Hi Jacob, Thank you so much for your reply!
Actually, I want to show how the virus HK97 evolve from Prohead (PDB ID: 1if0) to Head (PDB ID: 1ohg) state. There are some intermediate states from our calculation. All the PDB files are Biological Unit files. However, if you load a biological unit file to PyMOL, it will be put into separated states/frames. By applying the command, 'split_states', to the first PDB file, [1if0.pdb1], you will get a series of objects, e.g.: 1if0_0001 1if0_0002 1if0_0003 ...... 1if0_0060 After that if you now load the second PDB file, [1ohg.pdb1], and split it, you will get more objects: 1ohg_0001 1ohg_0002 ...... 1ohg_0060 All the above objects appear in the same state/frame. But we want to put the N'th file to the N'th frame. Is there an easy way to put the second Biological Unit PDB file to next states/frame? Thank you all! Best, Zheng -----Original Message----- From: Jacob Corn [mailto:jc...@berkeley.edu] Sent: Tuesday, May 23, 2006 11:12 AM To: proteiny...@gmail.com Subject: Re: [PyMOL] biological unit Hi Zheng, Sorry it's taken me a while to get back to you. I'm not entirely clear on your question. Precisely what is it that you're trying to do with the movie? I don't think split_states has an option to keep some of the states as separate states while splitting others, if that's what you're asking. You could split everything and then write a script to use only certain of those resulting models in the movie. Zheng Yang wrote: > Dear all, > > I want to create a movie of a virus capsid from N biological unit pdb files > (N frames). After loading and splitting the first pdb file, how to load the > remaining pdb files and put them in different states/frames? > > Is there any optional control on the command, 'split_states', e.g. splitting > to a certain state? > > Thanks a lot! > Zheng > > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Jacob Corn > Sent: Sunday, May 21, 2006 1:58 AM > To: surendra negi > Cc: PyMOL-users@lists.sourceforge.net > Subject: Re: [PyMOL] biological unit > > Hi Surendra, > Just to make sure, are you downloading the "biological unit" PDB from > RCSB? That should be a 5MB gzipped file. The normal PDB for 1c8e does > not contain coordinates for the biological unit (which you need to use > split_states); only a monomer and then info on crystal symmetry. If you > go to a PDB entry at the RCSB and open up the "Download Files" menu, > choose the last option in the list, "Biological Unit Coordinates". > Here is a direct link to the biological unit for 1c8e > http://www.rcsb.org/pdb/files/1c8e.pdb1.gz > The normal PDB is > http://www.rcsb.org/pdb/files/1c8e.pdb.gz > > Jacob > > surendra negi wrote: >> Ji Jacob, >> I am trying to produce the results shown in >> >> http://delsci.com/img/1c8e.jpg >> http://delsci.com/img/1c8e-screen.jpg >> >> using >> >> >>> split_states 1c8e >>> delete 1c8e >>> zoom >>> spectrum b >>> hide lines >>> set cartoon_sampling,3 >>> show cartoon >>> bg_color grey70 >>> set hash_max, 150 >>> ray >>> orient >>> zoom complete=1 >>> ray >> script in my linux machine but is is not working and >> also giving no error message. It is just showing me >> single molecule. Do you have any suggestions. >> thanks >> surendra >> >> __________________________________________________ >> Do You Yahoo!? >> Tired of spam? Yahoo! Mail has the best spam protection around >> http://mail.yahoo.com > > > ------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job > easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > ------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
