Re: [phenixbb] grouped occupancy definitions
Hi Pavel, I'm digging in docs and list serv but could not find out, and figured you probably know faster. I need to make an occ.params file for some groups of non adjacent side chains which interact with each other, and associated waters. 1) How do I select ACs 2) How do I constrain water occupancies so that their Q + that of coupled protein atomes does not exceed 1. If I match the AC flags for the waters and side chains will this take care of it. e.g. if residues 2 and 21 have coupled ACs and waters 101 and 102 move in when residue 21 is in one of its ACs how would I define below? refinement { refine { occupancies { constrained_group { selection = chain A and resseq 2 selection = chain A and resseq 21 selection = chain W and resseq 101 selection = chain W and resseq 102 } } Thanks !!! -- +++++++++++++++++++++++++++++++++++++++++++++++++++++++ Mark Mayer Ph.D.
Did Pavel reply to this already?
1) How do I select ACs
altloc A
2) How do I constrain water occupancies so that their Q + that of coupled protein atomes does not exceed 1. If I match the AC flags for the waters and side chains will this take care of it.
Not if they are in different residues; but it is important to match the altloc characters to get meaningful nonbonded interactions. You need to use Pavel's occupancies.constrained_group selections in addition. I hope Pavel will give you the details on those. Ralf
Ralf, Pavel's working on a suggestion (he's sick). using altlocs I can see how to build group selections that tie nonadjacent residues together, since occupancies for ACS within residues are constrained to 1.0, but I'm not sure if these is best way. It gets tricky when waters join the group. e.g constrained_group { selection = chain A and resseq 2 and altloc A selection = chain A and resseq 21 and altloc B } takes care of non adjacent residues, but then when I add a group containing a water constrained_group { selection = chain A and resseq 2 and altloc A selection = chain S and 101 and altloc B } how will phenix parse the combined groups ?
Did Pavel reply to this already?
1) How do I select ACs
altloc A
2) How do I constrain water occupancies so that their Q + that of coupled protein atomes does not exceed 1. If I match the AC flags for the waters and side chains will this take care of it.
Not if they are in different residues; but it is important to match the altloc characters to get meaningful nonbonded interactions. You need to use Pavel's occupancies.constrained_group selections in addition. I hope Pavel will give you the details on those.
Ralf _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
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participants (2)
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Dr. Mark Mayer -
Ralf W. Grosse-Kunstleve