Re: [PyMOL] How to store matrix settings for individual scenes?

...@schrodinger.com] Sent: Monday, March 07, 2016 2:51 PM To: Schubert, Carsten [JRDUS] Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] How to store matrix settings for individual scenes? Hi Carsten, What's your use case? Since movie frames can store object matrices, would creating an actual

Re: [PyMOL] how to get an atom coordinates information

Albert, there is no command line tool for that purpose per se, however you can use the iterate command for that purpose. http://pymolwiki.org/index.php/Iterate#Example:_Get_coordinates There are other ways to do this but this will get you going more quickly. -Original Message- From:

Re: [PyMOL] how can we make this kind of figure?

Albert, looks like it is from 'cutemol'. You can probably achieve a similar effect in Pymol -enable perspective -play around with occlusion (search in settings for occlusion) -display protein with 'cartoon loop' -show sidechains for selected residues -fog seems to have a tint of grey in there,

Re: [PyMOL] auto_show_cartoon or similar

Hi Ivan, you could either try to overload the “load” function in Pymol (not sure this is supported) or write your own custom load function under a different name, which loads the protein, assigns the name of the object, hides lines and shows the cartoon. Sorry, this is a rather generic answer

Re: [PyMOL] ColorByRMSD script

Hi Guilherme, the script is not a plugin, so you cannot install it since it is missing some software infrastructure to work as a plugin. Simply put the script into the directory you are working in and run it via ‘run colorbyrmsd.py’ . This will add the command to the scripting interface and

Re: [PyMOL] OBJECT argument in ALIGN command - color

Hi Tim, I ran into the same issue a while back as well. I gets complicated very quickly when you dive deeper into the subject. Your are right the colors of the CGO lines seem to be hardcoded. A way to get around this is to extract the matching residues with

Re: [PyMOL] light reposition

Darya, I have never used that feature, but do you see a difference when raytracing or drawing the scene? Could be that the regular display mode does not take these feature into account (this is a wild guess though) Cheers, Carsten From: Дарья Николаева

Re: [PyMOL] default fetch format

You may want to form you own opinion and take a look at this thread and others in CCP4 https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ccp4bb;8e513bea.1308 I hope the link works. There has been extensive and heated debate over the merits of mmCIF vs. PDB on the same BB. The wwPDB is pushing

Re: [PyMOL] on coloring residues based on y values in the x y z coordinates

If you have access to the incentive version, I would recommend looking at the new properties capabilities in Pymol. The distances can be nicely encoded in a property and rendered with spectrum w/o having to resort to messing with other properties like B-factors. I believe the docs at

Re: [PyMOL] Ray tracing on PBS queue with multiple cores?

Dan, pymol has a setting “max_threads” which (AFIK) controls the number of CPUs on a multicore machine used during rendering. The program tries to set these to a reasonable default value, but if that fails you can try to do this yourself. I don’t think it is possible to spread the same job

Re: [PyMOL] Phosphorylation

Hi Melanie, funny you ask. Just did this myself a week ago... To reverse the morph A-B to B-A to create a continuous loop you need a bit of python scripting, the same for gluing stuff together at the end. This example needs to be adapted for your needs, but should get you started. For

Re: [PyMOL] A strange mistake when working with files. KeyError: 'atomName' Selector-Error: Invalid selection name myFile

Alsa, it looks as if the error does not originate from within the script itself, but it caused in the chempy module, which reads the sdf files. It looks to me as if one of your SDF files is either corrupted or PyMol does not like it. Since you are logging, which file is read, why don’t you

Re: [PyMOL] How to forbid merging of files?

AE, you need to delete the loaded file before loading another. cmd.save will save ALL objects in the buffer by default as you have experienced yourself. Also your handling of the filename is slightly off, since pymol strips the extender upon loading, i.e. test01.pdb becomes test01 object. You

Re: [PyMOL] create bonds between selections within cutoff radius

Shamelessly hijacking this thread... ...but the index page for the Wiki http://www.pymolwiki.org/index.php/Category:Commands has not been updated for the last 10 year, according to the footer. In other words the find_pairs function is not on the index. Makes me wonder, what else is missing?!

[PyMOL] Handling of scene specific global settings?

Hi, with the current refactoring of the scene code was there any consideration given to the handling of scene specific global settings? For instance cartoon putty vs. cartoon automatic or settings like sphere_scale are only applied once on a global scope and carry over to all scenes, even

Re: [PyMOL] RMS over a MD trajectory.

, Schubert, Carsten [JRDUS] wrote: Hi Al, you would need to go through the Python API: python rms=cmd.align(mobCA,tarCA, quiet=0) print rms python end rms contains a tuple with various parameters related to the superposition. The first value in the tuple i.e. rms[0] should be the RMS value

Re: [PyMOL] RMS over a MD trajectory.

Hi Al, you would need to go through the Python API: python rms=cmd.align(mobCA,tarCA, quiet=0) print rms python end rms contains a tuple with various parameters related to the superposition. The first value in the tuple i.e. rms[0] should be the RMS value. HTH Carsten

Re: [PyMOL] when number of atoms changes, colors change in an uncontrolled manner

Hi Efrem, do you still see the same behavior if you disable automatic change of colors when loading your PDBs? The relevant setting would be auto_color set to off. Does not quite answer your question, but could be a work-around. HTH Carsten From: Efrem Braun

Re: [PyMOL] How to determine distance of matching atoms in aligned nonidentical structures?

, Schubert, Carsten [JRDUS] cschu...@its.jnj.com wrote: Hi, How can I best determine the distance between matching pairs of atoms in two or more aligned structures? Fairly easy to do when the two aligned structures are the same, but how does one go about when the structures

[PyMOL] How to determine distance of matching atoms in aligned nonidentical structures?

Hi, How can I best determine the distance between matching pairs of atoms in two or more aligned structures? Fairly easy to do when the two aligned structures are the same, but how does one go about when the structures are not the same? The problem is that I cannot figure out how to dependably

Re: [PyMOL] How do I undo my last command I executed in the PyMOL command line and viewer?

As far as I you cannot undo commands issued on the command line. This feature seems to be mostly targeted towards the builder interface or some other interactive features. For 'newbies' I would recommend opening up a session, starting to work on your presentation and saving frequently. That way

Re: [PyMOL] CGOs

Hi Bob, a while back I attempted to document the CGO capabilities, but never finished it. Attached is a bit of a write-up from that attempt. Hope it helps somewhat. Carsten From: Robert Hanson [mailto:hans...@stolaf.edu] Sent: Monday, December 22, 2014 12:27 PM To: David Hall Cc: pymol-users

Re: [PyMOL] How to draw clashes in pymol - integration/plug-in of Molprobity in PyMol???

Tim: Good suggestion, I would second this effort. Thanks for raising the issue Cheers, Carsten From: Tim Schulte [mailto:tim.schu...@ki.se] Sent: Wednesday, October 22, 2014 2:11 PM To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] How to draw clashes in pymol - integration/plug-in of

Re: [PyMOL] Other coloring strategies based on user-provided properties

Chen, not sure if this has made it yet into the open source version, but to quote the incentive version documentation “Beginning with incentive PyMOL 1.6, arbitrary object level and atom level properties are supported. Now, for each object and each atom you can possibly have an arbitrary

Re: [PyMOL] regarding APBS tools in PyMOL

Hi Vaheh, my recollection is a bit hazy, but I remember having some issues with the distributed APBS version earlier this year. Try downloading the latest APBS and run the plug-in generated input file using the latest version from the commandline. If that works you may have to swap the APBs

Re: [PyMOL] animation showing conformational change

Alternatively you could try the Morph server in Gerstein's lab and then load each intermediate structure into a separate state for animation purposes. http://morph2.molmovdb.org/ HTH Carsten From: Sampson, Jared [mailto:jared.samp...@nyumc.org] Sent: Wednesday, April 09, 2014

Re: [PyMOL] boundaries/outlines of overlapping regions on surface

Sid, I'm guessing here, but may be coloring by properties (new in 1.7) may be the way to go. Usually I would color the residues and if you want to show the underlying residues I would just make another object for those. HTH, Carsten From: Sridharan, Sudharsan

Re: [PyMOL] apbs plugin

Hi jpd, try running APBS directly just using the .in file generated from a failed run. That may provide a clue as to where the problem is, i.e. within APBS itself or within the plugin. If it is APBS, which is throwing the error you may want to try to grab an updated version or the source code

[PyMOL] List residues functionality ?

Hi All, probably a question for the developers, but may not hurt to ask publicly: Is there a functionality in Pymol to list the residues in a given selection? I am looking for the equivalent to the get_chains() function. I have scripted something up, but the code is not 100% clean and not

Re: [PyMOL] Error while starting Pymol 1.7

Hi Roy, I ran into the same issue last week. I am running Pymol of a laptop with an Intel chip driving the internal monitor and a Nvidia chip for the external monitor. The same error pops up when I ran Pymol using the intel graphics chip, but not when I run Pymol of the Nvidia head. According

Re: [PyMOL] Roving maps from scripting level?

Thanks Nat, that example worked nicely. Cheers, Carsten From: Nat Echols [mailto:nathaniel.ech...@gmail.com] Sent: Friday, January 24, 2014 3:13 PM To: Schubert, Carsten [JRDUS] Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Roving maps from scripting level? On Fri

[PyMOL] Roving maps from scripting level?

Dear All, I am trying to get the roving density features to work from a scripting level w/o invoking the Density Wizard. Setting up the following script loads fine, but does not enable roving. Is there anything else I need to define in the settings or am I stuck with using the Density Wizard?

Re: [PyMOL] APBS plug in (2.1) with PyMOL v1.7

Hi Seth, I had problems with the underlying APBS version (1.4 I believe) under Windows in Pymol 1.7. It croaked with an memory allocation error, which I only found after I ran the .in file manually in APBS. Try that. You can either install an upgraded version of APBS or switch to Pymol 1.8,

Re: [PyMOL] APBS plug in (2.1) with PyMOL v1.7

Sorry, I got my versions crossed. I had the same issues with 1.6, it worked again with 1.7. Nevertheless I'd try running the .in file separately to debug what is going on behind the scenes. -C. From: Schubert, Carsten [JRDUS] Sent: Wednesday, January 22, 2014 4:57 PM To: Seth Harris; pymol

Re: [PyMOL] How to automate RMSD calculation for large no of structures

Hi Om, asides from the usual list of suspects like access permissions try double backslashes or a raw string in your path-filenames. Python on Windows is a bit peculiar in that respect. Read up on raw strings in the Python docs. Try wt_file =

Re: [PyMOL] Selection algebra issue

Katherine, not sure if that is what you are looking for but you can select for non-polymer residues with: select lig, prot and organic That will select any non polymer (protein and R(D)NA) residues present in the pdb. You then would need to break the selection further into the individual

Re: [PyMOL] Creating coloured and transparent polyhedra

Hi Timo, I think you may have to switch to a different drawing primitive like TRIANGLES or TRIANGLE_STRIP. Since these are closed objects I assume that the enclosing area should be fillable with a color of choice. Unfortunately I have not actually had a chance to play with these primitives,

Re: [PyMOL] Creating coloured and transparent polyhedra

Hey Tsjerk, Good to know, I missed that feature. Wonder what else is hidden… Cheers, Carsten From: Tsjerk Wassenaar [mailto:tsje...@gmail.com] Sent: Monday, July 15, 2013 11:42 AM To: Schubert, Carsten [JRDUS] Cc: pymol-users@lists.sourceforge.net; Timo Stein Subject: Re: [PyMOL] Creating

Re: [PyMOL] Viewing PyMol in 3D

Hi Max, you are already pretty much spot on. Pymol stereo works under XP, Vista, W7 and as far as I know any Linux flavor, as long as you purchase a compatible NVIDIA quadro card and Nvidia 3D kit. The only caveat is that under Linux you need to have a card which supports the external 3 pin

Re: [PyMOL] Shrinking the sidebar

Alex, there is a little rectangle under the S of State in the lower left of the sidebar or to the left of the | button. You can use that as a slider for the sidebar From: Alex Truong [mailto:atru...@bu.edu] Sent: Monday, December 10, 2012 3:03 PM To: pymol-users@lists.sourceforge.net Subject:

Re: [PyMOL] Viewing PyMol in 3D

Thanks Sabuj, useful info indeed. -Original Message- From: Sabuj Pattanayek [mailto:sab...@gmail.com] Sent: Monday, December 10, 2012 4:18 PM To: Schubert, Carsten [JRDUS] Cc: Max Ferretti; pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Viewing PyMol in 3D You don't need

[PyMOL] Syntax for cmd.auto_arg.update

Hi, can someone please shed some light on the syntax for 'cmd.auto_arg.update'. I've seen this in a couple of scripts and it appears to be related to the command line completion feature, but the details are murky. I'd like to make better use of this for the tools I'm developing. Thanks

Re: [PyMOL] clipping planes

Christian, you should be able to get the values from the tuple returned by get_view(). Looking into this would be a good starting point. from my old notes (origin unknown...): 0-8 is the 3x3 rotation matrix 9-11 is the camera location (I think -- been a while...) 12-14 is the origin of rotation

Re: [PyMOL] Messed up structures in movie

Ritu, just an idea. It could be that your PDB files contains CONECT records for your ligands. Those bonds are defined by atom number or atom index I believe. There could be a conflict between the different files you are loading. Try stripping the CONECT records and see if that helps. HTH