RE: [PyMOL] question about ca trace

[Warren D. <wa...@de...>]

FYI: all. =20

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.                    =20
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> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Tsjerk Wassenaar
> Sent: Friday, April 14, 2006 5:04 AM
> To: pym...@li...
> Subject: Re: [PyMOL] question about ca trace
>=20
> Hi Tiger,
>=20
> Nick is largely right. The cause for the link to show up is=20
> that pymol just traces through all c-alphas in the object,=20
> regardless of chains or distances. So, selecting the linked=20
> residues and hiding the trace should solve your problem.=20
> Also, creating two files will do the trick. Alternatively,=20
> you can create two objects and draw the trace for each of these.
>=20
> Cheers,
>=20
> Tsjerk
>=20
>=20
> On 4/13/06, Noinaj <no...@uk...> wrote:
>=20
> 	Tiger,
> =09
> 	I am no expert by far, but can you select the linkage? =20
> If so, just select
> 	and hide.  Also, you might try just hiding the two=20
> residues that are linked,
> 	this might get rid of the link and you probably=20
> wouldn't notice the missing=20
> 	residues unless it is a small protein.  alternatively,=20
> and probably the best
> 	solution is to edit the pdb file to create two=20
> individual files, one for
> 	each dimer (this can be done in any text editor).  then=20
> open both in Pymol=20
> 	and you should then be able to edit independently.
> =09
> 	The problem may be, and again I remind you that I am no=20
> expert, that these
> 	atoms are two close to each other and may be getting=20
> mistaken for a covalent
> 	interaction, can't tell without actually seeing though.=20
> =09
> 	Hope any or all of this helps.  Good Luck!
> =09
> =09
> =09
> 	Cheers,
> 	Nick
> =09
> =09
> =09
> =09
> =09
> =09
> 	----- Original Message -----
> 	From: "Geng Tian" <gen...@ho... >
> 	To: <pym...@li...>
> 	Sent: Thursday, April 13, 2006 3:19 PM
> 	Subject: [PyMOL] question about ca trace
> =09
> =09
> 	> Hi, There:=20
> 	> I have a pdb file for a dimer. only coordinates of=20
> 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=20
> between the last=20
> 	> residue of chain a and first residue of chain b. I=20
> just can't remove this
> 	> ugly linkage. Do you have any idea? Thank you.=20
> Actually I tried ribbon
> 	> mode and no this weird linkage but I like the figure=20
> qualify of the=20
> 	> cartoon.
> 	> Tiger
> 	>
> 	>=20
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> --=20
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> Tsjerk A. Wassenaar, M.Sc.
> Groningen Biomolecular Sciences and Biotechnology Institute=20
> (GBB) Dept. of Biophysical Chemistry University of Groningen=20
> Nijenborgh 4 9747AG Groningen, The Netherlands
> +31 50 363 4336
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