Hi Robert,
You're exactly right. It's a chainid issue. If I load 2 PDBs with
different chainids, they "merge" without a problem. If they have a the
same chainid, lines display OK, but the sequence viewer and
ribbons/cartoon view makes the problem clear.
As background, what we were trying to do was use PyMOL as to model
multimers from several different monomers, using distantly related
structures as a template, and then create a composite model from the
monomers and it as one PDB. Basically just trying to save time, rather
than writing out several rotated/translated monomer PDBs and collating them.
I don't know about anyone else, but I think that task would be nice to
do in PyMOL. Would it be hard to alter the create command so that it
makes sure there are no clashes between atom/chain/etc. naming?
Jacob
Robert Campbell wrote:
Jacob,
* Jacob Corn <jc...@uclink.berkeley.edu> [2005-04-13 16:40] wrote:
I am trying to create one composite object from two separate objects.
When I issue the command
create objectx, object1 or object2
objectx is created and contains most of the two objects, but is missing
around 1/5-1/10 of the atoms (seemingly random stretches just gone).
Similarly, if I load just the two objects I want and try
create objectx, (all)
the problem still occurs. Since this has happened with two independent
pdbs, I'm wondering if any one else has run into the problem. If so, is
there a workaround?
I believe that this is a problem of trying to merge atoms that have the
same residue numbers and names. I don't really know as I've never tried
to do this. I always seem to be breaking up my objects, not merging
them!
Ok, so I just tried this and got *apparently* the same result when
displaying both structures as cartoons. There appeared to be parts
missing. When I displayed lines or sticks they appeared to be fine.
If you colour the two structure uniquely before creating the merged
object and turn on the sequence viewer, you will note that the sequences
are inter-mixed. This is probably the source of your problem. Try
setting a unique chain identifier for each structure first. If I save a
pdb file after doing that, the sequences are in the correct order, if I
don't then they are inter-mixed.
Cheers,
Rob
--
Jacob Corn
UC Berkeley - 315 Hildebrand Hall
jc...@uclink.berkeley.edu
phone: 510-643-8893
fax: 510-643-9290
