And what about PHENIX?
E

On Tue, 19 Nov 2019 at 15:33, Pierre Rizkallah <rizkall...@cardiff.ac.uk>
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
> in the a.u. contiguous in real space. Validation told me the centre of
> gravity as declared in the header is not the same as that produced from the
> coordinates. I edited the input TLS file, but it still produced the same
> outcome. I eventually realised that REFMAC reads the TLS blocks from the
> input PDB after reading all the other input instructions for the refinement
> run. This happening last, it overrides the declarations in the input TLS
> definitions file. In order to get the coordinates and the definitions to
> match, I had to remove the TLS blocks, produced by an earlier run of
> REFMAC, from the pdb input file, so that the new definitions can be
> followed, and appropriate TLS blocks produced. REFMAC would use
> pre-existing TLS blocks if they are in the PDB file.
>
> The mismatch notwithstanding, REFMAC still worked correctly, although the
> shifts from the group origins would have looked strange if one tries to
> analyse the TLS motions with TLSANL. I admit, I don't view them. Moral of
> the story is, be careful when you rename chains at the end of the
> refinement!
>
> Pierre Rizkallah
> *******************************************************
> Dr Pierre Rizkallah, Senior Lecturer Structural Biology
> Institute of Infection & Immunology, Sir Geraint Evans Building,
> School of Medicine, Heath Campus, Cardiff, CF14 4XN
> email: rizkall...@cardiff.ac.uk        phone: +44 29 2074 2248
> http://www.cardiff.ac.uk/people/view/126690-rizkallah-pierre
>
> -----Original Message-----
> From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Robbie
> Joosten
> Sent: 19 November 2019 15:14
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] TLS parameters
>
> 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 feature is
> hardly used.
> Parsing TLS records is not straightforward, particularly the sets from
> Buster suffered a lot from inconsistent manual editing in the early days of
> TLS refinement. PDB-REDO's extractor does a decent job in getting
> selections and changing those into Refmac format, but there are definitely
> cases that it cannot do. We also have a tool that does this for mmCIF files
> which is not written by me and (therefore) much more sophisticated in
> handling more complicated cases.
>
> Cheers,
> Robbie
>
> > -----Original Message-----
> > From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Eleanor
> > Dodson
> > Sent: Tuesday, November 19, 2019 3:59 PM
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: [ccp4bb] TLS parameters
> >
> > Does anyone know how reliably the different programs record and use
> > these blocks from the PDB file?
> >
> > Eleanor
> >
> > ________________________________
> >
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