[phenixbb] Refmac error using PDB coordinates generated by Phenix PDB File Editor

Pavel Afonine 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:
> Pavel,
> 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
>>     occupancy)?
>     This is addressed in the documentation:
>     http://phenix-online.org/documentation/reference/refinement.html#occupancy-refinement
>     as well as here:
>     "13 typical occupancy refinement scenarios and available options
>     in phenix.refine"
>     http://phenix-online.org/newsletter/
>     Pavel

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