And what about PHENIX?EI 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
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Dr Pierre Rizkallah, Senior Lecturer Structural Biology
Institute of Infection & Immunology, Sir Geraint Evans Building,
School of Medicine, Heath Campus, Cardiff, CF14 4XN
email: [log in to unmask] phone: +44 29 2074 2248
http://www.cardiff.ac.uk/people/view/126690-rizkallah-pierre
-----Original Message-----
From: CCP4 bulletin board <[log in to unmask]> On Behalf Of Robbie Joosten
Sent: 19 November 2019 15:14
To: [log in to unmask]
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 <[log in to unmask]> On Behalf Of Eleanor
> Dodson
> Sent: Tuesday, November 19, 2019 3:59 PM
> To: [log in to unmask]
> 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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