Here are a series of commands to help you produce a simple graphical representation of different classes of amino acids in protein structures (we have these scripts installed in a separate "function panel" that was written in house, but you can also save them as (name).pml scripts and run them when needed.....) Of course, if what you're looking for is a detailed analysis of packing interactions between specific residues, or types of amino acids, including numeric output of distance separations, et cetera, then your need is more complex than these admittedly very simple graphical representations........
Hopefully these will be of use to you or others, -Tom show_aromatics.pml: ---------------begin------------------------- # # Show side chain sticks for aromatic residues # # (script for PyMol) # Tom Stout, 08/05/2004 # mstop dss hide all #zoom all #orient show cartoon,all color gray,all select aromatics,(resn phe+tyr+trp+his) show sticks, (aromatics and (!name c+n+o)) color green,aromatics disable aromatics set cartoon_smooth_loops,0 ---------------end--------------------------- show_hydrophobics.pml: ---------------begin------------------------- # # Show side chain sticks for hydrophobic residues # # (script for PyMol) # Tom Stout, 08/05/2004 # mstop dss hide all #zoom all #orient show cartoon,all color gray,all select hydrophobes,(resn ala+gly+val+ile+leu+phe+met) show sticks, (hydrophobes and (!name c+n+o)) color orange,hydrophobes disable hydrophobes set cartoon_smooth_loops,0 ---------------end--------------------------- show_charged.pml: ---------------begin------------------------- # # Show side chain sticks for charged residues # # (script for PyMol) # Tom Stout, 08/05/2004 # mstop dss hide all #zoom all #orient show cartoon,all color gray,all select pos,(resn arg+lys+his) show sticks, (pos and !name c+n+o) color marine,pos disable pos select neg,(resn glu+asp) show sticks, (neg and !name c+n+o) color red,neg disable neg set cartoon_smooth_loops,0 ---------------end--------------------------- show_hydrophilic.pml: ---------------begin------------------------- # # Show side chain sticks for hydrophilic residues # # (script for PyMol) # Tom Stout, 08/05/2004 # mstop dss hide all #zoom all #orient show cartoon,all color gray,all select hydrophilics,(resn arg+lys+his+glu+asp+asn+gln+thr+ser+cys) show sticks, (hydrophilics and !name c+n+o) color green,hydrophilics disable hydrophilics set cartoon_smooth_loops,0 ---------------end--------------------------- -----Original Message----- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net]on Behalf Of Ferdinand Molnár Sent: Monday, March 07, 2005 4:19 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] hydrophobic interactions Hello, I would be interested whether there is a way to calculate and visualize the hydrophobic interaction such as Phe-Phe or Leu-Leu etc. Maybe it would be a good add to the program because there are not so many softwares which can do that. Regards Ferdinand -- -- Ferdinand Molnár, M.Sc. Department of Biochemistry University of Kuopio Savilahdentie 9F P.O. Box 1627 FIN - 70211 Kuopio Finland Phone: +358-17-163392 Fax: +358-17-2811510 e-mail: mol...@uku.fi ------------------------------------------------------- SF email is sponsored by - The IT Product Guide Read honest & candid reviews on hundreds of IT Products from real users. Discover which products truly live up to the hype. Start reading now. http://ads.osdn.com/?ad_ide95&alloc_id396&op=ick _______________________________________________ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
