I am a new user to phenix and have just started with Phenix.refine using GUI. I want to fix the co-ordinate of ligand atoms in my structure and then refine it. can anyone help me to do that in phenix GUI. Thanks in advance Regards INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL
Hi, From the phenix manual: Refinement with minimization (selected part of model): % phenix.refine data.hkl model.pdb strategy=individual_sites sites.individual="chain A" This will refine the coordinates of atoms in chain A while keeping fixed the atomic coordinates in chain B. So I think you probably need to have a different chain ID for your ligand, and the above should do the trick. Note that here, Phenix is run in command line mode, not the GUI. I haven't checked if it's possible to do this with the GUI. Fred. intekhab alam wrote:
I am a new user to phenix and have just started with Phenix.refine using GUI. I want to fix the co-ordinate of ligand atoms in my structure and then refine it. can anyone help me to do that in phenix GUI. Thanks in advance
Regards
INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL ------------------------------------------------------------------------
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From the phenix manual:
Refinement with minimization (selected part of model): % phenix.refine data.hkl model.pdb strategy=individual_sites sites.individual="chain A"
This will refine the coordinates of atoms in chain A while keeping fixed the atomic coordinates in chain B.
We have a pretty general atom selection syntax which lets you select for example sites.individual="resid 10:20" in case the moving and the fixed part have the same chain id. See the "Atom selection examples" in the phenix.refine docs. Ralf
On Tue, Jul 6, 2010 at 3:51 AM, Vellieux Frederic
Refinement with minimization (selected part of model): % phenix.refine data.hkl model.pdb strategy=individual_sites sites.individual="chain A"
This will refine the coordinates of atoms in chain A while keeping fixed the atomic coordinates in chain B.
So I think you probably need to have a different chain ID for your ligand, and the above should do the trick. Note that here, Phenix is run in command line mode, not the GUI. I haven't checked if it's possible to do this with the GUI.
In general, anything possible on the command line should be possible in the GUI as well. If you right-click on the check-box for "Individual sites" (or any other strategy) in the GUI, it should pop up a menu that will give you access to the relevant atom selection(s). Alternately, go to the Settings menu and open Atom selections->Individual sites. The first control isn't labeled very well (I think it just says "Atom selection"), but that's what you want to use - following the example above, just enter "chain A". If you click the "view/pick" button, it will let you verify that the atom selection does exactly what you want, or you can pick selections with the mouse. -Nat
participants (4)
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intekhab alam -
Nathaniel Echols -
Ralf W. Grosse-Kunstleve -
Vellieux Frederic