Re: [ccp4bb] ipmosflm not connecting to XQuartz on Mac.
Hi Francis It works okay for me on OSX Mavericks when I use the “official” Mosflm build rather than the CCP4 one (choose the “X11” option when downloading). I don’t think the CCP4 build of Mosflm includes the X11 GUI (since we’ve been trying for many years to wean people off it…). I’m assuming when you say you get a hang that it reads the commands but the X11 GUI doesn’t appear (but I could be wrong). It’s probably worth saying here that if people have features that they really do miss from the old GUI that they would like to see in iMosflm, then please let us know - if there’s enough demand we will do our best to oblige (particularly if it’s a straightforward addition to the code…). -- ** note change of address ** Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH Chairman of European Crystallographic Association SIG9 (Crystallographic Computing) On 15 Apr 2014, at 21:54, Francis Reyes francis.re...@colorado.edu wrote: Hi all, Anyone having issues getting ipmosflm to connect to XQuartz? I'm getting a hang when running go just when I expect the old GUI to load. Thanks, F - Francis E. Reyes PhD 215 UCB University of Colorado at Boulder --
Re: [ccp4bb] ipmosflm not connecting to XQuartz on Mac.
I had a similar problem with CCP4 generally after a recent computer upgrade. Re-installing xquartz worked for me, because some components had seemingly become deleted. HTH Mark On 15 Apr 2014, at 21:54, Francis Reyes francis.re...@colorado.edu wrote: Hi all, Anyone having issues getting ipmosflm to connect to XQuartz? I'm getting a hang when running go just when I expect the old GUI to load. Thanks, F - Francis E. Reyes PhD 215 UCB University of Colorado at Boulder --
[ccp4bb] Studentship in Crystallography and Parasitology
Applications are invited for a three-year University of Leeds 110-year Anniversary Ph. D. studentship to work in the Goldman and Muench groups. The project will involve structural and functional studies of integral membrane pyrophosphatases, focussing on ones from pathogenic parasites such as Leishmania and Toxoplasma. The goal will be to solve the structure of one of these proteins, and use the resulting structure for drug design with collaborators in Chemistry. Candidates with a strong background in parasitology and crystallography as an undergraduate are encouraged to apply. The deadline for applications is April 21st at 4pm, because the funding scheme closes on April 28th. Interested applicants should fill in the web form at: http://www.leeds.ac.uk/rsa/postgraduate_scholarships/UoLARS-AppForm14 and send an email to a.gold...@leeds.ac.uk and s.p.mue...@leeds.ac.uk. Informal enquiries can be addressed to both Goldman and Muench at the addresses above. Adrian Goldman and Stephen Muench
[ccp4bb] Rmerge, Rmeas, I/sigma, Mn(I/sd)
Hi, in the Rupp book the following relation is reported (on pag 415): Rmerge ≈ 0.8/I/σ(I) referring to a relation of the linear merging R-value with the signal-to-noise ratio. in a 2006 CCP4bb, Manfred Weiss reported: Rrim (or Rmeas) = 0.8*sd(i)/I so, First question: is it Rmerge or Rmeas (Rrim) that we are dealing with? Second question: at the denominator (of the Rupp way to write), it is the aimless Mn(I/sd) (usually indicated as the real signal-to-noise ratio) or the aimless I/sigma (very different from Mn(I/sd) with high redundancy)? Thank you very much for the clarification. Best, Roberto. Roberto Battistutta Associate Professor Department of Chemistry University of Padua via Marzolo 1, 35131 Padova - ITALY tel. +39.049.827.5262 fax. +39.049.827.5829 roberto.battistu...@unipd.it www.chimica.unipd.it/roberto.battistutta/ VIMM (Venetian Institute of Molecular Medicine) via Orus 2, 35129 Padova - ITALY tel. +39.049.7923.236 fax +39.049.7923.250 www.vimm.it
[ccp4bb] Validation reports for all X-ray structures in the PDB
Hi all, You may not have noticed, but 19 March 2014 was VR Day - the day that new style wwPDB validation reports for all X-ray structures were made publicly available - see http://www.wwpdb.org/news/news_2014.html#18-March-2014 The validation-related files for individual X-ray PDB entries can be accessed through the web sites and ftp sites of the various wwPDB partners. Speaking for PDBe, if you go to the summary page of an X-ray PDB entry, for instance: http://pdbe.org/1cbs you will see the percentile sliders displayed in the PDBportfolio widget (http://pdbe.org/portfolio) on the right of the page. (Clicking the big white arrow will start a slideshow of images related to this entry.) The legend of the percentile-slider plot contains a direct link to the validation report (as a PDF file; in this case http://www.ebi.ac.uk/pdbe/entry-files/1cbs_validation.pdf). If you are not yet familiar with these new style validation reports, have a look here: http://www.wwpdb.org/validation-reports.html - in particular the user guide may be of interest: http://www.wwpdb.org/ValidationPDFNotes.html If you want to download the full report (which lists all outliers for many of the validation criteria, instead of just the worst 5 or the first 5), or a graphic image of the percentile-slider plot, or an XML file with all validation data in machine-readable form, go to the downloads page of any X-ray PDB entry, either through clicking the Downloads link in the menu on the left, or directly by going to a URL of the form: http://pdbe.org/1cbs/downloads The section labelled Validation of the table provides the relevant links. Note that sites that include PDBportfolio in their pages now automatically display the percentile-slider plot and download link as well! To see this in action, go to the EDS page (if any) of your favourite X-ray PDB entry, e.g.: http://eds.bmc.uu.se/cgi-bin/eds/uusfs?pdbCode=1cbs Please send any comments, questions or suggestions on the new style validation reports to validat...@mail.wwpdb.org Questions about PDBe-specific pages and services can be sent to pdbeh...@ebi.ac.uk --Gerard --- Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK ger...@ebi.ac.uk . pdbe.org Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk
Re: [ccp4bb] regarding TLS records
Thanks Pavel. I was a little tired from an overnight Synchrotron run when I wrote that. Lesson: Stay off the internet when you are tired. Haha. I forgot that the TLS groups would be assigned per chain not per molecule. Thanks for the correction. I didn't know you could run find TLS groups as part of the refinement strategy. Very helpful. -Yarrow On Tue, Apr 15, 2014 at 8:36 PM, Pavel Afonine pafon...@gmail.com wrote: Hello Yarrow, in some refinement software (phenix.refine), if you run TLS refinement and you don't specify the TLS groups, the entire structure is considered one TLS group if you use TLS parameterization and do not specify TLS groups, two scenarios are possible: a) each chain will be treated as one TLS group, b) if you define tls.find_automatically=true (or check appropriate box in the GUI) it will find TLS groups as part of refinement similarly to TLSMD but ~100 times faster. This may be why the annotators could not find the TLS groups. In any case, if TLS refinement was used, then TLS matrices defining refined TLS parameters are always present in PDB file header (in REMARK 3 records). In case of just one group there will be just one set of T,L and S. Finally, if you've done TLS refinement and decided not to use TLS in the next refinement you do not need to remove ANISOU records manually - the program will figure this out. All the best, Pavel
[ccp4bb] GRC Diffraction 2014 Instruct fellowships
Dear all, Unfortunately something went wrong in email archiving, and I recall receiving more applications from specific people, than what are now in my mailbox. May I kindly ask the people that did send an application, to re-send me their PDF file by reply to this email? Sorry again to everybody for the double posting and the rather silly error on my side - Tassos
Re: [ccp4bb] Rmerge, Rmeas, I/sigma, Mn(I/sd)
The 2006 Weiss expression - I guess from the context- is for a single reflection h measured N times (and then is identical to my 8-23) while (8-24) is valid for the Rmerge (defined in 8-15) of averaging over a shell with h reflections each measured N times , which also explains why the two related expressions in aimless necessarily have to be different. Somehow crystallographers historically invented their own linear merging statistics instead of 'standard' descriptive statistics like the standard error of the mean...still an unresolved mess see the papers/threads on cc1/2, cc* etc... Best, BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Roberto Battistutta Sent: Wednesday, April 16, 2014 5:09 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Rmerge, Rmeas, I/sigma, Mn(I/sd) Hi, in the Rupp book the following relation is reported (on pag 415): Rmerge 0.8/I/s(I) referring to a relation of the linear merging R-value with the signal-to-noise ratio. in a 2006 CCP4bb, Manfred Weiss reported: Rrim (or Rmeas) = 0.8*sd(i)/I so, First question: is it Rmerge or Rmeas (Rrim) that we are dealing with? Second question: at the denominator (of the Rupp way to write), it is the aimless Mn(I/sd) (usually indicated as the real signal-to-noise ratio) or the aimless I/sigma (very different from Mn(I/sd) with high redundancy)? Thank you very much for the clarification. Best, Roberto. Roberto Battistutta Associate Professor Department of Chemistry University of Padua via Marzolo 1, 35131 Padova - ITALY tel. +39.049.827.5262 fax. +39.049.827.5829 roberto.battistu...@unipd.it www.chimica.unipd.it/roberto.battistutta/ VIMM (Venetian Institute of Molecular Medicine) via Orus 2, 35129 Padova - ITALY tel. +39.049.7923.236 fax +39.049.7923.250 www.vimm.it
