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 On Tue, Nov 19, 2019 at 4:36 PM Eleanor Dodson < 0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > 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 >> > >> > ________________________________ >> > >> > >> > To unsubscribe from the CCP4BB list, click the following link: >> > https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww. >> > jiscmail.ac.uk%2Fcgi-bin%2Fwebadmin%3FSUBED1%3DCCP4BB%26A%3D1&data >> > =01%7C01%7Crizkallahp%40CARDIFF.AC.UK%7Cf2a9834dd919481f28d508d76d030e >> > 63%7Cbdb74b3095684856bdbf06759778fcbc%7C1&sdata=BMwtQsLcQzHTeZcKqC >> > Yg5W7MLDM7Phk0MUx8ohylApI%3D&reserved=0 >> >> >> ######################################################################## >> >> To unsubscribe from the CCP4BB list, click the following link: >> >> https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2Fwebadmin%3FSUBED1%3DCCP4BB%26A%3D1&data=01%7C01%7Crizkallahp%40CARDIFF.AC.UK%7Cf2a9834dd919481f28d508d76d030e63%7Cbdb74b3095684856bdbf06759778fcbc%7C1&sdata=BMwtQsLcQzHTeZcKqCYg5W7MLDM7Phk0MUx8ohylApI%3D&reserved=0 >> >> ######################################################################## >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 >> > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
