Hi Christian, > I have a two chain protein and I want translat and rotate it using the > commands translate and rotate. It is complicate to choose the rigth angel, > because I cannot see the rotation axis. Is there a way to draw the axis system > for the objects to see around which axis and how much I must rotate every > single object. Does every object have is own axis system or is there a common > system for all objects?
See http://www.pymolwiki.org/index.php/Axes. Each object has its own transformation matrix. Rotate and translate can act upon that matrix. See http://www.pymolwiki.org/index.php/Get_object_matrix. > When I color my protein according to the B-values is it possible to include a > kind of a legend like for the elctrostatics when I use APBS to get an idea > about the minimum and maximum value? An easy way is the following, but has two problems: (1) you're not ensured the correct 1-1 mapping; (2) when you adjust the ramp the lines colors don't change. But, it does work: # fetch an example protein fetch 1foo, async=0 # color it by b-factor spectrum b, rainbow # get the list of b-factors x = [] cmd.iterate("1foo", "x.append(b)", space={'x':x}) # create the ramp across the range cmd.ramp_new("myRamp", "1foo", [min(x), max(x)], "rainbow") If I can recall the other way of mapping the ramp color to the lines, I'll let you know. Right now it escapes me. Cheers, -- Jason > Thanks in advance and Best Regards > > Christian > > > > ------------------------------------------------------------------------------ > All the data continuously generated in your IT infrastructure > contains a definitive record of customers, application performance, > security threats, fraudulent activity, and more. Splunk takes this > data and makes sense of it. IT sense. And common sense. > http://p.sf.net/sfu/splunk-novd2d > _______________________________________________ > 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 > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d _______________________________________________ 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
