Hi Francesco, I'm sure the Python script will work for you. However, it should be easy enough to select the B alternative positions with "@.b" and then use "Actions > Atom/Bonds > delete" to wipe them out. Then save the new PDB file. This will do exactly the same thing as the script you identified and may be easier for you. If you want to consider occupancy values, you may have to manually inspect the PDB file yourself. But maybe Elaine can come up with a clever way to do that in Chimera... Best of luck! Darrell Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62G, MSC 2135 Bethesda, MD 20892-2135 Office 301-402-0095 Mobile 301-758-3559 http://bioinformatics.niaid.nih.gov (Within NIH) http://exon.niaid.nih.gov (Public) Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. On 9/15/11 12:54 PM, "Francesco Pietra" <chiendarret@gmail.com> wrote:
At any event I am at Debian GNU-Linux. In the meantime I came across a possible solution that should work on both Linux and Darwin, although it does not take account of the occupancy values. Probably, however, in the case I am interested in, the occupancy values are not too dissimilar (have to check), otherwise the authors would have not published so many alternate locations.
http://www.biopython.org/wiki/Remove_PDB_disordered_atoms
francesco
On Thu, Sep 15, 2011 at 6:35 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hmm, that's very puzzling to me -- I'm using a Mac now and I tested exactly that before replying! Elaine
for example: open 2fma disp focus :170 ~disp @.b (or, ~disp :170@.b)
On Sep 15, 2011, at 9:28 AM, Hurt, Darrell (NIH/NIAID) [E] wrote:
Hi everyone,
It is my experience with Chimera on a Macintosh computer that the alternate designation must be case-sensitive. In other words:
~disp :42@.b - will NOT undisplay alternate location B atoms in residue 42
~disp :42@.B - will undisplay alternate location B atoms in residue 42
YMMV, Darrell
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