> | www.cdrd.ca<http://www.cdrd.ca>
>
>
>
>
>
>
> Follow us:
>
> This email and any files transmitted with it are confidential and intended
> solely for the addressee. If you are not the named addressee you should not
> disseminate, distribute, copy, or alter this email.
>
>
>
> --
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[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 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: This email and any files transmitted with it are confidential and intended solely for the addressee. If you are not the named addressee you should not disseminate, distribute, copy, or alter this email. -- New Year. New Location. New Benefits. New Data Center in Ashburn, VA. GigeNET is offering a free month of service with a new server in Ashburn. Choose from 2 high performing configs, both with 100TB of bandwidth. Higher redundancy.Lower latency.Increased capacity.Completely compliant. http://p.sf.net/sfu/gigenet ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
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? sure, you are welcome to update the PyMOLWiki page. Cheers, Thomas On 16 Oct 2014, at 15:57, Markus Heller wrote: > Aha, that makes sense now. > > Would it be worth to clarify this in the pymolwiki > (http://www.pymolwiki.org/index.php/Show)? That's where I got my version > from ... > > Cheers > Markus > > -Original Message- > From: Thomas Holder [mailto:thomas.hol...@schrodinger.com] > Sent: Thursday, October 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 rather want is to remove those non-polar > hydrogens, so that they will not be included in the surface calculation. > > # remove non-polar hydrogens > remove (h. and (e. c extend 1)) > > Hope that helps. > > Cheers, > Thomas > > On 16 Oct 2014, at 13:34, Markus Heller wrote: >> Thomas, >> >> If you comment out the h_add line in the pml script below, the surface looks >> good. If it's in there, it's broken for me. >> >> Cheers >> Markus >> >> >> >> # load the PDB file >> fetch 3CIY, async = 0 >> >> # add hydrogens >> h_add >> >> # hide everything but show cartoon >> hide lines >> #as cartoon >> >> # show protein surface >> show surface, all >> >> # deselect all to avoid little pink squares deselect >> >> # hide non-polar hydrogens >> hide (h. and (e. c extend 1)) >> >> # finally, raytrace and save a PNG >> ray >> png broken_surf.png >> >> >> >> -Original Message- >> From: Thomas Holder [mailto:thomas.hol...@schrodinger.com] >> Sent: 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, >>> >>> I updated to 1.7.2.3. I noticed that >>> >>> h_add >>> >>> breaks the surface rendering for me, meaning the surface representation >>> shows lots of holes/missing parts (before and after ray). It doesn't >>> matter if h_add is placed before or after the surface is generated. >>> >>> Has anybody else noticed 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.cdrd.ca -- Thomas Holder PyMOL Developer Schrödinger, Inc. -- Comprehensive Server Monitoring with Site24x7. Monitor 10 servers for $9/Month. Get alerted through email, SMS, voice calls or mobile push notifications. Take corrective actions from your mobile device. http://p.sf.net/sfu/Zoho ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Show all residues forming H-bonds
Hi Jared,
Thanks for your help. I have two issues with this script:
1. It only works once after I've started pymol; the second time, python.exe
crashes.
2. It does create an object with *distances*, not the actual residues.
Your other solution with the single word selectors should work 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 to run the python script from the wiki page (save it as, e.g.
polarpairs.py). Then, to run pure Python code within a pml file, you'll need
to enclose those lines in a python block
(http://www.pymolwiki.org/index.php/Python) using 'python' and 'python end'.
For example, to list all the H bonds between chains A and B:
###
run path/to/polarpairs.py
python
# the example from http://www.pymolwiki.org/index.php/Polarpairs
pairs = polarpairs('chain A', 'chain B')
for p in pairs:
dist = cmd.get_distance('(%s`%s)' % p[0], '(%s`%s)' % p[1])
print p, 'Distance: %.2f' % (dist)
python end
###
Hope that helps.
Cheers,
Jared
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/
On Oct 15, 2014, at 6:17 PM, Markus Heller wrote:
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.sourceforge.net
Subject: Re: [PyMOL] Show all residues forming H-bonds
Actually, an even better option is Thomas' polarpairs.py script:
http://www.pymolwiki.org/index.php/Polarpairs, which considers the H-bond angle
as well as distance.
Apologies for the multiple emails, but I hope that is closer to what you're
looking for.
Cheers,
Jared
On Oct 10, 2014, at 7:10 PM, Sampson, Jared wrote:
Hi Markus -
Ah, sorry, I misunderstood your request at first.
What about the "acceptors" and "donors" selectors?
http://www.pymolwiki.org/index.php/Single-word_Selectors
e.g.
select hbond_residues, byres ((acceptors within 3.5 of donors) or (donors
within 3.5 of acceptors))
Cheers,
Jared
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/
On Oct 10, 2014, at 6:41 PM, Markus Heller wrote:
Hi Jared,
Thanks for the reply.
This is NOT what I'm looking for. As you stated, distance mode 2 yields the
*distances* as dashes, but not the actual residues. I don't want the dashes,
but I want the residues (i.e. the donors and acceptors) in selectable objects.
I hope it'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, you'll find several
options which will create a new object with all the specified distances as
dashes.
This is also available with `distance` command.
http://www.pymolwiki.org/index.php/Distance
Hope that helps.
Cheers,
Jared
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/
On Oct 10, 2014, at 2:45 AM, Markus Heller wrote:
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/DistancesRH
Is this current state-of-the-art, true-and-tried, or is there something more
powerful hiding out there?
Thanks
Markus
--
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Re: [PyMOL] h_add breaks surface?
Aha, that makes sense now. Would it be worth to clarify this in the pymolwiki (http://www.pymolwiki.org/index.php/Show)? That's where I got my version from ... Cheers Markus -Original Message- From: Thomas Holder [mailto:thomas.hol...@schrodinger.com] Sent: Thursday, October 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 rather want is to remove those non-polar hydrogens, so that they will not be included in the surface calculation. # remove non-polar hydrogens remove (h. and (e. c extend 1)) Hope that helps. Cheers, Thomas On 16 Oct 2014, at 13:34, Markus Heller wrote: > Thomas, > > If you comment out the h_add line in the pml script below, the surface looks > good. If it's in there, it's broken for me. > > Cheers > Markus > > > > # load the PDB file > fetch 3CIY, async = 0 > > # add hydrogens > h_add > > # hide everything but show cartoon > hide lines > #as cartoon > > # show protein surface > show surface, all > > # deselect all to avoid little pink squares deselect > > # hide non-polar hydrogens > hide (h. and (e. c extend 1)) > > # finally, raytrace and save a PNG > ray > png broken_surf.png > > > > -Original Message- > From: Thomas Holder [mailto:thomas.hol...@schrodinger.com] > Sent: 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, >> >> I updated to 1.7.2.3. I noticed that >> >> h_add >> >> breaks the surface rendering for me, meaning the surface representation >> shows lots of holes/missing parts (before and after ray). It doesn't matter >> if h_add is placed before or after the surface is generated. >> >> Has anybody else noticed 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.cdrd.ca -- Thomas Holder PyMOL Developer Schrödinger, Inc. -- Comprehensive Server Monitoring with Site24x7. Monitor 10 servers for $9/Month. Get alerted through email, SMS, voice calls or mobile push notifications. Take corrective actions from your mobile device. http://p.sf.net/sfu/Zoho ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] h_add breaks surface?
Thomas, If you comment out the h_add line in the pml script below, the surface looks good. If it's in there, it's broken for me. Cheers Markus # load the PDB file fetch 3CIY, async = 0 # add hydrogens h_add # hide everything but show cartoon hide lines #as cartoon # show protein surface show surface, all # deselect all to avoid little pink squares deselect # hide non-polar hydrogens hide (h. and (e. c extend 1)) # finally, raytrace and save a PNG ray png broken_surf.png -Original Message- From: Thomas Holder [mailto:thomas.hol...@schrodinger.com] Sent: 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, > > I updated to 1.7.2.3. I noticed that > > h_add > > breaks the surface rendering for me, meaning the surface representation shows > lots of holes/missing parts (before and after ray). It doesn't matter if > h_add is placed before or after the surface is generated. > > Has anybody else noticed 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.cdrd.ca -- Thomas Holder PyMOL Developer Schrödinger, Inc. -- Comprehensive Server Monitoring with Site24x7. Monitor 10 servers for $9/Month. Get alerted through email, SMS, voice calls or mobile push notifications. Take corrective actions from your mobile device. http://p.sf.net/sfu/Zoho ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] h_add breaks surface?
Hi all, I updated to 1.7.2.3. I noticed that h_add breaks the surface rendering for me, meaning the surface representation shows lots of holes/missing parts (before and after ray). It doesn't matter if h_add is placed before or after the surface is generated. Has anybody else noticed 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.cdrd.ca Follow us: This email and any files transmitted with it are confidential and intended solely for the addressee. If you are not the named addressee you should not disseminate, distribute, copy, or alter this email. -- Comprehensive Server Monitoring with Site24x7. Monitor 10 servers for $9/Month. Get alerted through email, SMS, voice calls or mobile push notifications. Take corrective actions from your mobile device. http://p.sf.net/sfu/Zoho ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
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.sourceforge.net Subject: Re: [PyMOL] Show all residues forming H-bonds Actually, an even better option is Thomas' polarpairs.py script: http://www.pymolwiki.org/index.php/Polarpairs, which considers the H-bond angle as well as distance. Apologies for the multiple emails, but I hope that is closer to what you're looking for. Cheers, Jared On Oct 10, 2014, at 7:10 PM, Sampson, Jared wrote: Hi Markus - Ah, sorry, I misunderstood your request at first. What about the "acceptors" and "donors" selectors? http://www.pymolwiki.org/index.php/Single-word_Selectors e.g. select hbond_residues, byres ((acceptors within 3.5 of donors) or (donors within 3.5 of acceptors)) Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On Oct 10, 2014, at 6:41 PM, Markus Heller wrote: Hi Jared, Thanks for the reply. This is NOT what I'm looking for. As you stated, distance mode 2 yields the *distances* as dashes, but not the actual residues. I don't want the dashes, but I want the residues (i.e. the donors and acceptors) in selectable objects. I hope it'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, you'll find several options which will create a new object with all the specified distances as dashes. This is also available with `distance` command. http://www.pymolwiki.org/index.php/Distance Hope that helps. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On Oct 10, 2014, at 2:45 AM, Markus Heller wrote: 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/DistancesRH Is this current state-of-the-art, true-and-tried, or is there something more powerful hiding out there? Thanks Markus -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://p.sf.net/sfu/Zoho___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Comprehensive Server Monitoring with Site24x7. Monitor 10 servers for $9/Month. Get alerted through email, SMS, voice calls or mobile push notifications. Take corrective actions from your mobile device. http://p.sf.net/sfu/Zoho ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
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.C. Canada V6T 1Z3 Main: (604) 827-1147 Direct: (604) 827-1122 F: (604) 826-1299 E: mhel...@cdrd.ca<mailto:mhel...@cdrd.ca> www.cdrd.ca<http://www.cdrd.ca> On Oct 10, 2014, at 4:15 PM, "Sampson, Jared" mailto:jared.samp...@nyumc.org>> wrote: Actually, an even better option is Thomas’ polarpairs.py script: http://www.pymolwiki.org/index.php/Polarpairs, which considers the H-bond angle as well as distance. Apologies for the multiple emails, but I hope that is closer to what you’re looking for. Cheers, Jared On Oct 10, 2014, at 7:10 PM, Sampson, Jared mailto:jared.samp...@nyumc.org>> wrote: Hi Markus - Ah, sorry, I misunderstood your request at first. What about the “acceptors” and “donors” selectors? http://www.pymolwiki.org/index.php/Single-word_Selectors e.g. select hbond_residues, byres ((acceptors within 3.5 of donors) or (donors within 3.5 of acceptors)) Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On Oct 10, 2014, at 6:41 PM, Markus Heller mailto:mhel...@cdrd.ca>> wrote: Hi Jared, Thanks for the reply. This is NOT what I’m looking for. As you stated, distance mode 2 yields the *distances* as dashes, but not the actual residues. I don’t want the dashes, but I want the residues (i.e. the donors and acceptors) in selectable objects. I hope it’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, you’ll find several options which will create a new object with all the specified distances as dashes. This is also available with `distance` command. http://www.pymolwiki.org/index.php/Distance Hope that helps. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On Oct 10, 2014, at 2:45 AM, Markus Heller mailto:mhel...@cdrd.ca>> wrote: 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/DistancesRH Is this current state-of-the-art, true-and-tried, or is there something more powerful hiding out there? Thanks Markus -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net<mailto:PyMOL-users@lists.sourceforge.net>) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://p.sf.net/sfu/Zoho___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net<mailto:PyMOL-users@lists.sourceforge.net>) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://p.sf.net/sfu/Zoho___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Show all residues forming H-bonds
Hi Jared, Thanks for the reply. This is NOT what I'm looking for. As you stated, distance mode 2 yields the *distances* as dashes, but not the actual residues. I don't want the dashes, but I want the residues (i.e. the donors and acceptors) in selectable objects. I hope it'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, you'll find several options which will create a new object with all the specified distances as dashes. This is also available with `distance` command. http://www.pymolwiki.org/index.php/Distance Hope that helps. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On Oct 10, 2014, at 2:45 AM, Markus Heller mailto:mhel...@cdrd.ca>> wrote: 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/DistancesRH Is this current state-of-the-art, true-and-tried, or is there something more powerful hiding out there? Thanks Markus -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net<mailto:PyMOL-users@lists.sourceforge.net>) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://p.sf.net/sfu/Zoho___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[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/DistancesRH Is this current state-of-the-art, true-and-tried, or is there something more powerful hiding out there? Thanks Markus -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] CONECT table
Thanks, works beautifully! Just FYI, it's not my structure, I was tasked with making a few pretty pictures, that's all :) Markus From: Engin Özkan [mailto:eoz...@uchicago.edu] Sent: Tuesday, October 07, 2014 7:35 PM To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] CONECT table fetch hide everything show cartoon, all select NlinkedGlyco, resn NAG+BMA+MAN+FUC or byres (polymer within 2.0 of resn NAG+BMA+MAN+FUC) show sticks, NlinkedGlyco hide sticks, name C+CO+N This should do. Also, are you sure about NDG? If you are talking about N-linked glycosylation, as far as I know, there are no NDG (alpha monomer of N-actyl-D-glucosamine) in glycoproteins. NDG in N-linked sugars is usually an incorrectly modeled NAG (beta-N-acetyl-D-glucosamine), and the PDB is replete with this mistake (about a third of N-linked sugars are incorrectly named/modeled according to a paper by Thomas Lütteke). If this is your structure, I suggest you correct it. If you have to have NDG (because of an incorrect existing file from PDB), then add NDG to the two places I have common monomer names for sugars. Also, add galactose and sialic acid to that list; I don't remember 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. How do I do that? I show the protein as cartoon: Load foo.pdb Hide lines As cartoon Then I select the glycosides Select gluco, resn NDG Show sticks, gluco This only shows me the glycoside, but NOT the side chain it's attached to. I tried Select gluco, bound_to resn NDG Show sticks, gluco But that doesn't work, shows no side chains. Any help much appreciated! Thanks 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<mailto:pymol-users@lists.sourceforge.net> Subject: Re: [PyMOL] CONECT table http://www.pymolwiki.org/index.php/Connect_mode -David On Oct 6, 2014, at 6:35 PM, Markus Heller <mailto:mhel...@cdrd.ca> wrote: 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 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<mailto:mhel...@cdrd.ca> | www.cdrd.ca<http://www.cdrd.ca> Follow us: This email and any files transmitted with it are confidential and intended solely for the addressee. If you are not the named addressee you should not disseminate, distribute, copy, or alter this email. -- Slashdot TV. Videos for Nerds. Stuff that Matters. http://pubads.g.doubleclick.net/gampad/clk?id=160591471&iu=/4140/ostg. clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net<mailto:PyMOL-users@lists.sourceforge.net>) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net<mailto:PyMOL-users@lists.sourceforge.net>) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Engin Özkan, Ph.D. Assistant Professor Dept of Biochemistry and Molecular Biology University of Chicago Phone: (773) 834-5498 http://ozkan.uchicago.edu -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/os
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@lists.sourceforge.net Subject: Re: [PyMOL] CONECT table Hi, It appears that the following: Select gluco, bound_to resn NDG Show sticks, gluco does not work. I'm not sure if the glycosylation is handled as a separate residue, but you could try: select glucoasp, byres (neighbor (resn NDG)) show sticks, glucoasp FYI: There are pages on selection algebra on the Pymol wiki that may give more inspiration. Hope this gets you started, /Andreas On Oct 7, 2014 10:02 PM, "Markus Heller" mailto:mhel...@cdrd.ca>> 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. How do I do that? I show the protein as cartoon: Load foo.pdb Hide lines As cartoon Then I select the glycosides Select gluco, resn NDG Show sticks, gluco This only shows me the glycoside, but NOT the side chain it's attached to. I tried Select gluco, bound_to resn NDG Show sticks, gluco But that doesn't work, shows no side chains. Any help much appreciated! Thanks and Cheers Markus -Original Message- From: David Hall [mailto:li...@cowsandmilk.net<mailto:li...@cowsandmilk.net>] Sent: Monday, October 06, 2014 4:40 PM To: Markus Heller Cc: pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net> Subject: Re: [PyMOL] CONECT table http://www.pymolwiki.org/index.php/Connect_mode -David > On Oct 6, 2014, at 6:35 PM, Markus Heller > mailto:mhel...@cdrd.ca>> wrote: > > 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 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<mailto:mhel...@cdrd.ca> | > www.cdrd.ca<http://www.cdrd.ca> > > > > > > > Follow us: > > This email and any files transmitted with it are confidential and intended > solely for the addressee. If you are not the named addressee you should not > disseminate, distribute, copy, or alter this email. > > > > > -- > Slashdot TV. Videos for Nerds. Stuff that Matters. > http://pubads.g.doubleclick.net/gampad/clk?id=160591471&iu=/4140/ostg. > clktrk ___ > PyMOL-users mailing list > (PyMOL-users@lists.sourceforge.net<mailto:PyMOL-users@lists.sourceforge.net>) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: > http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net<mailto:PyMOL-users@lists.sourceforge.net>) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] CONECT table
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. How do I do that? I show the protein as cartoon: Load foo.pdb Hide lines As cartoon Then I select the glycosides Select gluco, resn NDG Show sticks, gluco This only shows me the glycoside, but NOT the side chain it's attached to. I tried Select gluco, bound_to resn NDG Show sticks, gluco But that doesn't work, shows no side chains. Any help much appreciated! Thanks 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 6:35 PM, Markus Heller wrote: > > 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 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: > > This email and any files transmitted with it are confidential and intended > solely for the addressee. If you are not the named addressee you should not > disseminate, distribute, copy, or alter this email. > > > > > -- > Slashdot TV. Videos for Nerds. Stuff that Matters. > http://pubads.g.doubleclick.net/gampad/clk?id=160591471&iu=/4140/ostg. > clktrk ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: > http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[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 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: This email and any files transmitted with it are confidential and intended solely for the addressee. If you are not the named addressee you should not disseminate, distribute, copy, or alter this email. -- Slashdot TV. Videos for Nerds. Stuff that Matters. http://pubads.g.doubleclick.net/gampad/clk?id=160591471&iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Select residues involved in H-bonds
Hi all, Is there an easy way to first detect H-bonds, either by using the distance command or a something a bit more elaborate (e.g. along the lines of http://www.pymolwiki.org/index.php/Displaying_Biochemical_Properties#Hydrogen_bonds_and_Polar_Contacts) *and* automagically select all 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 - 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: This email and any files transmitted with it are confidential and intended solely for the addressee. If you are not the named addressee you should not disseminate, distribute, copy, or alter this email. -- Slashdot TV. Videos for Nerds. Stuff that Matters. http://pubads.g.doubleclick.net/gampad/clk?id=160591471&iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Show DNA/RNA phosphate backbone
Greetings, I'm trying to visualize the phosphate backbone of DNA/RNA, so far to no avail. I've seen nuccyl, but I'm on WIndoze, and have found no mention of nuccyl running there. Any other straightforward way? Specifically, I'm trying to visualize interactions between the 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) 827-1122 | F: (604) 827-1299 | E: mhel...@cdrd.ca | www.cdrd.ca Follow us: This email and any files transmitted with it are confidential and intended solely for the addressee. If you are not the named addressee you should not disseminate, distribute, copy, or alter this email. -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] cartoon_transparency issue
D'uh!!! I need to get used to always "ray" before assuming anything. Sorry for the noise! -Original Message- From: Justin Lecher [mailto:j.lec...@fz-juelich.de] Sent: Tuesday, August 26, 2014 4:24 AM To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] cartoon_transparency 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 of it? > > Thanks and Cheers > Markus > > Here's my code: > > # reset everything > delete all > > # white background > bg_color white > > # show valences > set valence, 1 > > # show valences inside rings, 0 = centered, 1 = inside set valence_mode, 1 > > # antialias > set antialias = 1 > > # load the PDB files > > load ... example PDB > > # turn on grid mode and set it up > set grid_mode, 1 > > # hide everything > hide everything > > # select protein > select prot, polymer > > # color everything > color white > > # show cartoon ribbon for protein > show cartoon > > # don't show backbone for cartoons > set cartoon_side_chain_helper, on > > # keep standard helix, strand, loop representations # other options: cartoon > loop, cartoon rect, # cartoon oval , cartoon tube cartoon automatic > > # color cartoon white and set transparency set cartoon_color, white set > cartoon_transparency, 0.7 > > # select residue of interest > select roi, resi 27+31+34+37+41 > > # show sticks for ROIs > show sticks, roi > > # hide non-polar H > hide (h. and (e. c extend 1)) > > # 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 > > > > > -- > Slashdot TV. > Video for Nerds. Stuff that matters. > http://tv.slashdot.org/ > > > > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Hi markus, just raytrace you figure using the "ray" command. Justin -- Justin Lecher Institute of Complex Systems ICS-6 Structural Biochemistry Research Centre Juelich 52425 Juelich, Germany phone: +49 2461 61 2117 -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] cartoon_transparency issue
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 of it? Thanks and Cheers Markus Here's my code: # reset everything delete all # white background bg_color white # show valences set valence, 1 # show valences inside rings, 0 = centered, 1 = inside set valence_mode, 1 # antialias set antialias = 1 # load the PDB files load ... example PDB # turn on grid mode and set it up set grid_mode, 1 # hide everything hide everything # select protein select prot, polymer # color everything color white # show cartoon ribbon for protein show cartoon # don't show backbone for cartoons set cartoon_side_chain_helper, on # keep standard helix, strand, loop representations # other options: cartoon loop, cartoon rect, # cartoon oval , cartoon tube cartoon automatic # color cartoon white and set transparency set cartoon_color, white set cartoon_transparency, 0.7 # select residue of interest select roi, resi 27+31+34+37+41 # show sticks for ROIs show sticks, roi # hide non-polar H hide (h. and (e. c extend 1)) # 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 -- 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: This email and any files transmitted with it are confidential and intended solely for the addressee. If you are not the named addressee you should not disseminate, distribute, copy, or alter this email. -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Hbonds in grid mode
Hi, I've got another question where a google search came up empty. I'm displaying 4 proteins in grid mode. When I try to display H bonds (dist Hbo, resi 37, resi 41, mode = 2), the H bonds are displayed in a separate panel. How can I avoid this, i.e. how can I show H bonds without 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: (604) 827-1299 | E: mhel...@cdrd.ca | www.cdrd.ca Follow us: This email and any files transmitted with it are confidential and intended solely for the addressee. If you are not the named addressee you should not disseminate, distribute, copy, or alter this email. -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Coloring of helices
Hi all, I'm stuck. I'm trying to create a figure where I show a helix bundle, with select side chains shown as sticks. I would like the helices to be green, and the side chains in different colors. Easy enough, *but* the carbon color of the side chains supersedes the green color of the helices. I tried to duplicate the object and show sticks for one objects and helices for the other, which works in terms of color, *but* now the cartoon_side_chain_helper doesn't work, since I'm displaying sticks and helices from 2 different objects. How do I go about this? Thanks and Cheers Markus PS: Here's my attempt: # reset everything delete all # white background bg_color white # show valences set valence, 1 # show valences inside rings, 0 = centered, 1 = inside set valence_mode, 1 # antialias set antialias = 1 # don't show backbone for cartoons set cartoon_side_chain_helper, on # keep standard helix, strand, loop representations # other options: cartoon loop, cartoon rect, # cartoon oval , cartoon tube cartoon automatic # Molscript-like edges for helices set cartoon_fancy_helices = 1 # color inside of helices gray set cartoon_highlight_color, gray # load the PDB file load example.pdb, EXA # duplicate protein copy EXA_dup, EXA # hide everything hide everything # select protein select prot, polymer # show cartoon ribbon show cartoon, EXA # select helices select heli, (ss h and EXA) select heli_dup, (ss h and EXA_dup) # color everything limon color limon # select residue of interest select V27, (resi 27 and EXA) select S31, (resi 31 and EXA) select A34, (resi 34 and EXA) select H37, (resi 37 and EXA) select W41, (resi 41 and EXA) # show sticks for ROIs show sticks, (V27 or S31 or A34 or H37 or W41) # color ROIs color atomic, (V27 or S31 or A34 or H37 or W41) color yellow, (name C* and V27) color orange, (name C* and S31) color cyan, (name C* and A34) color magenta, (name C* and H37) color purple, (name C* and W41) # color helices properly show cartoon, EXA_dup color limon, EXA_dup # deselect all to avoid 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: This email and any files transmitted with it are confidential and intended solely for the addressee. If you are not the named addressee you should not disseminate, distribute, copy, or alter this email. -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Special word to select ligand?
This might help, thanks. I'm trying to write a script that will generate a view of a bound ligand in the active site and wanted to automate things as best as I could. I'll test something like byres (organic and symbol N) and see how far this will get me. Cheers! -Original Message- From: Gianluca Santoni [mailto:gianluca.sant...@ibs.fr] Sent: Wednesday, August 20, 2014 1:27 AM To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Special word to select ligand? Not sure if this could help, but if you know which particular kind of atom X characterizes your 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 other molecules that are artifacts from crystallization. Is there a way > (surely there must be, so I'd better say 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 > -- Gianluca Santoni, Dynamop Group Institut de Biologie Structurale 6 rue Jules Horowitz 38027 Grenoble Cedex 1 France _ Please avoid sending me Word or PowerPoint attachments. See http://www.gnu.org/philosophy/no-word-attachments.html -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Special word to select ligand?
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 other molecules that are artifacts from crystallization. Is there a way (surely there must be, so I'd better say 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 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: This email and any files transmitted with it are confidential and intended solely for the addressee. If you are not the named addressee you should not disseminate, distribute, copy, or alter this email. -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Show cation-pi/pi-pi interactions
Hi Jared, Thanks for your reply. I was aware of the distance command (polar contacts). The pseudo atom solution could work, but to be honest, I'd prefer a solution that would detect these interactions. I've found InteractionDetector.py (https://github.com/Pymol-Scripts/Pymol-script-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 PM To: Markus Heller Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Show cation-pi/pi-pi interactions Hi Markus - It's already possible to highlight polar interactions using the `distance` command with mode=2. http://www.pymolwiki.org/index.php/Distance For pi-cation stacking, it might be useful to create pseudo atoms at the average position of the atoms in each charged group or ring in question (e.g. `pseudoatom ring_Y102, resi 102 and name CG+CD1+CD2+CE1+CE2+CZ`) and use them to create sensibly positioned distance dashes between them. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On Aug 13, 2014, at 4:59 PM, Markus Heller mailto:mhel...@cdrd.ca>> wrote: Hello, There's a thread in the PyMol Wiki (http://www.pymolwiki.org/index.php/Ideas) that mentions the possible implementation of functionality to highlight H-bonds, salt bridges, Pi-stacking, Pi-cations. Has such a thing been implemented yet, and if not, what's the current status? 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<mailto:mhel...@cdrd.ca> | www.cdrd.ca<http://www.cdrd.ca> Follow us: This email and any files transmitted with it are confidential and intended solely for the addressee. If you are not the named addressee you should not disseminate, distribute, copy, or alter this email. -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net<mailto:PyMOL-users@lists.sourceforge.net>) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. = -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Show cation-pi/pi-pi interactions
Hello, There's a thread in the PyMol Wiki (http://www.pymolwiki.org/index.php/Ideas) that mentions the possible implementation of functionality to highlight H-bonds, salt bridges, Pi-stacking, Pi-cations. Has such a thing been implemented yet, and if not, what's the current status? 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: This email and any files transmitted with it are confidential and intended solely for the addressee. If you are not the named addressee you should not disseminate, distribute, copy, or alter this email. -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
