Tsjerk, Nice point, and probably easier to just create new objects in Pymol.
nick ----- Original Message ----- From: Tsjerk Wassenaar To: [email protected] Sent: Friday, April 14, 2006 4:29 AM Subject: Re: [PyMOL] question about ca trace Hi Tiger, Nick is largely right. The cause for the link to show up is that pymol just traces through all c-alphas in the object, regardless of chains or distances. So, selecting the linked residues and hiding the trace should solve your problem. Also, creating two files will do the trick. Alternatively, you can create two objects and draw the trace for each of these. Cheers, Tsjerk On 4/13/06, Noinaj <[email protected]> wrote: Tiger, I am no expert by far, but can you select the linkage? If so, just select and hide. Also, you might try just hiding the two residues that are linked, this might get rid of the link and you probably wouldn't notice the missing residues unless it is a small protein. alternatively, and probably the best solution is to edit the pdb file to create two individual files, one for each dimer (this can be done in any text editor). then open both in Pymol and you should then be able to edit independently. The problem may be, and again I remind you that I am no expert, that these atoms are two close to each other and may be getting mistaken for a covalent interaction, can't tell without actually seeing though. Hope any or all of this helps. Good Luck! Cheers, Nick ----- Original Message ----- From: "Geng Tian" <[email protected] > To: <[email protected]> Sent: Thursday, April 13, 2006 3:19 PM Subject: [PyMOL] question about ca trace > Hi, There: > I have a pdb file for a dimer. only coordinates of alph carbons are in the > pdb. In the pymol, I > set cartoon_trace, 1 > and > show cartoon > each monomer is fine but a weird linkage showed up between the last > residue of chain a and first residue of chain b. I just can't remove this > ugly linkage. Do you have any idea? Thank you. Actually I tried ribbon > mode and no this weird linkage but I like the figure qualify of the > cartoon. > Tiger > > _________________________________________________________________ > Express yourself instantly with MSN Messenger! Download today - it's FREE! > http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ > > > > ------------------------------------------------------- > This SF.Net email is sponsored by xPML, a groundbreaking scripting > language > that extends applications into web and mobile media. Attend the live > webcast > and join the prime developer group breaking into this new coding > territory! > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642 > _______________________________________________ > PyMOL-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/pymol-users > ------------------------------------------------------- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642 _______________________________________________ PyMOL-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/pymol-users -- Tsjerk A. Wassenaar, M.Sc. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336
