[phenixbb] Refmac error using PDB coordinates generated by Phenix PDB File Editor
pafonine at lbl.gov
Fri Apr 29 20:01:42 PDT 2016
If PDB formatting for alternative conformations or/and values of
occupancies obey some documented rules then as you say you may not need
to cast any parameters or compose any parameter files, this is correct!
On 4/29/16 19:57, Xiao Lei wrote:
> Thanks a lot! I found my situation in the letter you wrote:
> 4. Overlapping chains: It may happen that stretches of two or more
> chains overlap in space such that when one is present the other one
> isn’t . This situation is not recognized automatically by
> phenix.refine but can be dealt with successfully. This requires two
> actions. Firstly, overlapping atoms of both chains need to be assigned
> different altloc ; this will ensure that these atoms will not be
> pushed apart by non-‐bonded repulsion. Secondly, one needs to compose
> a parameter file telling phenix.refine what occupancies need to be
> coupled; this will override any default behavior applicable to these
> groups of atoms.
> But I feel I do not need to compose a parameter file telling
> phenix.refine what occupancies need to be couples as in your letter. I
> just edit it by Phenix PDB Editor set two chains with different ID and
> set Atloc for each chain, then set 0.5 occupancy for each chain and
> run Phenix.Refine, it seems Phenix.Refine can handle it well and not
> asking me to provide a parameter file about occupancies.
> On Fri, Apr 29, 2016 at 6:53 PM, Pavel Afonine <pafonine at lbl.gov
> <mailto:pafonine at lbl.gov>> wrote:
>> Is there any difference between using the same chain ID (Chain I,
>> atloc P and Q, half occupancy) or using the different chain ID
>> (Chain I, atloc P, half occupancy and then Chain K, atloc Q, half
> This is addressed in the documentation:
> as well as here:
> "13 typical occupancy refinement scenarios and available options
> in phenix.refine"
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