August 2018 - cctbxbb - phenix-online.org

Python 3 status
by Graeme.Winter＠Diamond.ac.uk 06 Sep '18

06 Sep '18

Hi Folks, Are there any updates on the progress to Python 3 compatibility? I know there is a project here https://github.com/cctbx/cctbx_project/projects/2 but I have lost the thread of activities since I have been out of the office much of the summer. At the very least I know no progress has been made from this side of the pond as we’ve put this work down for now. i would guess that a lot is on hold while the PHENIX release is done - however I thought I should check in case I have missed anything? Part of why I ask is that there is a PHENIX meeting in Cambridge real soon now (mid September) and I wonder if it is worth folks from DIALS and PHENIX getting together at that time to discuss this? Any thoughts? Thanks & best wishes Graeme -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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Adding more parameters to xray::scatterer for anharmonic thermal displacements
by Luc J. Bourhis 21 Aug '18

21 Aug '18

Hi, we are working with Michal Chodkiewicz (Warsaw University) to add anharmonic thermal tensors to smtbx refinement. I was thinking to add one pointer to xray::scatterer, which can be NULL. When it is not so, it would point to an object which can compute the value and the derivatives for that thermal factor. That means we would have a base class with virtual methods, but I would say that is our problem! The issue for the rest of the cctbx community is the extra storage of that pointer in that class. Would that be all right? I remember quite a few years ago Ralf saying he wanted to replace the ADP's by a pointer to an external storage to save space. Our idea is along the same line. Best wishes, Luc

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model selection
by Pavel Afonine 16 Aug '18

16 Aug '18

Currently model class has three selection methods: def selection(self, selstr, optional=True): def select(self, selection): def iselection(self, selstr): which is hideously confusing with zero chance to remember, and also inconsistent with the rest. Most objects in cctbx have ".select(self, selection)" methods, while being inconsistent about what they expect: iselection or boolean selection as "selection" argument. Some smart ones though can take both int or bool selections (figure out type automatically, which is trivial). Can we consolidate all three into one ".select()" that would allow taking bool or int or str? Or you think there are philosophical arguments against it? Pavel On 8/16/18 15:00, CCTBX commit wrote: > Repository : ssh://g18-sc-serv-04.diamond.ac.uk/cctbx > On branch : master > > ------------------------------------------------------------------------ > > > commit c98b44997e8eb7bf53ee828f510b933cd5167758 > Author: Oleg Sobolev <osobolev(a)lbl.gov> > Date: Thu Aug 16 15:00:20 2018 -0700 > > Proper use of model class > > > ------------------------------------------------------------------------ > > > c98b44997e8eb7bf53ee828f510b933cd5167758 > mmtbx/model/model.py | 3 +-- > 1 file changed, 1 insertion(+), 2 deletions(-) > > diff --git a/mmtbx/model/model.py b/mmtbx/model/model.py > index 6f2247452..87412f95c 100644 > --- a/mmtbx/model/model.py > +++ b/mmtbx/model/model.py > @@ -2312,8 +2312,7 @@ class manager(object): > sizes = flex.int() > h = self.get_hierarchy() > if(macro_molecule_only): > - asc = h.atom_selection_cache() > - s = asc.selection("protein or nucleotide") > + s = self.selection("protein or nucleotide") > h = h.select(s) > for r in h.residue_groups(): > sizes.append(r.atoms().size())

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Extracting data from MTZ
by David Waterman 14 Aug '18

14 Aug '18

Hi all, I have a script that extracts Fobs and Fcalc from an MTZ file produced by Refmac for some analysis. I was just doing this in a trivial way: fobs = m.extract_reals("F").data fc = m.extract_reals("FC_ALL").data and this worked fine, until I came across a file with missing observations, so that the lengths of fobs and fc do not match. Can anybody advise a better way to do this please? I'm inexperienced with iotbx.mtz. I don't need anything other than the values of the structure factors, but I need each element of fobs and fc to contain the equivalent values. Thanks -- David

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