Some comments: - We (the PHENIX developers) are working with the PDB to come up with a more streamlined deposition of TLS information for PHENIX. There are some other issues that need to be resolved first that have slowed this down a little. - I am in agreement with George (not unusual). - As far as I remember Garib was supportive of the idea of no longer depositing residual B-factors in the atomic iso-B column. - What phenix.refine writes in the PDB file is almost exactly the same as you would get by running TLSANL on a REFMAC PDB file. - It is my understanding that the EBI runs TLSANL on REFMAC deposited PDB files to extract the ANISOU records so that R-factors can be calculated. It would seems that this information is then discarded. [I could be mistaken about this whole process though] - Allowing ANISOU records only when atomic anisotropic displacement parameters have been refined seems very restrictive. There may be multiple ways to arrive at anisotropic displacements other than the traditional method (TLS is one, George mentioned TLS restraints instead of constraints, and we have some ideas about ADP refinement that would also result in anisotropic displacements). - It is good to remember that TLS refinement is constrained anisotropic displacement parameter refinement. - If we want bioinformaticians to analyze our structures then we should be writing something in the iso-B column that they can understand - I favour the iso-B equivalent of the total atomic B-factor. This I assume they can handle. I very much doubt that anyone other than a crystallographer will go to the trouble of extracting the TLS information and recalculating atomic displacements. - The biologists looking at structures from the PDB do not care about TLS or ANISOU records. If they choose to look at anything it will be the iso-B column (probably by colouring the atoms by B-factor in a display program). I'd like to give them a fighting chance of seeing something meaningful such as the iso-B equivalent of the total atomic B-factor rather than a residual B-factor (which has no meaning to them). - I will not be holding my breath waiting for any of the popular display programs to start interpreting TLS header information. - I agree that it is best for everyone if we have some clear standards for deposition and tags that make it clear to anyone looking at files from the PDB what is meant by the contents. The PDB is very aware of this and I expect things to be straightened out fairly soon in collaboration with the developers of phenix.refine and REFMAC. -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 510-486-4225, Fax: 510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. --