Right, the problem is that these three atoms form carboxyl group of Glu, and if I put them (I tried this option) in one occupancy constrained group, occupancies are still refined individually with the sum between three atoms =1. From chemistry point of view I think carboxyl group leaves as one entity, so occupancy should be the same between all three atoms. Is there another way how to constrain it between three atoms if it is not the case of alt conformation? Thank you On Tue, Nov 20, 2012 at 2:27 PM, Nathaniel Echols wrote:

On Tue, Nov 20, 2012 at 3:29 AM, Mikalai Lapkouski wrote:

...

I tried to set the occupancy for those atoms 0.8 and refine individually. But obviously occupancies for those atoms are individually refined to different values which I dont think is the right way. Is there a way of how to refine occupancies for those atoms so that they remain identical after refinement (say all have 0.6)?

I'm a little surprised that the atoms within a residue aren't already constrained to be the same occupancy, but that may only apply if they're labeled as an alternate conformer. But I think all you need to do this is to define them as a constrained group, as described here:

https://www.phenix-online.org/version_docs/dev-1218/refinement.htm#anch111

(scroll down to Example 4 for the messy details.) If you're using the GUI, you can find the relevant controls by selecting "Occupancy" from the menu labeled "Modify atom selections for" below the strategy choices.

-Nat

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Thank you very much! I was making it indeed incorrect. The one you showed works just fine. Thank you, On Tue, Nov 20, 2012 at 3:54 PM, Nathaniel Echols wrote:

On Tue, Nov 20, 2012 at 6:41 AM, Mikalai Lapkouski wrote:

...

Right, the problem is that these three atoms form carboxyl group of Glu, and if I put them (I tried this option) in one occupancy constrained group, occupancies are still refined individually with the sum between three atoms =1. From chemistry point of view I think carboxyl group leaves as one entity, so occupancy should be the same between all three atoms. Is there another way how to constrain it between three atoms if it is not the case of alt conformation?

I suspect you're specifying the selections incorrectly - each constrained group should have a single selection which includes all atoms in a group that you want to keep together, and not multiple selections (one per atom). If you're using parameter files, this means doing this:

refinement.refine.occupancies { constrained_group { selection = chain A and resseq 40 and (name CD or name OE1 or name OE2) } }

and not:

refinement.refine.occupancies { constrained_group { selection = chain A and resseq 40 and name CD1 selection = chain A and resseq 40 and name OE1 selection = chain A and resseq 40 and name OE2 } }

I tried the first version here and it appears to work as expected.

-Nat

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