If the correct atoms are in place, resetting the b factors of those atoms/residues to a constant e.g. 5.00 and refining in phenix with individual B-factors ON should take care of these.Best,RezaSent from my iPhoneOn Aug 2, 2023, at 7:42 AM, Thomas, Leonard M. wrote:
Hello All,
A general
Hello, is it definitely due to the TLS refinement? I guess you have tried
without TLS and don't see the same effect i.e. the B-factors are more
consistent. It would be good to know.
Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
Sent from Proton Mail mobile
Original Message
if the B-factor anomaly remains.
Cheers,
Robbie
> -Original Message-
> From: CCP4 bulletin board On Behalf Of Daniel M.
> Himmel, Ph. D.
> Sent: Wednesday, August 2, 2023 17:06
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] High Temperature Factors with TLS
>
>
So the Phosphates are actually the end of the ADP which the Sulfer atoms are
Cystiene suffers. The Fo-Fc maps show large positive peaks for each position
also. The TLS groups is the whole protein chain, there are 4 in the asymmetric
unit as the biological unit I think is a dimer of 2
One possible explanation for high B-factors, assuming the coordinates are
refined correctly, is partial occupancy and high mobility (dynamics) at
those heavy atom sites.
Also, one should check Fo-Fc maps of those positions. Are other atom types
substituting for some of those heavy atoms (such as
You need to tell us more details - is this a deposited structure?
Eleanor
On Wed, 2 Aug 2023 at 15:42, Thomas, Leonard M. wrote:
> Hello All,
>
> A general questions though phenix.refine is being used for refinement. A
> student I am working with has a structure that was solved and initially
>
Hello All,
A general questions though phenix.refine is being used for refinement. A
student I am working with has a structure that was solved and initially refined
using TLS and NCS parameters. They were given the structure to gain some
experience in refinement and they have been asking me
