[phenixbb] [ccp4bb] Deposition of riding H

Felix Frolow mbfrolow at post.tau.ac.il
Wed Sep 15 10:33:14 PDT 2010

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: mbfrolow at post.tau.ac.il
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 I was always wondering but never had a good occasion to ask (my Shelxl knowledge is limited and may be outdated so I apology in advance if my questions are too dummy; also I realize that I'm asking a non-CCP4 question on CCP4bb for which I apology again):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.

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