[PyMOL] compiling Open Source PyMOL v1.5.0.1

Hi All - I am trying to compile the open-source code for PyMOL for the first time (on CentOS) and running into all sorts of issues. Is there a listing somewhere of all the dependencies (and their versions) that I could use as a guide to get everything I need all at once, rather than continuin

[PyMOL] measuring distances in recent versions

Hi All -- I am prone to using "Ctrl-X" to measure the distance between two selected atoms (also, angles and dihedrals). Has this keystroke been eliminated in recent versions? I have tried versions 1.5.0.1 and 1.5.0.2 on both Windows and Linux and don't get any response to "Ctrl-X", but it work

RE: [PyMOL] saving files in pymol

Along these lines, PyMOL also allows one to quit the program without prompting that you may have unsaved work (i.e., the session has changed since the last time a .pse file was written). Is this also easily implemented? -Tom -Original Message- From: pymol-users-ad...@lists.sourceforge

[PyMOL] anybody have experience with the "get_area" command?

Does it work? We're running version 0.99rc6 on both windoze and linux (RHEL,WS4) and the "get_area" command returns nothing (no error, no value). I've tried this with a number of situations, including loading a single object with a single protein chain and issuing "get_area all", "get_area n+

RE: [PyMOL] RE: povray image mapping and default pigments

I'm glad you solved your problem, but more importantly when are we going to get to see this picture of an easter bunny on some wood-textured rendition of a half-submerged albumin glowing softly in the warm lights of a double sunset over an infinite lake lapping at the shores of a checkered bea

[PyMOL] bug in selections for "set ribbon_color"

Has anyone successfully set colors for ribbons via a non-trivial atom selection? The syntax is supposed to be: set ribbon_color, color, selection, state e.g., set ribbon_color, green, /obj01//B should set the ribbon color to green for only chain B of a multi-chain object. However, in practic

Re: [PyMOL] symmetry generation P21/n?

I have discovered that PyMOL is somewhat picky about the format of the name of the space group. The only way I have found to uncover which specific form(s) of the space group name PyMOL is looking for is to search within the binary (not a good solution). For example, P-1 will fail while "P -1"

[PyMOL] "report" or "clone" settings?

Does anyone know if there is a way of reporting all of the display settings for an object, or - conversely - "cloning" the display settings from one object onto another? Specifically, I am thinking about the situation where I have one elaborately displayed object that is protein A in complex wit

[PyMOL] viewport report?

Hi All -- I have a rather old session file that I would like to "replicate" in a new session file. Essentially, I want to carry the settings over in order to make a new figure using a different structure. One of the settings that I'm having trouble with is the size of the viewport: anyone know

Re: [PyMOL] viewport report?

Fantastic! That is EXACTLY what I needed - many thanks -Tom -Original Message- From: Andreas Forster [mailto:docandr...@gmail.com] Sent: Monday, November 05, 2007 9:46 AM To: Thomas Stout Cc: PyMOL-users@lists.sourceforge.net Subject: Re: [PyMOL] viewport report? Hey Thomas, try

[PyMOL] Isotropic thermal ellipsoids

Hi All -- Yes, I know I want to do something silly here, but does anyone know of a "jiffy" that will generate anisotropic thermal parameters for an isotropic atom? My end goal is to create a figure showing a ligand as ball-and-stick where the spheres are scaled by the B-factor. Since I'm not d

Re: [PyMOL] Isotropic thermal ellipsoids

:39 AM To: 'Tsjerk Wassenaar'; Thomas Stout Cc: PyMOL-users@lists.sourceforge.net Subject: RE: [PyMOL] Isotropic thermal ellipsoids Tsjerk, Close, but the relationship isn't linear. RMS displacement is c*sqrt(temperature-factor), where c is a constant. The following equation can be

[PyMOL] FW: Re: Isotropic thermal ellipsoids

Resending with a smaller attachment -Tom -Original Message- From: Thomas Stout Sent: Friday, February 22, 2008 9:57 AM To: 'Tsjerk Wassenaar' Cc: PyMOL-users@lists.sourceforge.net Subject: RE: [Junk released by Allow List] Re: [PyMOL] Isotropic thermal ellips

Re: [PyMOL] [Apbs-users] Strange behaviour with APBS

To follow up on one of Gilles least important questions: I was convinced that the PDB must contain structures for which there are more than two alternate conformations. I downloaded all structures with resolutions between 0.5 and 1.0A and with a bit of regexp grepping, quickly found the follo

[PyMOL] rotating "maps" ??

Hi All -- I've just stumbled into an odd behavior that is either a bug, or more likely my mis-understanding some aspect of how PyMOL works. I've created "low resolution" surfaces on a hetero-meric protein complex to illustrate the packing together of various protein chains. I've made these su

Re: [PyMOL] rotating "maps" ??

Ah Ha! Yes, that does the trick Many thanks to all for that solution! -Tom -Original Message- From: Mauricio Esguerra [mailto:esgue...@rci.rutgers.edu] Sent: Monday, November 10, 2008 1:23 PM To: Thomas Stout Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] rotating

[PyMOL] another odd PyMOL question....

Hi again everyone -- I have another odd PyMOL question: does anyone know if it is possible to make selections based on what color certain atoms are? I need to do some wholesale re-coloring of a series of complicated figures and it would be extremely useful if I could just say something like:

Re: [PyMOL] another odd PyMOL question....

So, a follow up question becomes: is there a way to report what color something is? :) -Tom -Original Message- From: matthew.frank...@imclone.com [mailto:matthew.frank...@imclone.com] Sent: Tuesday, November 11, 2008 1:52 PM To: Thomas Stout Cc: pymol-users@lists.sourceforge.net

Re: [PyMOL] another odd PyMOL question....

Ah! spectacular Thanks very much -- those two suggestions have just very likely saved me HOURS of work! -Tom -Original Message- From: DeLano Scientific [mailto:del...@delsci.info] Sent: Tuesday, November 11, 2008 6:15 PM To: Thomas Stout Cc: pymol-users@lists.sourceforge.net

Re: [PyMOL] Capping cut surface of map

Hi Neil -- Do you mean like this raster3d example? http://skuld.bmsc.washington.edu/raster3d/examples/slice.png I also think this would make a great feature addition to PyMOL ! (but probably not a priority for the developers...) -Tom From: Neil Ranson [mailt

Re: [PyMOL] POVRAY Usage

Hi Tsjerk -- What version of PyMOL does this work with? I've been trying your commands with versions 1.1 and 1.2b and while PyMOL reports that the primitives have been processed, nothing is written to the file "protein.pov" other than the header info: camera {orthographic location <0.0

Re: [PyMOL] POVRAY Usage

Ah ha! Yes, of course Many thanks to you & Rob for catching that! Note to self: *triple* shots of espresso next time :) -Tom -Original Message- From: Tsjerk Wassenaar [mailto:tsje...@gmail.com] Sent: Saturday, May 16, 2009 1:30 AM To: Thomas Stout Cc: pymol-users Sub

[PyMOL] is font_color universal?

Hi All -- In my reading of the documentation/wiki and experimenting with settings, it looks like "font_color" is universal, meaning that you can only have one font color for ALL objects in a session file -- correct? I was hoping to have different color labels for different objects, so if an

Re: [PyMOL] is font_color universal?

, red, elem c # note that the other label settings may not work below the per-object level Cheers, Warren From: Thomas Stout [mailto:tst...@exelixis.com] Sent: Wednesday, June 24, 2009 10:59 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] is font_

Re: [PyMOL] is font_color universal?

ch other material there as well... -Tom -Original Message- From: Warren DeLano [mailto:war...@delsci.com] Sent: Wednesday, June 24, 2009 11:05 AM To: Thomas Stout; pymol-users@lists.sourceforge.net Subject: RE: [PyMOL] is font_color universal? Tom, # per-object: set label-color, color-n

[PyMOL] de-speculating?

Hi All -- Would anyone happen to have a "recipe" handy for turning down/off the specularity (of CPK spheres especially) in PyMOL? I happen to be a fan of more "matte" surfaces and find the highlights to be rather extreme. I've been messing around with all of the parameters as found on PyMOLwi

Re: [PyMOL] de-speculating?

is a job for a printing house -Original Message- From: Warren DeLano [mailto:war...@delsci.com] Sent: Fri 8/7/2009 3:08 PM To: Thomas Stout; pymol-users@lists.sourceforge.net Subject: RE: [PyMOL] de-speculating? Hi Tom, set specular, 0 alone should be enough to do the job if all you w

[PyMOL] a Biotech job opportunity using PyMOL

w.exelixis.com/> . The position is Job ID #817. Cheers, Thomas Stout --- Thomas J. Stout Director, Structural Biology Exelixis, Inc. 210 East Grand Avenue, Box 511 South San Francisco, CA 94083-0511 USA Phone: 650-837-8129 FAX: 650-837-8181 This email (including any attachments) may contain mat

Re: [PyMOL] Saving high resolution images

Here's a crazy idea: if someone out there were clever at both python and manipulating orientation matrices, I would bet that a "scene" could be quartered or cut into eighths and "translated" such that each portion filled the viewport for rendering; then the individual images could be spliced bac

Re: [PyMOL] Saving high resolution images

er 3 | render 4 | | | | | | | --- I feel like I'm missing something important here! -Tom -Original Message- From: Tsjerk Wassenaar [mailto:tsje...@gmail.com] Sent: Thursday, October 22, 2009 11:45 AM To: Thomas Stout Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Saving high r

Re: [PyMOL] Rendering in parts

allows >> > you to break a large rendering job up into tiles pretty much just >> > like Tom suggests, so not so crazy of an idea! I think in that case >> > you can specify starting and ending x,y pixel coordinates from your >> > large scene. But not in Pymol as

Re: [PyMOL] PyMOL/CEAlign for Windows

A perhaps easier way is to right-click on a pdb file with the mouse and choose "Open with..." In that sub-menu select "Choose program". In the subsequent window that appears, select PymolWin as the program you want to open the PDB file with AND then also check the box underneath that says "Always

[PyMOL] acquisition of PyMOL by Schrodinger

All -- from the PyMOL web site: ANNOUNCEMENT On January 8, 2010 Schrödinger reached an agreement with the estate of the late Dr. Warren L. DeLano to acquire PyMOL. Schrödinger will take over continued development and maintenance

Re: [PyMOL] CEalign - PyMOL Build

Several +1s from all the people here !! -Tom From: Sean Law [mailto:magic...@hotmail.com] Sent: Thursday, January 28, 2010 12:47 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] CEalign - PyMOL Build Jason, I would LOVE to see CEalign built alo

Re: [PyMOL] CEalign - PyMOL Build

I thought that I had +1'd to this last week, but I don't see that note... If legal, I'm also +1-ing for 5 additional people here that do not subscribe to the mailing list... (or should that be +5-ing?) -Tom -Original Message- From: Sean Law [mailto:magic...@hotmail.com] Sent: Thursday

[PyMOL] List participation commentary......

Hi All -- Recently I've noticed a growing number of questions being posed to the PyMOL mailing list that never seem to get responses. I infer from this that one or both of two things are happening: either 1) list members that know the answers to these questions are not responding to the questions

RE: [PyMOL] cmd.read_pdbstr segfault

version 0.98 (beta 07 and beta 17) loads PDB IS 1DT7 just fine. It's a little slow, but it works! Are you sure you don't have "auto-zoom" off? I turn auto-zoom off by default and as a result some entries (like 1DT7) load but are not visible. Clicking the "zoom" button brings it into the cent

RE: [PyMOL] cmd.read_pdbstr segfault

11/20/2004 8:42 AM To: Thomas Stout Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] cmd.read_pdbstr segfault The application actually quits, hence the seg fault error. This happens for quite a few files, and the only trend I saw was file size since the smaller ones had no tro

RE: [PyMOL] animation in v. 0.98beta18

I definitely second Seth's praise for the animation feature. It may seem a little "hokey" at first, but in presentations it really helps to keep the viewers in register with the presenter... My only niggle with it is that it actually moves too fast (on my machine) - any way of throttling it, at

RE: [PyMOL] low res surfaces, CRYST headers, rotamers

Since we do this all the time, I can answer #3!

[PyMOL] Centrosymmetric symmetry?

Has anyone ever been able to use PyMOL to expand the symmetry of a centrosymmetric space group? I have tried twice, once in P-1 and once in P21/c. Both attempts result in a core dump, but before asking Warren to examine his code, I thought I should check with everyone else and see if it works

RE: [PyMOL] hydrophobic interactions

Here are a series of commands to help you produce a simple graphical representation of different classes of amino acids in protein structures (we have these scripts installed in a separate "function panel" that was written in house, but you can also save them as (name).pml scripts and run them w

[PyMOL] PyMOL versus WinXP, SP2

Has anyone on the list successfully installed PyMOL (especially v0.98) on a Win box running XP, Service Pack 2? We are considering allowing our IT department to "upgrade" all of our PCs from Win2K to XP, but as I remember earlier versions of PyMOL 0.98 betas were not compatible with SP2 ..

RE: [PyMOL] PyMOL versus WinXP, SP2

Thanks all for the positive feedback regarding XP SP2sounds like my earlier experiences with SP2 may have been due to "complicating factors" :} -Tom -Original Message- From: Pinotsis [mailto:pinot...@embl-hamburg.de] Sent: Friday, May 06, 2005 8:37 AM To: Thomas Stout

[PyMOL] Crystallographer position

of python and or java would be especially attractive. If you know - or are - someone like this, I would appreciate your passing the word along. I have included below the HR-speak version of the job ad. Many thanks, Thomas Stout NB: Applications must be directed to Exelixis Human