Hi Sean, On Mon, 09 Nov 2009 10:58:53 -0500 Sean Law <magic...@hotmail.com> wrote:
> > Robert, > > I would have to agree with you. I've used many of your scripts and have > also learned a lot from them and think that the color B script is pretty > robust and helpful. Thanks. > I could be wrong but I remember the original poster commenting about using > the "min & max" settings from the spectrum command and I wonder if that is > used to control the min/max of B-factor values to color (so that any values > outside of the range of min and max will be colored the extreme min/max > color values). Of course, I'm sure it's just as easy to add a couple of > lines of extra code into your script to account for that (if it isn't > already there). The color_b.py script has options called "minimum" and "maximum" just like the spectrum command. These are used to select the range of B-values to colour. So (using PDB code 1dvi as an example) if your actual B-values are between 2 and 55.98 and you set the minimum to 10 and maximum to 50, then use 8 bins (just to get nice numbers here!), by typing: color_b minimum=10, maximum=50, nbins=8 You'll see the following output from the color_b.py script: Minimum and Maximum B-values: 2.0 55.9799995422 Color select: n. ca and (b < 15 or b = 15) Color select: n. ca and b > 15 Color select: n. ca and b > 20 Color select: n. ca and b > 25 Color select: n. ca and b > 30 Color select: n. ca and b > 35 Color select: n. ca and b > 40 Color select: n. ca and b > 45 So yes, anything within the lowest range and below will be in colour 1 and anything within the highest range and above will be in colour 8. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821 Fax: 613-533-2497 <robert.campb...@queensu.ca> http://pldserver1.biochem.queensu.ca/~rlc ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
