Re: [ccp4bb] Removing TLS component of B factor of deposited PDB files to input to refmac
I must also credit Robbie with the easiest (most elegant?) solution to my question. You run 0 cycles of refmac with the mixed B factor model. Thanks all for your inputs. Best wishes Nick -- Prof Nicholas H. Keep Executive Dean of School of Science Professor of Biomolecular Science Crystallography, Institute for Structural and Molecular Biology, Department of Biological Sciences Birkbeck, University of London, Malet Street, Bloomsbury LONDON WC1E 7HX email n.k...@mail.cryst.bbk.ac.uk Telephone 020-7631-6852 (Room G54a Office) 020-7631-6800 (Department Office) Fax 020-7631-6803 If you want to access me in person you have to come to the crystallography entrance and ring me or the department office from the internal phone by the door
Re: [ccp4bb] Removing TLS component of B factor of deposited PDB files to input to refmac
Hi Eleanor, This is covered in PDB_REDO: we figure out whether the B-factors are totals or residuals. Wouter Touw has made the BDB (http://www.cmbi.ru.nl/bdb/) a databank in which all B-factors are represented as the isotropic component of the total B-factor. This is quite useful if you want to study patterns in B-factors. Cheers, Robbie > -Original Message- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Eleanor Dodson > Sent: Wednesday, March 08, 2017 15:35 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Removing TLS component of B factor of deposited PDB > files to input to refmac > > Actually I think it is pretty dangerous to trust the TLS stuff in the PDB > header - > there is a muddle between B_residual and B_merged and no adequate > description in the header. > > > Unless you are planning on doing many many repeats I would re-refine > before checking the map... > > eleanor > > > On 8 March 2017 at 14:16, Eleanor Dodson > wrote: > > > TLSANL? > > Eleanor > > > On 8 March 2017 at 14:08, Nicholas Keep > wrote: > > > It would be nice to be able to run zero cycles of refmac to get > a map etc direct from a PDB file. > > However due the PDB requiring the TLS component of B > factor to be included this does not work. > > Is there software to remove the TLS component so a zero > cycle of refmac can be run. > > Best wishes > > NIck > > > -- > Prof Nicholas H. Keep > Executive Dean of School of Science > Professor of Biomolecular Science > Crystallography, Institute for Structural and Molecular > Biology, > Department of Biological Sciences > Birkbeck, University of London, > Malet Street, > Bloomsbury > LONDON > WC1E 7HX > > email n.k...@mail.cryst.bbk.ac.uk > Telephone 020-7631-6852 (Room G54a Office) > 020-7631-6800 (Department Office) > Fax 020-7631-6803 > If you want to access me in person you have to come to the > crystallography entrance > and ring me or the department office from the internal > phone by the door > > >
Re: [ccp4bb] Removing TLS component of B factor of deposited PDB files to input to refmac
Normally, these days at least, a model that is result of TLS refinement contains total B factor in ANISOU records and its TLS component in TLS records (REMARK3), with Btotal = Btls+Bresidual. If TLS matrices are available, it's trivial to calculate Btls from TLS matrices in REMARK3 and subtract it from Btotal (ANISOU), which will give you Bresidual. Some of older PDB files are likely to have Bresidual in ATOM records and TLS component in REMARK3 as TLS matrices. In this case, to get total Btotal, you need to compute Btls from TLS and add to Bresidual. I guess TLSANAL is the CCP4 tool to do this, and phenix.tls will do conversion both ways as well. Pavel On Wed, Mar 8, 2017 at 6:34 AM, Eleanor Dodson wrote: > Actually I think it is pretty dangerous to trust the TLS stuff in the PDB > header - there is a muddle between B_residual and B_merged and no adequate > description in the header. > > Unless you are planning on doing many many repeats I would re-refine > before checking the map... > eleanor > > On 8 March 2017 at 14:16, Eleanor Dodson > wrote: > >> TLSANL? >> Eleanor >> >> On 8 March 2017 at 14:08, Nicholas Keep >> wrote: >> >>> It would be nice to be able to run zero cycles of refmac to get a map >>> etc direct from a PDB file. >>> >>> However due the PDB requiring the TLS component of B factor to be >>> included this does not work. >>> >>> Is there software to remove the TLS component so a zero cycle of refmac >>> can be run. >>> >>> Best wishes >>> >>> NIck >>> >>> >>> -- >>> Prof Nicholas H. Keep >>> Executive Dean of School of Science >>> Professor of Biomolecular Science >>> Crystallography, Institute for Structural and Molecular Biology, >>> Department of Biological Sciences >>> Birkbeck, University of London, >>> Malet Street, >>> Bloomsbury >>> LONDON >>> WC1E 7HX >>> >>> email n.k...@mail.cryst.bbk.ac.uk >>> Telephone 020-7631-6852 (Room G54a Office) >>> 020-7631-6800 (Department Office) >>> Fax 020-7631-6803 >>> If you want to access me in person you have to come to the >>> crystallography entrance >>> and ring me or the department office from the internal phone by the door >>> >> >> >
Re: [ccp4bb] Removing TLS component of B factor of deposited PDB files to input to refmac
Actually I think it is pretty dangerous to trust the TLS stuff in the PDB header - there is a muddle between B_residual and B_merged and no adequate description in the header. Unless you are planning on doing many many repeats I would re-refine before checking the map... eleanor On 8 March 2017 at 14:16, Eleanor Dodson wrote: > TLSANL? > Eleanor > > On 8 March 2017 at 14:08, Nicholas Keep > wrote: > >> It would be nice to be able to run zero cycles of refmac to get a map etc >> direct from a PDB file. >> >> However due the PDB requiring the TLS component of B factor to be >> included this does not work. >> >> Is there software to remove the TLS component so a zero cycle of refmac >> can be run. >> >> Best wishes >> >> NIck >> >> >> -- >> Prof Nicholas H. Keep >> Executive Dean of School of Science >> Professor of Biomolecular Science >> Crystallography, Institute for Structural and Molecular Biology, >> Department of Biological Sciences >> Birkbeck, University of London, >> Malet Street, >> Bloomsbury >> LONDON >> WC1E 7HX >> >> email n.k...@mail.cryst.bbk.ac.uk >> Telephone 020-7631-6852 (Room G54a Office) >> 020-7631-6800 (Department Office) >> Fax 020-7631-6803 >> If you want to access me in person you have to come to the >> crystallography entrance >> and ring me or the department office from the internal phone by the door >> > >
Re: [ccp4bb] Removing TLS component of B factor of deposited PDB files to input to refmac
TLSANL? Eleanor On 8 March 2017 at 14:08, Nicholas Keep wrote: > It would be nice to be able to run zero cycles of refmac to get a map etc > direct from a PDB file. > > However due the PDB requiring the TLS component of B factor to be included > this does not work. > > Is there software to remove the TLS component so a zero cycle of refmac > can be run. > > Best wishes > > NIck > > > -- > Prof Nicholas H. Keep > Executive Dean of School of Science > Professor of Biomolecular Science > Crystallography, Institute for Structural and Molecular Biology, > Department of Biological Sciences > Birkbeck, University of London, > Malet Street, > Bloomsbury > LONDON > WC1E 7HX > > email n.k...@mail.cryst.bbk.ac.uk > Telephone 020-7631-6852 (Room G54a Office) > 020-7631-6800 (Department Office) > Fax 020-7631-6803 > If you want to access me in person you have to come to the crystallography > entrance > and ring me or the department office from the internal phone by the door >
