Re: [ccp4bb] Translational non-crystallographic symmetry giving low R-factors

Hi Cat, If your pseudo-centering actually leads to significant change in your cumulative intensity distribution, you might have a convincing explanation as to why the R-values would remain on the high side. I had a pseudo-body centered case a long time ago (https://doi.org/10.1107/s09074449

Re: [ccp4bb] Translational NCS (tNCS)

Hi Bashir, It does look like you have translational pseudo-symmetry. If the translation vector happens to be body-centering, it could affect your intensity statistics so that the R-values would never go down as half of your reflections follow the distribution for centric reflections. I had thi

Re: [ccp4bb] To Trim or Not to To Trim

Dear Manfred, In addition to personal preference I think there are some philosophical differences in what the model actually means. I would argue that what we see in the density is stronger evidence of the chemical identity than what we believe we have used as a starting material. After all we

[ccp4bb] Job opening: Computational Crystallographer

Dear Colleagues, I would like to bring to your attention a job opening at the Data Management and Software Centre fo the European Spallation Source in Copenhagen, Denmark. In this role your main responsibility will be the design and development of a data processing pipeline optimized for

[ccp4bb] PhD position at Lund University

either myself or Prof. Ryde (ulf.r...@teokem.lu.se<mailto:ulf.r...@teokem.lu.se>) for questions. Best regards, Esko _ Esko Oksanen, PhD Instrument Scientist - Neutron Macromolecular Crystallography European Spallation Source ERIC P.O Box 176, SE-221 00 Lund, Sweden Vi

Re: [ccp4bb] Are there.cif dictionaries for deuterated aminoacids for Coot?

-file) should correspond to the third column of your pdb-file, so that coot know what hydrogen that should be. The only difference in your pdb-file compared to an X-ray structure with hydrogens is the element symbol in the last column. HTH, Esko _ Esko Oksanen, PhD

[ccp4bb] Support Scientist position for Macromolecular Crystallisation at the European Spallation Source

rmation about the recruitment process, please contact Linda Sima, linda.sima[at]esss.se (unavailable 2-25 August). We look forward to receiving your application. _____ Esko Oksanen, PhD Instrument Scientist - Neutron Macromolecular Crystallography European Spallation Source ESS AB P.O

Re: [ccp4bb] How to scale 2n+1 Weak and strong reflections

distribution; if it looks normal I don't think the separate scaling will help you. HTH, Esko _____ Esko Oksanen, PhD Instrument Scientist - Neutron Macromolecular Crystallography European Spallation Source ESS AB P.O Box 176, SE-221 00 Lund, Sweden Visiting address: Tunavägen 24,

Re: [ccp4bb] Temperature and crystallization

Dear Acoot, There is a paper by Monika Budayova-Spano (http://scripts.iucr.org/cgi-bin/paper?fw5105) on using temperature as a crystallisation variable that also has a number of useful references. HTH, Esko _ Esko Oksanen, PhD Instrument Scientist - Neutron

Re: [ccp4bb] Refinement with pseudo-translation

d any more. HTH, Esko _____ Esko Oksanen, PhD Instrument Scientist - Neutron Macromolecular Crystallography European Spallation Source ESS AB P.O Box 176, SE-221 00 Lund, Sweden Visiting address: Tunavägen 24, Lund Switchboard: +46 46 888 00 00 Phone: +46 46 888 30 36 Mobile:

Re: [ccp4bb] I/sigma for h+k=2n+1 and h+k=2n

and reflections with h+k=2n. Which software could do this job? A brief tutorial is appreciated. Yu -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904 Esko Oksanen, PhD Post-doctoral Fellow (EMBO) Groupe Synchrotron, Institut de

Re: [ccp4bb] Pseudo-symmetry/refinement

Seema, The problem actually originates from the scaling of the data that assumes a monomodal distritbution of the intensities. This is not the case with pseudotranslation and there are two sets of reflections: the weak, pseudo-absent reflections and the strong reflections. The scaling

Re: [ccp4bb] Pseudo-symmetry/refinement

Mike, You could try rigid body refinement against the weak reflections to get the position of the molecules right and then normal restrained refinement against the strong reflections. I had a case like this some years ago and that helped... Esko On 17.10.2010, at 6.48, Mike John wr

Re: [ccp4bb] From oscillation photographs to seeing specific sections of reciprocal lattice.

686F 78FD 6669 67BA 8D5D Esko Oksanen, M.Sc., researcher Macromolecular Structures Group Research Program in Structural Biology and Biophysics Institute of Biotechnology, University of Helsinki Viikinkaari 1 P.O. Box 65 FIN-00014 Helsinki FINLAND tel. +358-9-19158953 fax +358-9-19159940 mob

Re: [ccp4bb] first week of CCP4 community wiki

Would it be too much to ask that the person sending the summary email would also put that (or equivalent information) in the wiki? Esko Quoting Kay Diederichs <[EMAIL PROTECTED]>: > Andreas Förster schrieb: > > Hey Kay, > > > > I'm not even sure I see a problem with reposting. All ccp4 p

Re: [ccp4bb] 3D Glasses - Vuzix HMD by eDimensional

e and machining... Esko Esko Oksanen, M.Sc. European Molecular Biology Laboratory, Grenoble Outstation 6 rue Jules Horowitz BP 181 38042 Grenoble Cedex 9 FRANCE tel. +33-4-76207633 mob. +33-6-67416110 Skype ejoksane [EMAIL PROTECTED] Quoting Harry Powell <[EMAIL PROTECTED]>: > Hi > >

Re: [ccp4bb] Format convertion ccp4 to spider

Francesco, I recently had the same problem and I had to convert the ccp4 map to xplor format first (with mapman) and then to situs format with map2map. A bit annoying but it worked. HTH, Esko Esko Oksanen, M.Sc. European Molecular Biology Laboratory, Grenoble Outstation 6 rue Jules

Re: [ccp4bb] Solving a structure by MR with a pseudo-translation vector

ainst the even (strong) reflections. In the presence of significant pseudo- symmetry, the structure is probably never going to refine very well, at least in terms of R-value, because it is no longer a very good indicator of structure correctness... HTH, Esko Esko Oksanen, M.Sc., resea