[ccp4bb] crystals disappear
Hi forks, I got some membrane protein crystals in DDM. However, after one month, these crystals change to Irregular shape, and have not birefringent in polarized Light. Do anybody know why? Does the effect of DDM? Contain too much detergent? Thanks, Zhang Peng
Re: [ccp4bb] Concerns about statistics
Dear Ed, Thankyou for this. Indeed I have not pushed into the domain of as low as 0.4 or CC1/2 as low as 0.012. So, I do not have an answer to your query at these extremes. But I concede I am duly corrected by your example and indeed my email did not tabulate specifically how far one could investigate the plateau of DPI and certainly I was not considering such an extreme as you have investigated. Best wishes, Yours sincerely, John Prof John R Helliwell DSc On 15 Jun 2013, at 15:31, Ed Pozharski wrote: > On 06/14/2013 07:00 AM, John R Helliwell wrote: >> Alternatively, at poorer resolutions than that, you can monitor if the >> Cruickshank-Blow Diffraction Precision Index (DPI) improves or not as more >> data are steadily added to your model refinements. > Dear John, > > unfortunately the behavior of DPIfree is less than satisfactory here - in a > couple of cases I looked at it just steadily improves with resolution. > Example I have in front of me right now takes resolution down from 2.0A to > 1.55A, and DPIfree goes down from ~0.17A to 0.09A at almost constant pace > (slows down from 0.021 A/0.1A to 0.017 A/0.1A around 1.75A). > > Notice that in this specific case I/sigI at 1.55A is ~0.4 and CC(1/2)~0.012 > (even this non-repentant big-endian couldn't argue there is good signal > there). > > DPIfree is essentially proportional to Rfree * d^(2.5) (this is assuming > that No~1/d^3, Na and completeness do not change). To keep up with > resolution changes, Rfree would have to go up ~1.9 times, and obviously that > is not going to happen no matter how much weak data I throw in. > > The maximum-likelihood e.s.u. reported by Refmac makes more sense in this > particular case as it clearly slows down big time around 1.77A (see > https://plus.google.com/photos/113111298819619451614/albums/5889708830403779217). > Coincidentally, Rfree also starts going up rapidly around the same > resolution. If anyone is curious what's I/sigI is at the "breaking point" > it's ~1.5 and CC(1/2)~0.6. And to bash Rmerge a little more, it's 112%. > > So there are two questions I am very much interested in here. > > a) Why is DPIfree so bad at this? Can we even believe it given it's erratic > behavior in this scenario? > > b) I would normally set up a simple data mining project to see how common > this ML_esu behavior is, but there is no easily accessible source of data > processed to beyond I/sigI=2, let alone I/sigI=1 (are structural genomics > folks reading this and do they maybe have such data to mine?). I can look > into all of my own datasets, but that would be a biased selection of several > crystal forms. Perhaps others have looked into this too, and what are your > observations? Or maybe you have a dataset processed way beyond I/sigI=1 and > are willing to either share it with me together with a final model or run > refinement at a bunch of different resolutions and report the result (I can > provide bash scripts as needed). > > Cheers, > > Ed. > > -- > Oh, suddenly throwing a giraffe into a volcano to make water is crazy? >Julian, King of Lemurs >
Re: [ccp4bb] Concerns about statistics
On 06/14/2013 07:00 AM, John R Helliwell wrote: Alternatively, at poorer resolutions than that, you can monitor if the Cruickshank-Blow Diffraction Precision Index (DPI) improves or not as more data are steadily added to your model refinements. Dear John, unfortunately the behavior of DPIfree is less than satisfactory here - in a couple of cases I looked at it just steadily improves with resolution. Example I have in front of me right now takes resolution down from 2.0A to 1.55A, and DPIfree goes down from ~0.17A to 0.09A at almost constant pace (slows down from 0.021 A/0.1A to 0.017 A/0.1A around 1.75A). Notice that in this specific case I/sigI at 1.55A is ~0.4 and CC(1/2)~0.012 (even this non-repentant big-endian couldn't argue there is good signal there). DPIfree is essentially proportional to Rfree * d^(2.5) (this is assuming that No~1/d^3, Na and completeness do not change). To keep up with resolution changes, Rfree would have to go up ~1.9 times, and obviously that is not going to happen no matter how much weak data I throw in. The maximum-likelihood e.s.u. reported by Refmac makes more sense in this particular case as it clearly slows down big time around 1.77A (see https://plus.google.com/photos/113111298819619451614/albums/5889708830403779217). Coincidentally, Rfree also starts going up rapidly around the same resolution. If anyone is curious what's I/sigI is at the "breaking point" it's ~1.5 and CC(1/2)~0.6. And to bash Rmerge a little more, it's 112%. So there are two questions I am very much interested in here. a) Why is DPIfree so bad at this? Can we even believe it given it's erratic behavior in this scenario? b) I would normally set up a simple data mining project to see how common this ML_esu behavior is, but there is no easily accessible source of data processed to beyond I/sigI=2, let alone I/sigI=1 (are structural genomics folks reading this and do they maybe have such data to mine?). I can look into all of my own datasets, but that would be a biased selection of several crystal forms. Perhaps others have looked into this too, and what are your observations? Or maybe you have a dataset processed way beyond I/sigI=1 and are willing to either share it with me together with a final model or run refinement at a bunch of different resolutions and report the result (I can provide bash scripts as needed). Cheers, Ed. -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs
[ccp4bb] sigma value of a structure file
Dear all After PDB deposition i got a reply from the annotator to verify and review the sigma value in the structure file which in my case is -0.03. My first question is, what actually is a "sigma value" of a structure file. 2nd) where it is mentioned i mean where and how to see this value. 3rd) What is the optimum sigma value range ? -- Regards Faisal School of Life Sciences JNU
[ccp4bb] announcement: (another) GUI for XDS
Hi everybody, I developed a GUI for academic users of XDS which is documented at http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/XDSgui . This XDSwiki article also has the links to binaries of xdsGUI (or XDSgui or xds-gui; this has not been decided yet ...), for Linux 32 and 64 bit (compiled on a RHEL 6 clone), and Mac OS X (compiled on 10.7). The 'added value' of the GUI is that it produces informative plots which should greatly help to make decisions in data processing. The GUI is simple, tries to be self-explanatory and should be straightforward to operate. Noteworthy may be the TOOLS tab which offers a means to run commandline scripts upon a click with the mouse. This tab accepts user modifications which should make it attractive also for expert users - they can run their own scripts. This is the first version made publicly available. There are probaby bugs and I would like to learn about these. In particular, Mac experts please tell me how to solve the problems explained at the bottom of the Wiki article ... thanks, Kay -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: kay.diederi...@uni-konstanz.de Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box 647, D-78457 Konstanz
