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" <noi...@uky.edu>
To: "Tsjerk Wassenaar"
<tsje...@gmail.com>,<pymol-users@lists.sourceforge.net>
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: pymol-users@lists.sourceforge.net
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 <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
>
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Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
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