[phenixbb] grouped occupancy definitions

Dr. Mark Mayer mayerm at mail.nih.gov
Thu Oct 15 16:07:50 PDT 2009


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
>phenixbb at phenix-online.org
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