[phenixbb] fix part of structure during refinement
eckhard.hofmann at bph.ruhr-uni-bochum.de
Mon Apr 7 14:04:20 PDT 2014
But could you not just switch on tight reference model restraints or
harmonic restraints for this part of your structure?
Of course this is not leaving them untouched, but if you set sigma to
0.01, then they should pretty much stay the same.
(In main: set reference_model_restraints = True
and adjust parameters in section reference_model)
Am 07.04.2014 05:56, schrieb Pavel Afonine:
> Yes, SA and real-space refinement are done (if enabled) for all atoms.
> No particular reason for this. It just needs to be fixed.
> On 4/6/14, 6:03 PM, Nathaniel Echols wrote:
>> On Sun, Apr 6, 2014 at 4:47 PM, Jorge Iulek <iulek at uepg.br
>> <mailto:iulek at uepg.br>> wrote:
>> I want to test a refinement in which I fix part of my
>> structure (say, residues 1 to 244 in chains C and D, and chains A
>> and B completely) while the rest is to be refined with annealing.
>> I thought atoms out of the selection in the output structure
>> (chains A and B + residues 1 to 244 in chains C and D) would keep
>> the same coordinates as they were input. But I see all structure
>> atoms changed coordinates. I also tried to turn off tls and ncs
>> usage, but the picture is the same.
>> What do I miss here, to be able to fix some atoms during
>> I think the annealing may only work with the entire model and ignore
>> the atom selection completely.
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Eckhard Hofmann <eckhard.hofmann at bph.ruhr-uni-bochum.de>
AG Proteinkristallographie, LS Biophysik, ND04/318
Tel: +49-(0)234/32-24463, Sekr. -24461, FAX: -14762
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