[PyMOL] Problems with set solvent_radius

2011-04-15 Thread Ian Slaymaker
I am trying to change the solvent radius for the surface of about 20 objects
in my scene simultaneously. I "set solvent_radius, 4" and pymol seems to
take the time to do all the calculations, but at the end of the processing
the surface only displays for one out of the 20 objects. "rebuild" does not
fix the issue. Any suggestions would be very helpful.
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[PyMOL] Ray tracing problems

2011-04-15 Thread Mark A Saper
When I ray trace a surface, the colors on the surface appear to have a smaller 
color depth.  In other words, there are finite boundaries between different 
shades of colors rather than a smooth gradient.  Could the problem be 
color-dependent?  Has anyone seen this?  Any ideas how to fix it?

Mark
_
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry
University of Michigan

Biophysics, 3040 Chemistry Building
930 N University Ave
Ann Arbor MI  48109-1055 U.S.A.

sa...@umich.edu phone (734) 764-3353 fax (734) 764-3323
http://www.biochem.med.umich.edu/?q=saper   http://www.strucbio.umich.edu/



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[PyMOL] hydrogen bonds delete

2011-04-15 Thread ZHAO Lina
Hi,

when I use dist selename, select1, select2, mode=2

which produced one hydroge bond between oxygen of residues with anothe
oxygen of phosphate groups.

I wonder,

Which reason cause dist recognize the O-O forming hydrogen bonds in pymol?

Another question, are there some simple ways to just get those contact
residues output into a file simply, without examine one by one using eyes.

Thanks for any answer,

lina
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