[PyMOL] Alignment Problems

2009-08-07 Thread Buz Barstow
Hi All, I'm having some trouble fitting to sets of residues in Pymol (1.2r0 - installed with Fink on MacOSX 10.5.8). I'm also having almost identical trouble using MacPymol as well (the version based on Pymol 1.1). I'm trying to align 2 sets of 4 cysteine residues. I have tried align, sup

[PyMOL] de-speculating?

2009-08-07 Thread Thomas Stout
Hi All -- Would anyone happen to have a "recipe" handy for turning down/off the specularity (of CPK spheres especially) in PyMOL? I happen to be a fan of more "matte" surfaces and find the highlights to be rather extreme. I've been messing around with all of the parameters as found on PyMOLwi

Re: [PyMOL] de-speculating?

2009-08-07 Thread Warren DeLano
Hi Tom, set specular, 0 alone should be enough to do the job if all you want to do is turn off specular lighting -- you can ignore all those other spec_* settings. However, for a more matte appearance I'd be more inclined to try: set shininess,10 set specular_intensity, 0.2

Re: [PyMOL] de-speculating?

2009-08-07 Thread Thomas Stout
Thanks very much, Warren. Perhaps I've dorked something in my other settings, but I'm getting rather horrid results even with your suggestions; I'm going to start with a fresh session and see -Tom PS - I'm "trapped" in CYMK color space since this is a job for a printing house -