[phenixbb] fix part of structure during refinement
iulek at uepg.br
Tue Apr 8 06:36:45 PDT 2014
Yes, good advice, to use harmonic restraints does enough to what I
Nevertheless, I have not managed to use the model restraints yet,
but I will study it better.
On 04/07/2014 06:04 PM, Eckhard Hofmann wrote:
> 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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>>> phenixbb at phenix-online.org
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