Here is what is going on: PyMOL's atom selection mechanism has a set of keywords (name,resi,chain,model,etc), which includes "b" and "q" -- B-factor and occupancy. An object named "b" gets confused with the "b" keyword. Normally you are able to simply use an object name in a selection, but with a object named "b", you'll need to prefix it with the "model" keyword to make it clear what you're asking for...
load b.pdb # ambiguous: color red,(b) # unambiguous: color red,(model b) It is an embarassing design deficiency, but most of the time, the convenience of not using the "model" keyword is probably worth it. However, PyMOL should probably inform you if/when there is a name-space conflict like this : ) Cheers, Warren On Wed, 13 Mar 2002, Robert Campbell wrote: > > Lari Lehti? <leh...@mappi.helsinki.fi> [2002-03-13 08:40] wrote: > > Just a funny thing... > > > > If I try to color my cartoon with rainbow. The file name can't be b.pdb. I > > get > > an error: > > > > Selector-Error: Misplaced ). > > Selector-Error: Malformed selection. > > ( ( ( byres ( b )<-- > > > > If I rename the file and load it, coloring works fine. > > > > I noticed the same problem if I had read in any file name, but created a > selection named "b". I don't do that now! :) I guess "b" must be some > other predefined object? > > Cheers, > Robert >
