alternate side chains conjugated with water molecules
Dear all, I have a 1.70 A resolution dataset in which I observe, with certain confidence, that some (few) side chains are alternated with waters. Though managing to tie occupancies of each alternate side chain with a water molecule to give an overall occupancy of 1.00, phenix refine still pushes them (water from side chain) apart as if there were bumping restraints (but their occupancies sum up to no more than 1.00). The closest to this I could find is: http://www.phenix-online.org/pipermail/phenixbb/2009-May/013354.html But I could not find how to turn off specific bumping restraints. I would be thankful if someone could point me to the recipe to do this. Jorge
Hi Jorge, I'm sorry for delay with replying. I was (and am) traveling May 18-29, so it happens I miss emails by accident or do not reply promptly. Sorry. What you describe is definitely possible to do in Phenix, I have helped others to do similar things in the past and all worked just fine. I think it is easiest if you send me model and data files and tell what particular residues need to be couples with water, and then I will send you back a working example. Once again, I am sorry for the delay and I'm looking forward to help you with this problem. Pavel On 5/16/15 9:29 PM, Jorge Iulek wrote:
Dear all,
I have a 1.70 A resolution dataset in which I observe, with certain confidence, that some (few) side chains are alternated with waters. Though managing to tie occupancies of each alternate side chain with a water molecule to give an overall occupancy of 1.00, phenix refine still pushes them (water from side chain) apart as if there were bumping restraints (but their occupancies sum up to no more than 1.00). The closest to this I could find is:
http://www.phenix-online.org/pipermail/phenixbb/2009-May/013354.html
But I could not find how to turn off specific bumping restraints. I would be thankful if someone could point me to the recipe to do this.
Jorge
Dear Pavel, Thank you for responding. I put this structure in stand by for a while, then I retook now. I tried some alternate possibilities. It seems to be mandatory that the in constrained group selection, sidechain altloc B is in a selection together with water altloc B (and then so for altloc A). Therefore water altloc B lies "over" sidechain altloc A. I had not figured that yet. This seems to naturally make due antibumping restraints. I was about to make some more tests, but this seems to have worked then. By the way, I was prompted to test this way due to the comments at strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Phenix, which I found later. Yours, Jorge
Hi Jorge,
I'm sorry for delay with replying. I was (and am) traveling May 18-29, so it happens I miss emails by accident or do not reply promptly. Sorry.
What you describe is definitely possible to do in Phenix, I have helped others to do similar things in the past and all worked just fine.
I think it is easiest if you send me model and data files and tell what particular residues need to be couples with water, and then I will send you back a working example.
Once again, I am sorry for the delay and I'm looking forward to help you with this problem.
Pavel
On 5/16/15 9:29 PM, Jorge Iulek wrote:
Dear all,
I have a 1.70 A resolution dataset in which I observe, with certain confidence, that some (few) side chains are alternated with waters. Though managing to tie occupancies of each alternate side chain with a water molecule to give an overall occupancy of 1.00, phenix refine still pushes them (water from side chain) apart as if there were bumping restraints (but their occupancies sum up to no more than 1.00). The closest to this I could find is:
http://www.phenix-online.org/pipermail/phenixbb/2009-May/013354.html
But I could not find how to turn off specific bumping restraints. I would be thankful if someone could point me to the recipe to do this.
Jorge
participants (2)
-
Jorge Iulek -
Pavel Afonine