Re: [ccp4bb] Careless and negative Wilson B-factor

Dear Jon and Gyuhyeok the real connaisseurs (e.g. Kay Diedrichs, et al) will certainly respond much better to this! Redundancy is really high here (which is good of course), likely explaining the high-ish Rmerge. Indeed, “redundancy-aware“ indices, like Rpim, are much better, and actually

Re: [ccp4bb] Labeling centric and acentric reflections

Hi AndreI think you can use SFTOOLS. Check it with the documentation (cause not sure exactly), but after reading your mtz, you can use the command CALC. This  calculates lots of stuff, and even has some builtin functions, including the one you want (which  I think can be called with a

Re: [ccp4bb] Some questions on tools for CCP4i2cloud: pdbset, pdbcur, coordconv, sftools

Hi Robbie I also use them quite regularly (less so coordconv, although I do use it), typically from the command line Thanks, Alejandro > On Aug 30, 2021, at 17:38, James Holton wrote: > > I use pdbset, coordconv and sftools a LOT. Usually for things no other > programs do, like converting

Re: [ccp4bb] (scattering factors) f and f" for Sr Heavy atom

Hi check out the site http://www.bmsc.washington.edu/scatter/ set up by Ethan Merritt, it has lots of valuable info, and online tools to calculate stuff such as f'/f" for any desired element, etc HTH Alejandro El 22 ene. 2021, a la(s) 16:36, rohit kumar escribió: > Hello All, > > I have

Re: [ccp4bb] Using SFall for map conversion

Oh…maybe I suggested the wrong order then (Y X Z - for SG 20) ? …I do realize YXZ is not an XYZ cyclic permutation (whereas ZXY is)…I dug it from an old script of mine, so now rechecked the FFT doc …but yes, FFT says that Y X Z is the std axis ordering for SGs higher-than 18…I’m probably

Re: [ccp4bb] Using SFall for map conversion

Hi Bernhard I don’t know how you actually calculated your map. But it seems as thus it is not following the conventional requirement for the FFT calculation, with regards to the order of the map’s axes (, , , which must be some permutation of X Y Z). This shouldn’t normally happen, except if

Re: [ccp4bb] Macromolecular Crystallography workshop in South America 2020

gt; > > > > From: CCP4 bulletin board on behalf of Alejandro > Buschiazzo > Sent: Tuesday, February 4, 2020 7:30 PM > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] Macromolecular Crystallography workshop in South America > 2020 > > Dear colleagues,

[ccp4bb] Macromolecular Crystallography workshop in South America 2020

refinement and validation; · introduction to crystallography + cryo-electron microscopy integration Confirmed speakers and tutors (so far... a few more will join the crew): Alejandro Buschiazzo (Institut Pasteur de Montevideo, Uruguay) Paul Emsley (Laboratory of Molecular Biology MRC, Cambridge,

[ccp4bb] Macromolecular Crystallography workshop in South America

- 23, 2017 Confirmed speakers and tutors (so far... a few more may join the crew): Alejandro Buschiazzo, Montevideo, Uruguay Paul Emsley, Cambridge, UK Richard Garrat, São Carlos, Brazil Ronan Keegan, Oxford, UK Eugene Krissinel, Oxford, UK Andrey Lebedev, Oxford, UK Andrew Leslie, Cambridge

Re: [ccp4bb] Crystallography Workshop in South America - CCP4 / Institut Pasteur de Montevideo 2015

Dear all, nasty auto-corrector”-driven mistake affecting Kay Diederichs’ name! My apologies! Sorry for the duplication…now duly written below (+ extra advertisement as well! ;) ) best wishes Alejandro On Jan 23, 2015, at 20:42, Alejandro Buschiazzo ale...@pasteur.edu.uy wrote: Dear

[ccp4bb] Crystallography Workshop in South America - CCP4 / Institut Pasteur de Montevideo 2015

...@pasteur.edu.uy Organizers: Alejandro Buschiazzo, PhD. Institut Pasteur de Montevideo, Uruguay Ronan Keegan, PhD. CCP4, STFC Rutherford Appleton Laboratory, United Kingdom We look forward to welcoming you soon in Montevideo! -- Alejandro Buschiazzo, PhD Research Scientist Unit of Protein Crystallography

[ccp4bb] Institut Pasteur/CCP4 Joint Macromolecular Crystallography School From data processing to structure refinement and beyond

Pasteur de Montevideo. Organizers: Alejandro Buschiazzo, PhD. Institut Pasteur de Montevideo, Uruguay Ronan Keegan, PhD. CCP4, STFC Rutherford Appleton Laboratory, United Kingdom Applicants: 24 students will be selected among the applications. The Course will provide financial support

[ccp4bb] Workshop announcement @ Inst Pasteur Montevideo - Uruguay : Modern Approaches in Drug Discovery for Neglected Infectious Diseases

speakers:* Wim Hol (University of Washington, Seattle, USA), Paul Michels (University of Edinburgh, Edinburgh, UK), Celerino Abad-Zapatero (University of Illinois at Chicago, Chicago, USA), Hugo Cerecetto (UdelaR), Marcelo Comini (IP Montevideo), Sergio Pantano (IP Montevideo), Alejandro Buschiazzo

[ccp4bb] Workshop announcement @ Inst Pasteur Montevideo - Uruguay : Modern Approaches in Drug Discovery for Neglected Infectious Diseases

speakers:* Wim Hol (University of Washington, Seattle, USA), Paul Michels (University of Edinburgh, Edinburgh, UK), Celerino Abad-Zapatero (University of Illinois at Chicago, Chicago, USA), Hugo Cerecetto (UdelaR), Marcelo Comini (IP Montevideo), Sergio Pantano (IP Montevideo), Alejandro Buschiazzo

[ccp4bb] CeBEM-CCP4 Macromolecular Crystallography Workshop 2013 at Montevideo: Application deadline extended

://www.pasteur.edu.uy/mx2013 Please address further inquiries to mx2...@pasteur.edu.uy mailto:mx2...@pasteur.edu.uy Ronan Keegan and Alejandro Buschiazzo -- Alejandro Buschiazzo, PhD Research Scientist Unit of Protein Crystallography Institut Pasteur de Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone

[ccp4bb] REMINDER: Joint CeBEM/CCP4 Macromolecular Crystallography School announcement 2013 in Uruguay

Please address further inquiries to mx2...@pasteur.edu.uy mailto:mx2...@pasteur.edu.uy Ronan Keegan and Alejandro Buschiazzo -- Alejandro Buschiazzo, PhD Research Scientist Unit of Protein Crystallography Institut Pasteur de Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +598

[ccp4bb] Macromolecular Crystallography School announcement : 2013 in Uruguay

Please address further inquiries to mx2...@pasteur.edu.uy mailto:mx2...@pasteur.edu.uy Ronan Keegan and Alejandro Buschiazzo -- Alejandro Buschiazzo, PhD Research Scientist Unit of Protein Crystallography Institut Pasteur de Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +598

[ccp4bb] Int'l Workshop of Macromolecular Crystallography - South America

, to be evaluated on a case by case basis. *APPLICATION DEADLINE* All applications should be received until March 7 2010. They should be sent as a single pdf document to : crystallogra...@pasteur.edu.uy *ORGANIZERS* Dr. Alejandro Buschiazzo Unidad de Cristalografía de Proteínas Institut Pasteur de

[ccp4bb] Int'l Crystallography Course in Latin America

. * *APPLICATION DEADLINE* * All applications should be received until March 7 2010. They should be sent as a single pdf document to :crystallogra...@pasteur.edu.uy * *ORGANIZERS** Dr. Alejandro Buschiazzo Unit of Protein Crystallography Institut Pasteur de Montevideo Dr. Pedro Alzari Dept

Re: [ccp4bb] Peak wavelength of SeMet and the corresponding f_prime and f_doubleprime.

got it is 0.97905 A and Phenix manual shows f_prime and f_doubleprime to be -3 and 4 respectively. How can one deduce f_prime and f_doubleprime for any HA at a particular wavelength. Thanks. James. -- Alejandro Buschiazzo, PhD Research Scientist Laboratory of Protein Crystallography Pasteur

Re: [ccp4bb] SAD questions

Debajyoti Dutta http://sigads.rediff.com/RealMedia/ads/click_nx.ads/www.rediffmail.com/signatureline@middle? -- Alejandro Buschiazzo, PhD Research Scientist Laboratory of Protein Crystallography Pasteur Institute of Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +5982 5220910 int

Re: [ccp4bb] SAD questions

... is still valid though!! -- Alejandro Buschiazzo, PhD Research Scientist Laboratory of Protein Crystallography Pasteur Institute of Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +5982 5220910 int. 120 Fax: +5982 5224185

[ccp4bb] TLSANL gives zero off-diagonal ANISOU matrix in CCP4 6.1

been done, otherwise REFMAC5 will just leave the residual B fac on the ATOM card, giving somewhat 'misleading', frequently extremely low values) Any help on this TLSANL problem will be very much appreciated! Best, -- Alejandro Buschiazzo, PhD Research Scientist Laboratory of Protein

Re: [ccp4bb] H3 to 2.0A but low observations:parameter ratio

...) (and then of course you should be adding the 'extra' observations that you'll most probably be using, since at this resolution unrestrained refinement would not be a sensible idea...) HTH -- Alejandro Buschiazzo Unit of Protein Crystallography Pasteur Institute of Montevideo On Thu, 23 Apr 2009, Francis E

Re: [ccp4bb] Back-Fourier transforming an EM map with SFALL

: 0033.388.65.57.55 Tel. inside France: 03.88.65.57.55 Fax from abroad: 0033.388.65.32.76 Fax inside France: 03.88.65.32.76 e-mail: [EMAIL PROTECTED] websites: http://www.igbmc.fr/ http://igbmc.fr/recherche/Dep_BSG/Eq_BKlah/index_uk.html -- Alejandro Buschiazzo Research Scientist Laboratory

Re: [ccp4bb] self-rotation interpretation, 5 minutes

en liberté Dans les jardins mal fréquentés! Georges Brassens -- Alejandro Buschiazzo, PhD Research Scientist Laboratory of Structural Biology Pasteur Institute of Montevideo Mataojo