Occupancy Refinement of substrate and product occupying the same coordinates.
Dear Phenix community, I have a crystal structure which I believe involves the substrate and product of the enzymatic reaction occupying the same space within the active site. Ideally, I would like to refine their occupancies to sum to a value less than or equal to 1, as one would for alternate conformations of the same molecule. Phenix does not recognize that they both have partial occupancies however, and the steric repulsion consequently drives them apart during refinement. Does anyone have any advice on achieving this? This is a 1.6Å structure using Phenix version 1.6.1-353. Many thanks for all your help in advance, Joe. _________________________________________________________________ Browse profiles for FREE! Meet local singles online. http://clk.atdmt.com/NMN/go/150855801/direct/01/
Hi Joe,
I have a crystal structure which I believe involves the substrate and product of the enzymatic reaction occupying the same space within the active site. Ideally, I would like to refine their occupancies to sum to a value less than or equal to 1, as one would for alternate conformations of the same molecule. Phenix does not recognize that they both have partial occupancies however, and the steric repulsion consequently drives them apart during refinement. Does anyone have any advice on achieving this?
Did you consider assigning "altloc" identifiers in column 17 of your PDB file? Note that phenix supports multiple residue names for the same resid. See the newsletter article that just came out: http://www.phenix-online.org/newsletter/ Maybe all you need to do is assign the same resid to the substrate and the product, and give one altloc "A" and the other "B". Then the occupancies are automatically constrained to add up to one. Ralf
Hi Joe,
I have a crystal structure which I believe involves the substrate and product of the enzymatic reaction occupying the same space within the active site. Ideally, I would like to refine their occupancies to sum to a value less than or equal to 1,
you can do it in phenix.refine. If you assign one molecule an altLoc A and the other one altLoc B, and have them under the same residue name and chain id, their occupancies will be refined and the sum of them will be constrained to exactly 1. This is explained in phenix.refine manual: http://www.phenix-online.org/documentation/refinement.htm#anch20 If you still having trouble with this, then you can just send me your PDB file or its fraction containing the ligands in question, and I will help you from there. Pavel.
Hi Joe, below I meant residue number and NOT residue name. Sorry for the confusion. Pavel. On 7/12/10 9:29 PM, Pavel Afonine wrote:
Hi Joe,
I have a crystal structure which I believe involves the substrate and product of the enzymatic reaction occupying the same space within the active site. Ideally, I would like to refine their occupancies to sum to a value less than or equal to 1,
you can do it in phenix.refine. If you assign one molecule an altLoc A and the other one altLoc B, and have them under the same residue name and chain id, their occupancies will be refined and the sum of them will be constrained to exactly 1. This is explained in phenix.refine manual:
http://www.phenix-online.org/documentation/refinement.htm#anch20
If you still having trouble with this, then you can just send me your PDB file or its fraction containing the ligands in question, and I will help you from there.
Pavel.
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participants (3)
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Joseph Brock -
Pavel Afonine -
Ralf W. Grosse-Kunstleve