Hi Spyros, > Because I wish to determine if I can > correlate the database motifs with ligand-binding residues, what I would > like is some way of superimposing (if possible) one selection onto the > other. I would color-code the selections (if possible, again) so that I > could see if one was "on top" of the other in 3D or if they occur at > different regions of the protein.
If you're using PyMOL for the alignments, then please understand the differences between align, super and cealign. Lots of documentation on this can be found on these pages: http://www.pymolwiki.org/index.php/Align; http://www.pymolwiki.org/index.php/Super; http://www.pymolwiki.org/index.php/Cealign. > Creating selections the default way places pixel-size pink dots on the > structure, so I was wondering if there is some way to control this for more > complex visualization tasks? You can modify the indicators, the pixel-size pink dots, and their activity just a little (see selection_round_points, and selection_overlay settings). But this is best done by color-coding your selected atoms, not by modifying the indicator dots. > Is there a way to color-code my selections, and visualize them > simultaneously on the structure to see if there is any overlap? The most flexible way to do this is as Tsjerk suggested: changing the colors, or representations of your selections. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of 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-d2d-c2 _______________________________________________ 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
