Hi Sri, if you have your structure loaded into PyMOL, you can make named selections for your peptide sequences like this:
select pep1, pepseq RMFLS select pep2, pepseq KGHGK select pep3, pepseq ALSDL There are also scripts available for pattern matching, for example: http://pymolwiki.org/index.php/FindSeq Highlighting the selections with colors: color white color red, pep1 color blue, pep2 color green, pep3 You can query these selections on various properties: # (approximate) surface area set dot_solvent get_area pep1 # secondary structure print [a.ss for a in cmd.get_model('pep1 and name CA').atom] Doing this on a large number of structures is possible if you write a python script, which requires general programming skills. All the commands shown above are accessible from the PyMOL python API. Examples: from pymol import cmd cmd.select('pep1', 'pepseq RMFLS') cmd.color('red', 'pep1') print cmd.get_area('pep1') Hope that helps. Cheers, Thomas Sri Ramarathinam wrote, On 11/22/12 08:16: > Hi All > I am very new to using Pymol. I am wondering if anyone can point me towards > the right direction with the following: > 1) I have a list of peptides and would like to know what their location is on > their respective proteins which already have structures in PDB (surface > exposed, buried, helix, loop or beta sheet?) > I guess I could do it manually but the peptide list could go into > hundreds and would be nice to see if there a command line or a script I could > use. > 2) Can i ask Pymol to show the peptide's location on the 3d structure of the > protein? perhaps in a different colour to highlight location? > Manually I would select on the sequence and show as whatever I want but > is there a command to automate a huge list? > > Is it possible to do these tasks with Pymol or is there any other software I > could be using? > > Thanks very much for your help, > Cheers > Sri -- Thomas Holder PyMOL Developer Schrödinger Contractor ------------------------------------------------------------------------------ Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov _______________________________________________ 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
