Re: [PyMOL] Secondary structure labeling
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 bsub...@btk.fimailto:bsub...@btk.fi -- 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
Re: [PyMOL] Secondary structure labeling
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
Re: [PyMOL] Secondary structure labeling
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
