On Sun, 9 Sep 2012 22:54:57 +0800 (SGT) Anindito Sen <emailanindito@yahoo.co.in> wrote:
Dear All,
I have a Chimera session where 4 different atomic structures (pdb files) are docked in the computed density map of a macromolecular complex. I need to select multiple amino acids positioned at different places of the different docked atomic structures.
To explain the situation-
Say the 4 docked Atomic structures are A, B, C & D
I need to select 276aa of A, 15aa of B, 246aa of C and so on...
How can I do that ?
Thanks
Hi Anindito! Just playing around with the select command on a session with 2 loaded pdb files gave me the following: select #0:105.a #1:77.c #1:82 #:5 In other words, spaces between the different residues being picked allows you to pick from multiple models on the same line. With this command, I selected residue 105 on chain A of model 0, residue 77 on chain C of model 1, residue 82 on all chains of model 1, and residue 5 on all chains on both models. Since you label your pdb files as A, B, C, ... I assume that these would be numbered as 0, 1, 2, ... by Chimera, depending on the order they were read into the session. You would then enter the following: select #0:276 #1:15 #2:246 ... While I have not played with such situations, the origin of your particular set of pdb structures may have Chimera classify the chains as submodels of one large model, instead of distinctly different molecules. If that is true, then I believe the above becomes: select #.0:276 #.1:15 #.2:246 ... This is explained (much) more fully on the Atom Specification page of the help system. Final thought: if you know which residues you want to grab because you can see them in the structure, and this is a one time sort of thing, I'd honestly just select the residues with the mouse (with a cleared selection, Ctrl-Shift click on an atom of each residue, then up-arrow the results to grab the whole residues) ... Hope this works for you! Kenward -- In a completely rational society, the best of us would aspire to be _teachers_ and the rest of us would have to settle for something less, because passing civilization along from one generation to the next ought to be the highest honor and the highest responsibility anyone could have. - Lee Iacocca