HETATM automated chain assignment
Hello to the Phenix bulletin board community, I would like to know if I could find a tool to automatically assign HETATM atom (or even, water molecules) to the nearest protein chain ? In my case, I have 4 protein chains in the asymmetric unit : A, B, C and D. I would like to assign each ions and each ligands (which are numerous) with the chain letter of the nearest residue that coordinate them. Usually, I rename everything by hand but as the in-house program of the PDBe AutoDep deposition tool automatically do that... I beg your pardon if this question has just been posted here. I didn't find any tool either in the Phenix Suite or in the "Extensions" and "Calculate" menus of the Coot program (v0.7). Best regards. Romain Talon
Hi Talon, In the Phenix GUI under model tools, the program "Sort hetero atom groups" shopuld do what you want. You may have to enable alpha-test programs in the GUI preferences setttings. Regards, Rob On Feb 15 2013, Talon Romain wrote:
Hello to the Phenix bulletin board community,
I would like to know if I could find a tool to automatically assign HETATM atom (or even, water molecules) to the nearest protein chain ?
In my case, I have 4 protein chains in the asymmetric unit : A, B, C and D. I would like to assign each ions and each ligands (which are numerous) with the chain letter of the nearest residue that coordinate them. Usually, I rename everything by hand but as the in-house program of the PDBe AutoDep deposition tool automatically do that...
I beg your pardon if this question has just been posted here. I didn't find any tool either in the Phenix Suite or in the "Extensions" and "Calculate" menus of the Coot program (v0.7).
Best regards.
Romain Talon _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
-- Robert Oeffner, Ph.D. Research Associate, The Read Group Department of Haematology, University of Cambridge Cambridge Institute of Medical Research Wellcome Trust / MRC Building, Hills Road, Cambridge, CB2 0XY www-structmed.cimr.cam.ac.uk, tel:01223763234, mobile:07712 887162
On Fri, Feb 15, 2013 at 8:39 AM, R.D. Oeffner
In the Phenix GUI under model tools, the program "Sort hetero atom groups" shopuld do what you want. You may have to enable alpha-test programs in the GUI preferences setttings.
Also available on the command line as "phenix.sort_hetams". You will need the latest nightly build for this (1.8.1 doesn't have it), and Rob is correct that you need to enable alpha-test features (but I'm changing that now). There is one potential flaw in the method that I only realized yesterday, which is that covalently bound HETATMs such as carbohydrate groups will be treated as free ligands unless they are already part of a contiguous protein chain (i.e. the chain IDs are the same and there are no TER records or other atoms intervening in the PDB file). In the future we need to take connectivity into account. However, for now you can specify an atom selection to be left unmodified if you wish. -Nat
participants (3)
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Nathaniel Echols -
R.D. Oeffner -
Talon Romain