[phenixbb] NCS restraints with TLS

sbiswas2 at ncsu.edu sbiswas2 at ncsu.edu
Mon Sep 28 08:40:11 PDT 2009

Hi Joe,
Thanks for answering Pavel's question.I think there is no problem in using
phenix if you want (whatever works for you).

> I think the conclusion may be that you should first try to get good
> convergence with NCS, and then include TLS. The choice of CNS+REFMAC
> versus PHENIX is probably not important.
> Joe
> Pavel Afonine wrote:
>> Shya,
>> as PHENIX developer I would be delighted to know what exactly did not
>> work in phenix.refine so you decided to create some extra work for you
>> and follow the detour you mentioned below.
>> Thanks!
>> Pavel.
>> On 9/25/09 1:03 PM, sbiswas2 at ncsu.edu wrote:
>>> Hi Joe,
>>> Try doing NCS refinement in CNS and then when you have done
>>> considerable
>>> refinement use the final pdb file (when you think your model is
>>> complete)
>>> for TLS refinement in REFMAC. This has worked for me.You just need to
>>> define a TLS unit and use that as an input.
>>> Shya
>>>> I am using NCS restraints with TLS. It seems that the NCS B-factor
>>>> restraints are applied to the overall B-factor, rather than just the
>>>> non-TLS part. Is this correct?
>>>> In my structure, the disorder varies quite a bit among equivalent
>>>> molecules, and I don't get good results unless the b_factor_weight is
>>>> about 1e-3 or less.
>>>> I am experimenting with NCS restraints in CNS, where each pair of
>>>> coordinates allows an LSQ fit of B-factor scale and offset to be
>>>> excluded from the B restraints. It would probably work even better
>>>> with
>>>> TLS, which CNS does not have. I don't know if anyone has tried this,
>>>> but
>>>> I think that overall molecular B-factor differences are fairly common.
>>>> Joe Krahn
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