"Use starting structure as reference" for homo-multimers
Hi, I've noticed that when I choose the option to use the starting structure as a reference model and my structure is a homo-multimeric protein, Phenix uses only the first chain as the reference for all chains during refinement. Personally I'd much prefer it if instead it ran a true 1:1 reference throughout the structure, since I tend to use this for final very fine-scale refinement of structures where I've already identified and modelled differences between NCS copies. Others' mileage may vary, of course. Best regards, Tristan
Hi Tristan, could you please send me the PDB file? I guess I can just try any multi-chain file but it would be good to use the one you have just in case there is something special about it.. Thanks, Pavel On 2/9/16 07:55, Tristan Croll wrote:
Hi,
I've noticed that when I choose the option to use the starting structure as a reference model and my structure is a homo-multimeric protein, Phenix uses only the first chain as the reference for all chains during refinement. Personally I'd much prefer it if instead it ran a true 1:1 reference throughout the structure, since I tend to use this for final very fine-scale refinement of structures where I've already identified and modelled differences between NCS copies. Others' mileage may vary, of course.
Best regards,
Tristan
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Hi Tristan,
Thank you for pointing this out, I will change this behavior.
In the mean time, as a work-around, you can use the input file as reference
model file and specify reference groups by hand to achieve the desired
behavior.
Best regards,
Oleg Sobolev.
On Tue, Feb 9, 2016 at 7:55 AM, Tristan Croll
Hi,
I've noticed that when I choose the option to use the starting structure as a reference model and my structure is a homo-multimeric protein, Phenix uses only the first chain as the reference for all chains during refinement. Personally I'd much prefer it if instead it ran a true 1:1 reference throughout the structure, since I tend to use this for final very fine-scale refinement of structures where I've already identified and modelled differences between NCS copies. Others' mileage may vary, of course.
Best regards,
Tristan
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participants (3)
-
Oleg Sobolev -
Pavel Afonine -
Tristan Croll