Re: [PyMOL] Problem starting Pymol in a Python script
On Fri, Nov 07, 2003 at 01:52:42PM +, Tom Walsh wrote: Hi, I'm trying to start Pymol (version 0.93) in a Python script, using the first method described in __init__.py i.e.: import pymol pymol.finish_launching() I've set the PYTHONPATH and PYMOL_PATH variables as required but I get this error message: - Traceback (innermost last): File pymol.py, line 3, in ? import pymol File pymol.py, line 5, in ? pymol.finish_launching() AttributeError: finish_launching - So what am I doing wrong? It seems like you might have named your python script pymol.py, and the import pymol statement just tries to import pymol.py instead of the Pymol package. Try renaming your script to something other than pymol.py. -- Truls - kerfue+pymol-us...@herocamp.org
[PyMOL] aa residues disconnected from 'fancy helices'?
Hi all, I'm just starting to try out PyMOL (fink package 0.90-2, running through Apple's X11beta2, on a Lombard G3PB, MacOS 10.2.4). Its much easier to learn that I thought it would be! Well done Warren, and codevelopers! One puzzling thing I've noticed: when I build a model of my protein of interest using 'set cartoon_fancy_helices,1' and then show sidechains for several key catalytic residues, I find that the amino acids that reside along beta sheet or alpha helix regions appear properly connected to the alpha carbon backbone representation, but sidechains of amino acids that reside on 'strand' regions appear to float in midair and do not connect to the strand backbone. Anyone else seen this behaviour? Thanks! --Michael Bovee University of Vermont
Re: [PyMOL] aa residues disconnected from 'fancy helices'?
Friday, November 7, 2003, 8:50:13 AM, you wrote: MB ...I built a model of my protein of interest using 'set cartoon_fancy_helices,1'...but sidechains of MBamino acids that reside on 'strand' regions appear to float in midair and do not connect to the strand MBbackbone... On Friday, November 7, 2003, at 12:37 PM, Jacob Corn wrote: snip turn off Smooth Loops under the Cartoon menu... Jacob Ayup, that did the trick. Thanks! --Michael
[PyMOL] resolution
Hi, will PyMol only save images at 72dpi, or can I dial that up somehow? thanks Avram Slovic -- Avram M. Slovic Biochemistry and Molecular Biophysics University of Pennsylvania 420 Curie Blvd. 1010 Stellar Chance Bldg. Philadelphia, PA 19104 L:215-898-3496
