Hi Elaine, The problem I have is actually not whith chimera. itself. I can display all the models etc nicely within it. However, I want to make now a PDB file of a multi-protein complex in a format that can be deposited in the PDB database. Then I run into problems if the models are separated by Model ENDMDL lines or have chains with the same letter identifier. I was hoping to be able to generate a multi-protein PDB file from my chimera fitting without having to manually edit a lot of lines in the multimodel PDB file. Any suggestions on how to best do this would be appreciated. Thanks Hernando Elaine Meng wrote:
Hi Hernando, Sorry, Chimera does not have an option for changing chain IDs.
However, in Chimera I find it more convenient to work with structures read as multiple models as opposed to multiple chains in a single model:
- you can easily toggle which are shown and which are active (movable with the mouse) using the Model Panel http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html
- you can move one relative to another, whereas you cannot move one chain relative to another chain in the same model
- just like different chains, you can specify them independently in commands, rainbow-color to give each its own color, etc. In commands, the different models read from a single PDB file are specified as #0.1, #0.2, ... (and residues within them specified using something like #0.1:23,350-355 ) http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#hierarc...
- further, each model can include several of its own chains, and it is OK if another model in the same file also uses the same chain IDs, as they are still distinguishable (#0.1:23.a is different than #0.2:23.a)
Now I'm actually disappointed when a Web server gives me multiple models as different chains in a single model, because it is less convenient.
I do agree there may be situations in which you want the models as different chains, such as for input to another program, but currently Chimera does not include that type of editing. Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
-- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa@aecom.yu.edu -----------------------------------