Re: [PyMOL] Mac Flicker Issue Workaround

The new beta works fine on my new Powerbook now. No flickering anymore. Thanks. On Nov 5, 2005, at 11:33 PM, Warren DeLano wrote: Hmm... Working now. -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 US

[PyMOL] pymol -M ?

Hi Mark: I just tried the command with -M and it didn't help, but for the record, you can use /Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL or if you are a nerd, you might prefer this shell script, which you can call pymol and put in your $path array. It finds wherever you put it

RE: [PyMOL] Mac Flicker Issue Workaround

Hmm... Working now. -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailt

RE: [PyMOL] Discreet cartoon representation for overlapping secondary structure ?

Indraneel, PyMOL's cartoon generation code is some of the worst "production" code I have ever written in my life. It consists of one huge 2,000 line function with numerous one or two-letter variables and all kinds of implicit assumptions about the linear structure of the protein and the discrete

[PyMOL] Mac Flicker Issue Workaround

Mac users: We lucked out and obtained a little help from an off-duty Apple engineer today who figured out how to work around the issue in 10.4.3. It was one of these combined bugs -- we weren't doing things sensibly in PyMOL, and the ATI driver wasn't quite complying with normal OpenGL behavior w

[PyMOL] Discreet cartoon representation for overlapping secondary structure ?

Hi, Is changing cartoon representation a major work? My program PALSSE defines overlapping Secondary Structural Elements and it would be nice if I could see cartoons without having consecutive elements merged. It is technically possible for consecutive helices or consecutive strands or helices an

RE: [PyMOL] Loading tetramer

Multiple ways to go: load tetramer.pdb1 set all_states is most memory-efficient However, load tetramer.pdb1 split_states tetramer delete tetramer Would give you the ability to manipulate each subunit independently. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Sc

[PyMOL] Loading tetramer

Hi everyone, I want to load a biological assembly (tetramer) in pdb1 format. However, when I load it, I can only see one chain not the tetramer. On Command Line: ObjectMolecule: Read secondary structure assignments. ObjectMolecule: Read crystal symmetry information. Symmetry: Found 8 symmetry o

RE: [PyMOL] OS 10.4.3

MacPyMOL users: Just to let everyone know, we are aware of the screen fliker problem with the 10.4.3 update and working with Apple to resolve it ASAP. I have a favor to ask though: Could those who are expericing this issue please send me their machine info? Mac OS X has a comprehensive system p

RE: [PyMOL] get color of atom ?

Indraneel, iterate sele-name, print color Will dump out the color name. If you need this in a Python variable, the process is a bit more convoluted: from pymol import cmd, stored stored.list = [] cmd.iterate(sele-str, "stored.list.append(color)") print stored.list Cheers, Warren -- Warren L

[PyMOL] New PyMOL plugin

Hi, I've develop a new plugin. It offers the ability to do a PDB advance search. You can search directly keywords into the PDB entries file. For this, the PDB entries file is downloaded (the file is stored into the home directory). The results are diplayed into a spreadsheet. By a double click on