Re: [ccp4bb] Removing TLS component of B factor of deposited PDB files to input to refmac

2017-03-08 Thread Nicholas Keep
I must also credit Robbie with the easiest (most elegant?) solution to my question. You run 0 cycles of refmac with the mixed B factor model. Thanks all for your inputs. Best wishes Nick -- Prof Nicholas H. Keep Executive Dean of School of Science Professor of Biomolecular Science

Re: [ccp4bb] Removing TLS component of B factor of deposited PDB files to input to refmac

2017-03-08 Thread Robbie Joosten
Hi Eleanor, This is covered in PDB_REDO: we figure out whether the B-factors are totals or residuals. Wouter Touw has made the BDB (http://www.cmbi.ru.nl/bdb/) a databank in which all B-factors are represented as the isotropic component of the total B-factor. This is quite useful if you want

Re: [ccp4bb] Removing TLS component of B factor of deposited PDB files to input to refmac

2017-03-08 Thread Pavel Afonine
Normally, these days at least, a model that is result of TLS refinement contains total B factor in ANISOU records and its TLS component in TLS records (REMARK3), with Btotal = Btls+Bresidual. If TLS matrices are available, it's trivial to calculate Btls from TLS matrices in REMARK3 and subtract

Re: [ccp4bb] Removing TLS component of B factor of deposited PDB files to input to refmac

2017-03-08 Thread Eleanor Dodson
Actually I think it is pretty dangerous to trust the TLS stuff in the PDB header - there is a muddle between B_residual and B_merged and no adequate description in the header. Unless you are planning on doing many many repeats I would re-refine before checking the map... eleanor On 8 March 2017

Re: [ccp4bb] Removing TLS component of B factor of deposited PDB files to input to refmac

2017-03-08 Thread Eleanor Dodson
TLSANL? Eleanor On 8 March 2017 at 14:08, Nicholas Keep wrote: > It would be nice to be able to run zero cycles of refmac to get a map etc > direct from a PDB file. > > However due the PDB requiring the TLS component of B factor to be included > this does not work.

[ccp4bb] Removing TLS component of B factor of deposited PDB files to input to refmac

2017-03-08 Thread Nicholas Keep
It would be nice to be able to run zero cycles of refmac to get a map etc direct from a PDB file. However due the PDB requiring the TLS component of B factor to be included this does not work. Is there software to remove the TLS component so a zero cycle of refmac can be run. Best wishes