FYI: all. This is a bug that has been fixed in the source and will not occur with future releases.
Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Tsjerk Wassenaar > Sent: Friday, April 14, 2006 5:04 AM > To: pymol-users@lists.sourceforge.net > 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 <noi...@uky.edu> 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" <gengt...@hotmail.com > > To: <pymol-users@lists.sourceforge.net> > 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 > / <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 <http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944> &bid=241720&dat=121642> > > _______________________________________________ > > PyMOL-users mailing list > > PyMOL-users@lists.sourceforge.net > <mailto:PyMOL-users@lists.sourceforge.net> > > 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 > PyMOL-users@lists.sourceforge.net > 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 > >
