Re: [PyMOL] question about ca trace

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

Tsjerk,

Nice point, and probably easier to just create new objects in Pymol. =20



nick


  ----- Original Message -----=20
  From: Tsjerk Wassenaar=20
  To: pym...@li...=20
  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=20
    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=20
    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.=20

    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:=20
    > 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=20
    > 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=20
    > cartoon.
    > Tiger
    >
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  --=20

  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