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 -- Robert L. Campbell, Ph.D. <r...@post.queensu.ca> Senior Research Associate phone: 613-533-6821 Dept. of Biochemistry, Queen's University, fax: 613-533-2497 Kingston, ON K7L 3N6 Canada http://adelie.biochem.queensu.ca/~rlc PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2
