Re: [PyMOL] PyMOL-users Digest, Vol 27, Issue 3

I agree with Warren. Basically, you could use desaturate or "convert to grayscale" options of GIMP or photoshop, but there are ways to achieve much nicer results. See the following for ideas: http://www.gimp.org/tutorials/Color2BW/ - Show quoted text - On Tue, Aug 19, 2008 at 6:19 AM, DeLano Scien

Re: [PyMOL] colour by model

The different PDB MODELs are actually PyMol states. Thus: fetch 1oei set all_states,0 # The magic is done in the next line split_states 1oei # Now you should have separate objects for each state (MODEL) # Remove the original multistate object delete 1oei # Color util.color_objs('all') # Beutify as

[PyMOL] creating comand panels within pymol scripts

Continuing my thread 'reloading wizards' (started on Feb 24). Sometimes, in my pml scripts, I want to produce 'command buttons' like those obtained by get_panel( .. ) function that is present in all the wizards. The functionality of those scripts do not justify converting them to built-in wizards.

[PyMOL] reload modified wizard

Hello, I develop several custom PyMol wizards. Is there any way to reload a modified wizard, without restarting PyMol? Thank you.

Re: [PyMOL] trouble selecting residues with mouse

I also have such a problem (on Linux). Couldn't find any solution though. On 2/8/07, Heidi Privett wrote: I have been trying to run the latest version of MacPyMOL on my new iMac with an Intel Core 2 Duo processor and the latest version of OSX. I have noticed problems trying to select residues

Re: [PyMOL] Selecting nearby atoms

Atom's ID is specific to a molecule (or object - can someone please correct me?), thus if you have several molecules, and all of them contain atom with the specified ID, they all will be selected. Regarding listing the atoms within a selection (from http://www.rubor.de/bioinf/tips_advanced.html):

[PyMOL] chempy documentation

Hello, all. Is there any chempy documentation available? I've searched the web for a while, but couldn't find anything relevant. Do PyMol subscribers have access to extra documentation? Thank you

[PyMOL] pymol licensing questions

After searching the pymol site for two hours I'm still very confused about the license issue. I understand that using (and from recently - downloading) the binary PyMol package requires subscription. Now what about the source code? May I compile it and use it without any subscription? May I re-dis

Re: [PyMOL] Hydrogen bonds

Take a look at this link: http://www.rubor.de/bioinf/tips_modeling.html#addhbond It contains two simple examples and one python script. On 8/23/06, selva raj wrote: Dear Pymol users, Would anyone tell me how to draw hydrogen bonds between interacting atoms in a crystal structure of small

[PyMOL] creating frames from an existing structure

Hello, There are plenty examples of how to create frames by loading several structures (i.e one file, one frame). What I want is to do something like this: - load a structure - set it as frame 1 - change representation and coloring - set the view as frame 2 - show/hide several atoms, - set t he vi

[PyMOL] red - blue stereo mode

Is it possible to add the possibilty to make PyMol's stereo mode work with old fasioned red/bkue(or green or whatever) glasses? Something like this: http://www.3dchem.com/stereoglasses.asp

[PyMOL] internal GUI: letters vanish on window enlargement

Hello, I am experiencing a pretty annoying problem: when enlarging the PyMol window, the letters inside the internal gui slowly disappear. I've done several screenshots that demonstrate the problem: the full view: http://dl13.rapidshare.de/files/10017550/146939542/vanish.png focus on the disappear

[PyMOL] Correction: X server to crashes, when working with pymol

Correction, the X server crashes on each attempt to resize the pymol window On 12/21/05, bgbg bg wrote: > > Hello, list. > This is my setup: > Mandriva Linux 2006.0, > X Window System Version 6.8.99.900 (6.9.0 RC 0) > X Protocol Version 11, Revision 0, Release 6.8.99.900 > B

[PyMOL] X server to crashes, when working with pymol

Hello, list. This is my setup: Mandriva Linux 2006.0, X Window System Version 6.8.99.900 (6.9.0 RC 0) X Protocol Version 11, Revision 0, Release 6.8.99.900 Build Operating System: Linux 2.6.12-12mdksmp i686 [ELF] I used PyMol 0.98 both installed from Mandriva's rpm's and from sources. The problem

[PyMOL] loading multiple structures from one file

Hello, list. When loading a mol2 file (or an SDF file) with multiple structures in it, I see only one structure displayed, although the following lines are printed in the external GUI window. ObjectMolReadMOL2Str: read molecule 1 ObjectMolReadMOL2Str: read molecule 2 ObjectMolReadMOL2Str: read