Re: [PyMOL] question about ca trace

[Geng T. <gen...@ho...>]

Hi, there:
The problem was temporarily solved by putting each monomer in a separated 
file and load into pymol. Hiding the two residues doesn't work. The weird 
linkage will just jump to the next residues.
Thank you all.
Tiger









>From: "Noinaj" <no...@uk...>
>To: "Tsjerk Wassenaar" 
><ts...@gm...>,<pym...@li...>
>Subject: Re: [PyMOL] question about ca trace
>Date: Fri, 14 Apr 2006 11:23:52 -0400
>
>Tsjerk,
>
>Nice point, and probably easier to just create new objects in Pymol.
>
>
>
>nick
>
>
>   ----- Original Message -----
>   From: Tsjerk Wassenaar
>   To: pym...@li...
>   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 <no...@uk...> 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" <gen...@ho... >
>     To: <pym...@li...>
>     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
>     > PyM...@li...
>     > 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
>     PyM...@li...
>     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

_________________________________________________________________
Don’t just search. Find. Check out the new MSN Search! 
http://search.msn.click-url.com/go/onm00200636ave/direct/01/