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

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! Pavel 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 mailto:[email protected]> 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-r...

as well as here:

"13 typical occupancy refinement scenarios and available options in phenix.refine" http://phenix-online.org/newsletter/

Pavel