[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 works

[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

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

[PyMOL] acquisition of PyMOL by Schrodinger

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

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 use

Re: [PyMOL] Rendering in parts

Subject: Re: [PyMOL] Saving high resolution images To: Thomas Stout tst...@exelixis.com Cc: pymol-users@lists.sourceforge.net Message-ID:        8ff898150910230227k12719cedv8656233c7e67d...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Hi Thomas, You can also zoom

[PyMOL] a Biotech job opportunity using PyMOL

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 material that is confidential

[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 PyMOLwiki:

Re: [PyMOL] de-speculating?

-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 want to do is turn off specular

[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

Re: [PyMOL] is font_color universal?

, 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_color

Re: [PyMOL] is font_color universal?

-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-name, object-name # per-atom: set label-color

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 Subject: Re

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] 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

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

[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

[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

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

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

Re: [PyMOL] Isotropic thermal ellipsoids

'; 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 found in crystallography texts: B = U * 8

[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 ellipsoids Yes

[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

[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] 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 with

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] 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+c,

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] 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] 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

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

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

RE: [PyMOL] cmd.read_pdbstr segfault

/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 troubles