Hi Hena, if you only have CA atoms, you probably need this as well:
# assign secondary structure alter all, ss="L" alter resi 10-36, ss="H" alter resi 50-56, ss="S" # show cartoon set cartoon_trace_atoms as cartoon # and eventually... set cartoon_discrete_colors Cheers, Thomas Sampson, Jared wrote, On 07/10/12 19:50: > Hi Hena - > > You can type the following commands in the command line of the pymol > graphics window, one at a time. > > > color red, ss h > color yellow, ss s > color white, ss l+'' > > > If you don't mind the loops being green, you could also use the first > preset under the Color menu for your object. > > [C] > by ss > helix sheet loop (choose the colors you want) > > Hope that helps, > Jared > > -- > Jared Sampson > Xiangpeng Kong Lab > NYU Langone Medical Center > 550 First Ave MSB 398 > New York, NY 10016 > 212-263-7898 > http://kong.med.nyu.edu/ > > On Jul 10, 2012, at 1:39 PM, Hena Dutta wrote: > >> Hi, >> >> Sorry, I forgot to mention that, I have only C-alpha coordinates of 60 >> chains in one pdb file. >> >> I have 60 identical chains. Each chain is about 140 residues. Residues >> from 10-36 is helix and residues from 50-56 is beta sheet. I want to >> prepare a cartoon diagram displaying helix and sheet in red and yellow >> color respectively and the rest part(loop) in white. I need to do this >> for all 60 chains in diagram. Can someone help me? what commands I can >> use for this? >> Regards... -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ 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
