[phenixbb] NCS restraints with TLS

Joe Krahn krahn at niehs.nih.gov
Mon Sep 28 08:26:58 PDT 2009

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.


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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