Re: [ccp4bb] microdiffraction data assembly method
For serial crystallography at the SLS, the procedures that were in place more than a year ago are described in https://www.ncbi.nlm.nih.gov/pubmed/28573576 . I'd say these procedures are an order of magnitude more straightforward than what is in the paper that you cite, and give better results. Since then, a procedure was developed that made it possible to easily cluster (or select) similar data sets (https://www.ncbi.nlm.nih.gov/pubmed/28375141). This is available, for datasets processed with XDS, as xscale_isocluster, from XDSwiki. This opens new opportunities to work with serial crystallographic data (also those from XFEL), and if nothing else will result in better merged data through better selection. The methods development in this field is ongoing, and the current state will be displayed at next week's ISSX2 workshop at the SLS ( http://indico.psi.ch/conferenceDisplay.py?confId=5553 ). It will also be one topic at the forthcoming 2018 CCP4 Study Weekend (https://eventbooking.stfc.ac.uk/news-events/ccp4-study-weekend-2018-384). HTH, Kay On Tue, 21 Nov 2017 09:50:39 -0800, Ethan A Merritt wrote: >On Tuesday, November 21, 2017 9:32:15 AM PST CPMAS Chen wrote: >> Hi, CCP4ers, >> >> I came across this paper about improving data by microdiffraction data >> assembly method from Raymond C. Stevens group, >> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3338336/#SD1. >> >> By reading their methods, this seems to me like manually selecting data >> based on Rmerge. After almost 5 years, do we have a better/quicker >> script-based method to do so? > >The difficulty they faced was essentially identical to that faced by all >the nanocrystal + XFEL experiments performed since then. >The data processing software being developed for XFEL probably does >what you are asking for. You might start here: > > http://viper.lbl.gov/cctbx.xfel/index.php/Main_Page > >The issue is that each crystal contributes only a small slice of >reciprocal space to the data. In the case of XFEL data this is only >a still image. In the paper you cite it was more than that, but still >very small compared to "normal" data sets. > > Ethan > >> Their data improved not only in resolution, but also in the statistics. The >> method seems impressive. >> Thanks! >> >> Charles >> >> > > >-- >Ethan A Merritt >Biomolecular Structure Center, K-428 Health Sciences Bldg >MS 357742, University of Washington, Seattle 98195-7742
Re: [ccp4bb] microdiffraction data assembly method
Hi Charles, a couple of years ago a colleague and I put together a perl script based on this paper. It worked pretty well in our hands. I'd be happy to share it with you if you'd like. Best wishes Kevin -- Kevin Jude, PhD Structural Biology Research Specialist, Garcia Lab Howard Hughes Medical Institute Stanford University School of Medicine Beckman B177, 279 Campus Drive, Stanford CA 94305 Phone: (650) 723-6431 On Tue, Nov 21, 2017 at 9:32 AM, CPMAS Chen wrote: > Hi, CCP4ers, > > I came across this paper about improving data by microdiffraction data > assembly method from Raymond C. Stevens group, https://www.ncbi.nlm. > nih.gov/pmc/articles/PMC3338336/#SD1. > > By reading their methods, this seems to me like manually selecting data > based on Rmerge. After almost 5 years, do we have a better/quicker > script-based method to do so? > > Their data improved not only in resolution, but also in the statistics. > The method seems impressive. > > Thanks! > > Charles > > -- > > *** > > Charles Chen > > Research Associate > > University of Pittsburgh School of Medicine > > Department of Anesthesiology > > ** > >
Re: [ccp4bb] [Off-topic] Comparison of the same structure built by many people
Perhaps this can be automated: https://www.phenix-online.org/papers/wd5073_reprint.pdf Software doesn't get tired or bored, and thus potentially can try more and produce more plausible interretations. Then one can hire a number of people of various expertise to choose "best" result according to their subjective interpretations. Pavel On Mon, Nov 20, 2017 at 12:25 PM, Shintaro Aibara wrote: > Dear All, > > Apologies for the slightly off-topic, but I was wondering if anybody knew > of a paper/textbook where a protein model was built by multiple people > (ranging from novice to experienced builders) and compared. I believe the > conclusion was that while the overall trace was broadly correct, > experienced builders maintained better geometry compared to beginners. > > I distinctly remember reading it a couple of years ago but cannot seem to > find the figure. If anybody knows of this figure/paper/textbook it would be > much appreciated if you could point me in the direction. > > Yours faithfully, > Shintaro >
Re: [ccp4bb] [Off-topic] Comparison of the same structure built by many people
It sounds a bit like this paper from a year ago: https://www.nature.com/articles/ncomms12549 apart from the conclusion: here the point is that amateurs build higher quality models than crystallographers. On 20 November 2017 at 20:25, Shintaro Aibara wrote: > Dear All, > > Apologies for the slightly off-topic, but I was wondering if anybody knew of > a paper/textbook where a protein model was built by multiple people (ranging > from novice to experienced builders) and compared. I believe the conclusion > was that while the overall trace was broadly correct, experienced builders > maintained better geometry compared to beginners. > > I distinctly remember reading it a couple of years ago but cannot seem to > find the figure. If anybody knows of this figure/paper/textbook it would be > much appreciated if you could point me in the direction. > > Yours faithfully, > Shintaro
Re: [ccp4bb] microdiffraction data assembly method
On Tuesday, November 21, 2017 9:32:15 AM PST CPMAS Chen wrote: > Hi, CCP4ers, > > I came across this paper about improving data by microdiffraction data > assembly method from Raymond C. Stevens group, > https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3338336/#SD1. > > By reading their methods, this seems to me like manually selecting data > based on Rmerge. After almost 5 years, do we have a better/quicker > script-based method to do so? The difficulty they faced was essentially identical to that faced by all the nanocrystal + XFEL experiments performed since then. The data processing software being developed for XFEL probably does what you are asking for. You might start here: http://viper.lbl.gov/cctbx.xfel/index.php/Main_Page The issue is that each crystal contributes only a small slice of reciprocal space to the data. In the case of XFEL data this is only a still image. In the paper you cite it was more than that, but still very small compared to "normal" data sets. Ethan > Their data improved not only in resolution, but also in the statistics. The > method seems impressive. > Thanks! > > Charles > > -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg MS 357742, University of Washington, Seattle 98195-7742
[ccp4bb] microdiffraction data assembly method
Hi, CCP4ers, I came across this paper about improving data by microdiffraction data assembly method from Raymond C. Stevens group, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3338336/#SD1. By reading their methods, this seems to me like manually selecting data based on Rmerge. After almost 5 years, do we have a better/quicker script-based method to do so? Their data improved not only in resolution, but also in the statistics. The method seems impressive. Thanks! Charles -- *** Charles Chen Research Associate University of Pittsburgh School of Medicine Department of Anesthesiology **
Re: [ccp4bb] [Off-topic] Comparison of the same structure built by many people
Thanks Mark for the paper, it kind of catches the essence of what I was looking for. I do however remember it was more people and I think I'm looking for a figure where all the builds (which if I remember correctly was in the 10's rather than 3) were superimposed over each other to make what looked similar to an NMR ensemble. On Mon, Nov 20, 2017 at 10:04 PM, Mark J. van Raaij wrote: > > This one? > http://scripts.iucr.org/cgi-bin/paper?SE0260 > > > Mark J van Raaij > CNB-CSIC > wwwuser.csic.es/~mjvanraaij > > Original message > From: Shintaro Aibara > Date: 20/11/2017 21:25 (GMT+01:00) > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] [Off-topic] Comparison of the same structure built by > many people > > Dear All, > > Apologies for the slightly off-topic, but I was wondering if anybody knew > of a paper/textbook where a protein model was built by multiple people > (ranging from novice to experienced builders) and compared. I believe the > conclusion was that while the overall trace was broadly correct, > experienced builders maintained better geometry compared to beginners. > > I distinctly remember reading it a couple of years ago but cannot seem to > find the figure. If anybody knows of this figure/paper/textbook it would be > much appreciated if you could point me in the direction. > > Yours faithfully, > Shintaro > -- Yours Sincerely, Shintaro Aibara
