Hi Bishwa, what you want is to label one representative atom per secondary structure element. So figure out chain and residue number of those atoms, and label each of them individually:
PyMOL> label A/42/CA, "beta1" PyMOL> label A/117/CA, "alpha1" PyMOL> label A/147/CA, "alpha2" For changing label font, size, color etc., see: http://pymolwiki.org/index.php/Label Cheers, Thomas Bishwa Subedi wrote, On 05/08/13 21:50: > Dear Thomas, > > Thank you. The one you said is to show molecule as cartoon and color > according to the secondary structure. But I would like to label/name the > alpha helices as alpha1...and beta strands as Beta1 and so on. Can that > be done using Pymol. > > Best > > Bishwa Subedi, M.Sc Bioinformatics > University of Turku > Finland > > On May 8, 2013, at 5:33 PM, Thomas Holder wrote: > >> Hi Bishwa, >> >> can you be more precise what you mean by "label"? If the secondary >> structure is defined in the header of your PDB file, PyMOL can show >> cartoon representation, show text labels on C-alpha atoms and color by >> secondary structure. >> >> PyMOL> as cartoon >> PyMOL> label name CA, ss >> PyMOL> color red, ss H >> PyMOL> color yellow, ss S >> >> Cheers, >> Thomas >> >> Bishwa Subedi wrote, On 05/08/13 13:33: >>> Hi All, >>> >>> I am using Pymol to make figures for my publication. I am not sure if >>> there has been a discussion earlier but I would like to know how we >>> can label the secondary structures (helices and strands) using Pymol. >>> I have them defined in my header file using DSSP. >>> >>> Thank you in advance. >>> >>> Bishwa Subedi -- Thomas Holder PyMOL Developer Schrödinger Contractor ------------------------------------------------------------------------------ Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. This 200-page book is written by three acclaimed leaders in the field. The early access version is available now. Download your free book today! http://p.sf.net/sfu/neotech_d2d_may _______________________________________________ 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
