Hi Francesco, If I understand correctly, you have a structure with a single copy, but there are some parts you don't want to duplicate in the multimer. You didn't say whether you are deleting part of the protein, or some other subunits, or ligands, but I will try to answer generally. You also did not say what method you would be using to assemble the multimer. I mentioned PQS fetch, Unit Cell, and Multiscale Models in this previous message to you: http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-October/001897.html Another possibility is a "manual" approach where you open the structure multiple times and move the copies around yourself, or superimpose them on some other structure already available as a multimer that you believe is similar. With PQS fetch, the only choice is to perform the deletions from the already assembled multimer. With Unit Cell and Multiscale Models, I don't think it matters whether you delete the extra atoms before or after. With the manual approach, deleting before assembling the multimer would be better, as it would make the display less confusing, especially if you are doing clash checking while moving things around. Whether the file header is appropriate for the abridged subunit and/ or multimer depends on the file, of course, but also on what you want to do with that file. Often the header is merely for your own information and will have no effect on your subsequent work. Some tools will make use of symmetry matrix, HELIX/STRAND, and/or SEQRES information. Even if you delete the header entirely, however, Chimera will cope, for example by recomputing helix and strand assignments. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html P.S. registering your copy of Chimera, subscribing to chimera-users, and subscribing to chimera-announce are three different things. I believe one may be prompted to re-register after a fairly long period of time has elapsed or if the registration information was deleted from your computer. However, the email subscriptions do not expire and you should remain signed up until you unsubscribe. On Jul 12, 2008, at 10:38 AM, Francesco Pietra wrote:
I am posting again after having once again subscribed
In order to create an abridged multimer made of non covalently bound subunits (from available pdb of subunit) which is the preferable route?
(1) Load the monomer, delete substructures, and then assemble an abridged multimer? Are the headers furnished with the monomer OK for the abridged subunit?
(2) Build the unabridged multimer and proceed to simplify each subunit the same way?
Thanks
francesco pietra