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Does anyone know how reliably the different programs record and use these
blocks from the PDB file?
Eleanor
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Hi Eleanor,
The blocks are reliably recorded in PDB entries but in some cases the
renumbering of residues was not pushed through to TLS groups. Certain
selections cannot be captured in the PDB format, for instance the split in main
chain and side chain that Refmac allows. Fortunately that featu
I can vouch for TLS blocks being used by REFMAC and the PDB validation servers,
after some frustration I had with a deposition recently:
Towards the end of a refinement, I renamed some chains, to make oligomers in
the a.u. contiguous in real space. Validation told me the centre of gravity as
dec
And what about PHENIX?
E
On Tue, 19 Nov 2019 at 15:33, Pierre Rizkallah
wrote:
> I can vouch for TLS blocks being used by REFMAC and the PDB validation
> servers, after some frustration I had with a deposition recently:
> Towards the end of a refinement, I renamed some chains, to make oligomers
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Purely from memory, I think TLS is refined in Phenix on the fly and the
groups are updated in every run. It does split the B-Facs in isotropic and
anisotropic part in the putput pdb file. I do not recall the tls groups to
be recorded separately in a phenix pdb. But again distant memory.
Christian
Dear Eleanor,
Phenix reads and writes TLS records, both PDB and mmCIF format. It can also
read (but not write) TLS records in REFMAC and BUSTER format.
In ATOM records Phenix outputs complete B factors, which includes both
individual and TLS components (this is why they have ANISOU).
Phenix won'
