Pavel, Shelxl is working in correct coordinates - fractional... Many things are easier in fractional coordinates. Are you sure that Phenix does not go orthogonal -> fractional -> orthogonal in internal calculations? When fixing of parameter is made in fractional coordinates it does not produce confusion. Shelxl also make fractional -> orthogonal (AKA PDB) which is also correct. Constrain is not transferred there. BTW Shelxl knows symmetry very well and will constrain atoms that occupying symmetry elements. Shortly Shelxl knows crystallography best. When you will see number of lines in Shelxl Fortran code ( do not kill Fortran to early) you will be surprised. There are not so many of them. No graphical user interface yet, but COOT is of great help.
Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: [email protected] Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Sep 15, 2010, at 19:11 , Pavel Afonine wrote: > Hi Tim, > >> The pdbe.org, for example allows to upload auxiliary files and in my opinion >> the >> uploading of the final .ins-file (not the .res-file!) should be made >> mandatory >> in the case of shelxl refinement. >> >> Since coot has now become utterly convenient even for shelxl refinement, >> there >> is no reason one should not deposit the .ins-file ([flame] and the PDB-file >> probably for legacy reasons [/flame]). > > I was always wondering but never had a good occasion to ask (my Shelxl > knowledge is limited and may be outdated so I apology in advance if my > questions are too dummy; also I realize that I'm asking a non-CCP4 question > on CCP4bb for which I apology again): > > - how .ins file encodes the information about NCS groups used in refinement > (atom selection for NCS groups, restraint weights for different groups, etc? > > - how .ins file encodes the information about TLS (again, atom selections for > TLS groups, TLS matrices, etc)? Related, does it have a concept of having TLS > and other components to the total atomic displacement parameter (ADP)? > > - If I recall it correctly, to fix (=not refine) a certain parameter (say > occupancy or B-factor) in Shelxl you need to add a number 10 to it. Is it > true? IMHO, this might lead to confusion if such a file gets deposited to PDB. > > All the best! > Pavel.
