Re: [PyMOL] question about ca trace

[Noinaj <no...@uk...>]

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
>
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