And what about PHENIX? E On Tue, 19 Nov 2019 at 15:33, Pierre Rizkallah <[email protected]> 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: [email protected] phone: +44 29 2074 2248 > http://www.cardiff.ac.uk/people/view/126690-rizkallah-pierre > > -----Original Message----- > From: CCP4 bulletin board <[email protected]> On Behalf Of Robbie > Joosten > Sent: 19 November 2019 15:14 > To: [email protected] > 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 <[email protected]> On Behalf Of Eleanor > > Dodson > > Sent: Tuesday, November 19, 2019 3:59 PM > > To: [email protected] > > 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
