[ccp4bb] Diffraction images compression and long-term storage
Hello everyone, I have a couple of questions about images compression and storage: 1)do someone use it in routine work and does it works well for them? 2)I found this page by google: http://bl831.als.lbl.gov/~jamesh/lossy_compression/ http://bl831.als.lbl.gov/%7Ejamesh/lossy_compression/ And want to ask about reports of usage of this program (of course if someone already uses it) 3)Is there any advice for long-term diffraction image storage? Thank you for your attention, -- Eugene Osipov Junior Research Scientist Laboratory of Enzyme Engineering A.N. Bach Institute of Biochemistry Russian Academy of Sciences Leninsky pr. 33, 119071 Moscow, Russia e-mail: e.m.osi...@gmail.com
[ccp4bb] Diffraction image compression
Hello everyone, I have a couple of questions about images compression and storage: 1)do someone use it in routine work and does it works well for them? 2)I found this page by google: http://bl831.als.lbl.gov/~jamesh/lossy_compression/ And want to ask about reports of usage of this program (of course if someone already uses it) 3)Is there any advice for long-term diffraction image storage? Thank you for your attention, -- Eugene Osipov Junior Research Scientist Laboratory of Enzyme Engineering A.N. Bach Institute of Biochemistry Russian Academy of Sciences Leninsky pr. 33, 119071 Moscow, Russia e-mail: e.m.osi...@gmail.com
Re: [ccp4bb] Diffraction image compression
Dear Eugene, Personally I have a habit of using bzip2 for archival of data. Negative points: very slow. Positive points: universally supported, lossless. I have lots of data. To be honest most of it I keep in the native format. I expect to see plenty of comments of lossless vs. lossy compression now :o) N.B. well processed unmerged raw-from-integration .x, INTEGRATE.HKL, mosflm mtz represents pretty good lossy compression. Long term storage: depends on your definition of long term, which will also depend on what you want to do with them... I would guess useful-long-term would correspond to ~ 10 years to ~ 20 years tops. In the past I have written data to tape which I have never attempted to recover. Everything I now have on central file servers (raid systems) on local fast drives and local cheap USB drives which sit unplugged on my desk. Local fast drives fail (more frequently than the manufacturers would admit), raids fail (less frequently but more catastrophically), local cheap USB drives fail. I bank on them not all failing at the same time :o) esp. the ones I leave unplugged. The cheap drives store about 2TB in something the size of a paperback book and are relatively universal with USB connections. But they will fail one day. You weigh up how sad you will be at the loss against the cost of being more certain of not losing the data... Cheerio, Graeme On 11 March 2013 08:39, Eugene Osipov e.m.osi...@gmail.com wrote: Hello everyone, I have a couple of questions about images compression and storage: 1)do someone use it in routine work and does it works well for them? 2)I found this page by google: http://bl831.als.lbl.gov/~jamesh/lossy_compression/ And want to ask about reports of usage of this program (of course if someone already uses it) 3)Is there any advice for long-term diffraction image storage? Thank you for your attention, -- Eugene Osipov Junior Research Scientist Laboratory of Enzyme Engineering A.N. Bach Institute of Biochemistry Russian Academy of Sciences Leninsky pr. 33, 119071 Moscow, Russia e-mail: e.m.osi...@gmail.com
[ccp4bb] Postdoc position at MDC-Berlin / HZB-BESSY
The Helmholtz Zentrum Berlin für Materialien und Energie, the Max-Delbrück-Center for Molecular Medicine Berlin, the Freie Universität Berlin, the Humboldt Universität zu Berlin and the Leibniz-Institute for Molecular Pharmacology jointly operate three experimental stations for bio-macromolecular crystallography within the Joint Berlin MX-Laboratory cooperation at BESSY II, one of the world’s most modern synchrotron radiation sources for VUV and soft X-rays. The Macromolecular Structure and Interaction Group of the Max-Delbrück-Center is seeking a Post Doctoral Research Assistant to conduct research on various structural biology / biochemistry projects of the MDC group (headed by Prof. Dr. Udo Heinemann). Additionally, the candidate shall work on the development of the automated diffraction data evaluation pipeline XDSAPP (www.helmholtz-berlin.de/bessy-mxhttp://www.helmholtz-berlin.de/bessy-mx). The successful candidate will be involved in the operation of the BESSY II bio-macromolecular crystallography beamlines (headed by Dr. Uwe Müller Dr. Manfred Weiss) and will take part in graduate student education. Initially, a three-year contract will be offered to the successful candidate with the possibility for an extension. The salary will be based on German federal TvOD. The position is available immediately, and applications will be considered until the position is filled. The MDC is an equal-opportunity employer committed to excellence through diversity. Applications of women are explicitly encouraged. Applicants should hold a Ph.D. in the biological, chemical or physical sciences and have a background in bio-macromolecular crystallography, biochemistry or computational sciences. The position also requires the documented ability to conduct independent research as well as excellent communication and interpersonal skills. Please send applications (CV, list of publications, .pdf-file format) in electronic form, with the Code MDC-MX-2013/1 to: Dr. Uwe Müller (u...@helmholtz-berlin.demailto:u...@helmholtz-berlin.de) Dr. Uwe Mueller Soft Matter and Functional Materials Macromolecular Crystallography (BESSY-MX) | Group leader Elektronenspeicherring BESSY II Albert-Einstein-Str. 15, D-12489 Berlin, Germany Fon: +49 30 8062 14974 Fax: +49 30 8062 14975 url: www.helmholtz-berlin.de/bessy-mxhttp://www.helmholtz-berlin.de/bessy-mx email:u...@helmholtz-berlin.demailto:u...@helmholtz-berlin.de Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de
[ccp4bb] Is there a way of assessing how much of a structure is 'modelable'?
Hi all, I'm having great trouble building/refining a structure which has several regions of obvious flexibility/disorder... Regions where the density is fragmented and I have no clear way of building the chain (at least with any confidence). The protein is dimeric with some variation in the extent of those regions which are not interpretable, and simply copying from the ncs mate does not work! So the question is how far can one refine such a structure - is there a measure of 'completion''? I recall that there is, but I must be getting old. Am I miss-remembering? Cheers in advance Dean
Re: [ccp4bb] stereo monitor for DELL T7600
Yes, it works with PyMOL and COOT using the 'quad buffered stereo' / 'hardware stereo' option, respectively. Best wishes, Christoph Hi Christoph, Thanks so much for your information. This is very helpful for us. One more question, will the *ASUS VG278H work with Pymol and coot?* Thanks so much! Jinyu On Fri, Mar 1, 2013 at 9:15 AM, Christoph Parthier cparth...@googlemail.com mailto:cparth...@googlemail.com wrote: We use the ASUS VG278 monitor with built-in IR emitter under linux.Stereo works perfectly without 3 pin connector. Monitor is connected via (dual-link) DVI cable (stereo option 10 in xorg.conf). This should work with any Quadro card. The monitor is big and esp. bright in 3D due to it's NVIDIA 3D LightBoost technology (3D Vision 2). Much better for use of 3D in not so dark rooms. Christoph Andrew Purkiss schrieb: And that is because the emitter is powered by the screen and its presence is detected via the HDMI monitor cable (and the signal to the emitter is sent the same way). Use of these screens is via different driver option (stereo option of 12) and there is a more limited range available. I have no experience of running with this option, as being early(ish) adopters, we have a mix of Alienware OptX AW2310 and Samsung SyncMaster 2233RZ screens. I would be interested in how stable the stereo is, when a low powered graphics card is under heavy load. Having a graphics card with more power is not a waste of money (the CUDA drivers used by the molecular simulation groups show what can be done). The extra cost is quite small compared to the costs of getting crystals in the first place!! On Fri, 2013-03-01 at 13:21 +0100, Joachim Reichelt wrote: On Linux here the ASUS Monitor with build in Emitter runs fine even on a FX 380 Quadro without 3pin connection! Am 01.03.13 13:17, schrieb Andrew Purkiss: On Fri, 2013-03-01 at 12:52 +0100, mesters wrote: Why a quadro 4000? For coot, pymol, etc., a quadro 2000 is more than sufficient. Even the quadro 600 will do fine.
[ccp4bb] qtrview command line options
Is there some way of opening a log file (specifically, the pointandscale.log that imosflm bridge to scala generates) with qtrview from command line? I tried, of course, this qtrview pointandscale.log but it opens empty, no log-file. I tried qtrview -h and qtrview --help and man qtrview but there is seemingly no documentation. I found the source code (yes, I can google) and can deduce that available options at startup are --log-file --report-xml --report-xrt --inp-file The only thing that works is qrtview --log-file pointandscale.log but that only shows me the log-file itself, i.e. no graphs etc. I understand that the program was designed primarily for ccp4 gui and I know loggraph (and it works). By the way, checkout instructions for the qtrview repository at https://fg.oisin.rc-harwell.ac.uk/projects/qtrview/ don't work throwing this error bzr: ERROR: Connection error: curl connection error (server certificate verification failed. CAfile: /etc/ssl/certs/ca-certificates.crt CRLfile: none) on https://fg.oisin.rc-harwell.ac.uk/anonscm/bzr/qtrview/.bzr/smart Cheers, Ed. -- Hurry up before we all come back to our senses! Julian, King of Lemurs
[ccp4bb] DSSR: Software for Defining the (Secondary) Structures of RNA
We are pleased to announce the beta testing release of DSSR (http://forum.x3dna.org/rna-structures/): a software program for Defining the (Secondary) Structures of RNA. DSSR is implemented in ANSI C as a stand-alone command-line program, and is self-contained. Compiled versions for Linux (32bit/64bit), Mac OS X, and Windows (MinGW/Cygwin) are available from the 3DNA Forum site (http://forum.x3dna.org/), and the executables have zero dependencies on third-party libraries to run. The download size is tiny (~0.5MB) and no setup is necessary: simply put the program into a folder of your choice (preferably one on your command PATH), and it *should* work. Starting from an RNA structure in PDB format, DSSR employs a set of simple criteria to identify all existent base pairs (bp): both canonical Watson–Crick (WC) pairs and non-canonical pairs with one or more H-bonds, made up of normal or modified bases, regardless of tautomeric or protonation state. The classification is based on the six standard rigid-body bp parameters (shear, stretch, stagger, propeller, buckle, and opening), which together rigorously quantify the spatial disposition of any two interacting bases. Moreover, the program characterizes each bp by commonly used names (WC, reverse WC, Hoogsteen, reverse Hoogsteen, wobble, sheared, imino, Calcutta, dinucleotide platform), the Saenger classification scheme of 28 types, and the Leontis-Westhof nomenclature of 12 basic geometric classes. DSSR detects triplets, quadruplets, and higher-order base associations by searching horizontally in the plane of the associated bp for further H-bonding interactions. The program determines helical regions by exploring each bp’s neighborhood vertically for base-stacking interactions, regardless of backbone connection (e.g., coaxial stacking of helices, or pseudo helices). DSSR calculates commonly used backbone (including the virtual eta/theta) torsion angles, identifies A-minor interactions (types I and II), G quartets, and bulges, internal loops and multi-branch loops. It also detects the existence of pseudo-knots, and outputs RNA secondary structures in the dot-bracket notation. The program is currently under active development. Nevertheless, the beta testing version has been checked against all RNA/DNA-containing entries in the PDB as of March 2013, and should be robust enough for real-world applications. As always, we greatly appreciate your feedback. Please report all DSSR-related issues to the open 3DNA Forum website (http://forum.x3dna.org/), and I strive to promptly respond to any questions posted there. [Posted to CCP4BB and pdb-l mailing list on Monday, 2013-03-11] Xiang-Jun PS. DSSR is a new component of the 3DNA (http://x3dna.org/) suite of programs for the analysis, rebuilding, and visualization of three‐dimensional nucleic acid structures. -- Xiang-Jun Lu (PhD) Email: xiang...@x3dna.org Web: http://x3dna.org/ Forum: http://forum.x3dna.org/
Re: [ccp4bb] Diffraction image compression
I use bzip2 as well. In addition, I generally store md5sums of the images (before and after compression) because it's quicker to check the hash for validity than load up the images - but this may be overkill. Pete Graeme Winter wrote: Dear Eugene, Personally I have a habit of using bzip2 for archival of data. Negative points: very slow. Positive points: universally supported, lossless. I have lots of data. To be honest most of it I keep in the native format. I expect to see plenty of comments of lossless vs. lossy compression now :o) N.B. well processed unmerged raw-from-integration .x, INTEGRATE.HKL, mosflm mtz represents pretty good lossy compression. Long term storage: depends on your definition of long term, which will also depend on what you want to do with them... I would guess useful-long-term would correspond to ~ 10 years to ~ 20 years tops. In the past I have written data to tape which I have never attempted to recover. Everything I now have on central file servers (raid systems) on local fast drives and local cheap USB drives which sit unplugged on my desk. Local fast drives fail (more frequently than the manufacturers would admit), raids fail (less frequently but more catastrophically), local cheap USB drives fail. I bank on them not all failing at the same time :o) esp. the ones I leave unplugged. The cheap drives store about 2TB in something the size of a paperback book and are relatively universal with USB connections. But they will fail one day. You weigh up how sad you will be at the loss against the cost of being more certain of not losing the data... Cheerio, Graeme On 11 March 2013 08:39, Eugene Osipov e.m.osi...@gmail.com wrote: Hello everyone, I have a couple of questions about images compression and storage: 1)do someone use it in routine work and does it works well for them? 2)I found this page by google: http://bl831.als.lbl.gov/~jamesh/lossy_compression/ And want to ask about reports of usage of this program (of course if someone already uses it) 3)Is there any advice for long-term diffraction image storage? Thank you for your attention, -- Eugene Osipov Junior Research Scientist Laboratory of Enzyme Engineering A.N. Bach Institute of Biochemistry Russian Academy of Sciences Leninsky pr. 33, 119071 Moscow, Russia e-mail: e.m.osi...@gmail.com
Re: [ccp4bb] Is there a way of assessing how much of a structure is 'modelable'?
Dear Dean, I have not done any systematic studies, but I have struggled quite a bit with disordered regions and I can give you some practical tips: The first thing to remember is that when you have true disorder (in contrast to fitting errors), if you do things right (not introducing exessive model bias), your density never will be great and the best you can do is a least bad fit. What I do in these cases is first delete the disordered residues, and then do a fair number if refinement cycles to get rid of model bias. Then I rebuild the deleted residues from both ends of the gap, one or two residues at a time, with further refinement cycles in between. If at least the main-chain density stays continuous, I continue building, as soon as it gets broken I stop. I find that below a contour level 0.6 sigma one is looking at noise and fitting is generally not successful. However from 0.6 sigma upwards, fitting is usually succesful. It depends, of course, on the type of disorder. If there are a few discrete conformations, density may look very good, even at lower contour levels. However, if the loop is moving all over the place, density will be very bad. So for me, the measure of completion is when the density gets broken and/or, the levels drops below 0.6 sigma. At this point, there will still be many isolated blobs of density visible, which clearly must belong to disordered loops, but I am afraid that is something you will have to live with. One can spend forever unsuccessfully trying to fit these. If there is a paper of someone who did a systematic study on a measure of completetion, I would be interested as well. My two cents, Herman From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dean Derbyshire Sent: Monday, March 11, 2013 2:16 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Is there a way of assessing how much of a structure is 'modelable'? Hi all, I'm having great trouble building/refining a structure which has several regions of obvious flexibility/disorder... Regions where the density is fragmented and I have no clear way of building the chain (at least with any confidence). The protein is dimeric with some variation in the extent of those regions which are not interpretable, and simply copying from the ncs mate does not work! So the question is how far can one refine such a structure - is there a measure of 'completion''? I recall that there is, but I must be getting old. Am I miss-remembering? Cheers in advance Dean
[ccp4bb] statistical or systematic? bias or noise?
Salve, I would like to solicit opinions on a certain question about the relationship between statistical and systematic error. Please read and consider the following in its entirety before commenting. Statistical error (experiment precision) is determined by the degree to which experimental measurement is reproducible. It is derived from variance of the data when an experiment is repeated multiple times under otherwise identical conditions. Statistical error is by its very nature irremovable and originates from various sources of random noise, which can be reduced but not entirely eliminated. Systematic error (experiment accuracy) reflects degree to which precise average deviates from a true value. Theoretically, corrections can be introduced to the experimental method that eliminate various sources of bias. Systematic error refers to some disconnect between the quantities one tries to determine and what is actually measured. The issue is whether the classification of various sources of error into the two types depends on procedure. Let me explain using an example. To determine the concentration of a protein stock, I derive extinction coefficient from its sequence, dilute it 20x to and take OD measurement. The OD value is then divided by extinction coefficient and inflated 20 times to calculate concentration. So what is the statistical error of this when I am at the spectrophotometer? I can cycle sample cuvette in and out of the holder to correct for reproducibility of its position and instrument noise. This gives me the estimated statistical error of the OD measurement. Scaled by extinction coefficient and dilution factor, this number corresponds to the statistical error (precision) of the protein concentration. There are two sources of the systematic error originating from the two factors used to convert OD to concentration. First is irremovable inaccuracy of the extinction coefficient. Second: dilution factor. Here main contribution to the systematic error is pipetting. Importantly, this includes both systematic (pipettor calibration) and statistical (pipetting precision) error. Notice that I only prepared one sample, so if on that particular instance I picked up 4.8ul and not 5.0ul, this will translate into systematically underestimating protein concentration, even though it could have equally likely been 5.2ul. So if pipetting error could have contributed ~4% into the overall systematic error while the spectrophotometer measures with 0.1% precision, it makes sense to consider how this systematic error can be eliminated. The experiment can be modified to include multiple samples prepared for OD determination from the same protein stock. An interesting thing happens when I do that. What used to be a systematic error of pipetting now becomes statistical error, because my experiment now includes reproducing dilution of the stock. In a nutshell, Whether a particular source of error contributes to accuracy or precision of an experiment depends on how experiment is conducted. And one more thing. No need to waste precious protein on evaluating error of pipetting. I can determine that from a separate calibration experiment using lysozyme solution of comparable concentration/surface tension. Technically, a single measurement has accuracy of said 4% (padded by whatever is error in extinction coefficient). But one can also project that with actual dilution repeats, the precision would be this same 4% (assuming that this is a dominant source of error). So, is there anything wrong with this? Naturally, the question really is not about extinction coefficients, but rather about semantics of what is accuracy and what is precision and whether certain source of experimental error is rigidly assigned to one of the two categories. There is, of course, the wikipedia article on accuracy vs precision, and section 3.1 from Ian's paper (ActaD 68:454) can be used as a point of reference. Cheers, Ed. -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore -- When the great Tao is abandoned, Ideas of humanitarianism and righteousness appear. When intellectualism arises It is accompanied by great hypocrisy. When there is strife within a family Ideas of brotherly love appear. When nation is plunged into chaos Politicians become patriotic. -- / Lao Tse /
Re: [ccp4bb] Diffraction image compression
I keep meaning to get back to that algorithm and make it a bit more slick so that people don't need all the third-party stuff to use it. In fact, I have a better idea for how to do it now I'm calling noise replacement compression, but that is awaiting something I like to call time which appears to be in increasingly short supply these days. Enthusiasm for lossy compression has also been somewhat dampened by things like this: http://blog.backblaze.com/2013/02/20/180tb-of-good-vibrations-storage-pod-3-0/ That's 180 TB for 2000 USD. Admittedly not exactly the fire-hardened highly available redundant fault-tolerant archive that you might want to preserve your data for all time. But if you build one of these things and (ulp) install Windoze on it, then backblaze.com will be your off-site redundant copy and maintain that copy for only $5/month. Also has a nice web interface for retrieving your files. Which, I suppose, you might be able to tell someone at TARDIS the password for the particular backblaze account on this pod machine and make all the image data you want freely available to the crystallographic community. Of course, if EVERYONE does this, then backblaze might decide to change their pricing schedule, but it looks like some astronomers have already done something like this to them and they thought it was cool enough to put it on their blog. I suppose if it really is a problem for them, they might be interested in licensing my lossy-compression algorithm. ;) -James Holton MAD Scientist On 3/11/2013 7:50 AM, Pete Meyer wrote: I use bzip2 as well. In addition, I generally store md5sums of the images (before and after compression) because it's quicker to check the hash for validity than load up the images - but this may be overkill. Pete Graeme Winter wrote: Dear Eugene, Personally I have a habit of using bzip2 for archival of data. Negative points: very slow. Positive points: universally supported, lossless. I have lots of data. To be honest most of it I keep in the native format. I expect to see plenty of comments of lossless vs. lossy compression now :o) N.B. well processed unmerged raw-from-integration .x, INTEGRATE.HKL, mosflm mtz represents pretty good lossy compression. Long term storage: depends on your definition of long term, which will also depend on what you want to do with them... I would guess useful-long-term would correspond to ~ 10 years to ~ 20 years tops. In the past I have written data to tape which I have never attempted to recover. Everything I now have on central file servers (raid systems) on local fast drives and local cheap USB drives which sit unplugged on my desk. Local fast drives fail (more frequently than the manufacturers would admit), raids fail (less frequently but more catastrophically), local cheap USB drives fail. I bank on them not all failing at the same time :o) esp. the ones I leave unplugged. The cheap drives store about 2TB in something the size of a paperback book and are relatively universal with USB connections. But they will fail one day. You weigh up how sad you will be at the loss against the cost of being more certain of not losing the data... Cheerio, Graeme On 11 March 2013 08:39, Eugene Osipov e.m.osi...@gmail.com wrote: Hello everyone, I have a couple of questions about images compression and storage: 1)do someone use it in routine work and does it works well for them? 2)I found this page by google: http://bl831.als.lbl.gov/~jamesh/lossy_compression/ And want to ask about reports of usage of this program (of course if someone already uses it) 3)Is there any advice for long-term diffraction image storage? Thank you for your attention, -- Eugene Osipov Junior Research Scientist Laboratory of Enzyme Engineering A.N. Bach Institute of Biochemistry Russian Academy of Sciences Leninsky pr. 33, 119071 Moscow, Russia e-mail: e.m.osi...@gmail.com
Re: [ccp4bb] statistical or systematic? bias or noise?
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Ed, only prepared one sample, so if on that particular instance I picked up 4.8ul and not 5.0ul, this will translate into systematically I don't share your opinion about a single measurement translating into a systematic error. I would call it a poorly designed experiment in case you were actually iterested in how accurately you determined the protein concentration. Best, Tim On 03/11/2013 04:46 PM, Ed Pozharski wrote: Salve, I would like to solicit opinions on a certain question about the relationship between statistical and systematic error. Please read and consider the following in its entirety before commenting. Statistical error (experiment precision) is determined by the degree to which experimental measurement is reproducible. It is derived from variance of the data when an experiment is repeated multiple times under otherwise identical conditions. Statistical error is by its very nature irremovable and originates from various sources of random noise, which can be reduced but not entirely eliminated. Systematic error (experiment accuracy) reflects degree to which precise average deviates from a true value. Theoretically, corrections can be introduced to the experimental method that eliminate various sources of bias. Systematic error refers to some disconnect between the quantities one tries to determine and what is actually measured. The issue is whether the classification of various sources of error into the two types depends on procedure. Let me explain using an example. To determine the concentration of a protein stock, I derive extinction coefficient from its sequence, dilute it 20x to and take OD measurement. The OD value is then divided by extinction coefficient and inflated 20 times to calculate concentration. So what is the statistical error of this when I am at the spectrophotometer? I can cycle sample cuvette in and out of the holder to correct for reproducibility of its position and instrument noise. This gives me the estimated statistical error of the OD measurement. Scaled by extinction coefficient and dilution factor, this number corresponds to the statistical error (precision) of the protein concentration. There are two sources of the systematic error originating from the two factors used to convert OD to concentration. First is irremovable inaccuracy of the extinction coefficient. Second: dilution factor. Here main contribution to the systematic error is pipetting. Importantly, this includes both systematic (pipettor calibration) and statistical (pipetting precision) error. Notice that I only prepared one sample, so if on that particular instance I picked up 4.8ul and not 5.0ul, this will translate into systematically underestimating protein concentration, even though it could have equally likely been 5.2ul. So if pipetting error could have contributed ~4% into the overall systematic error while the spectrophotometer measures with 0.1% precision, it makes sense to consider how this systematic error can be eliminated. The experiment can be modified to include multiple samples prepared for OD determination from the same protein stock. An interesting thing happens when I do that. What used to be a systematic error of pipetting now becomes statistical error, because my experiment now includes reproducing dilution of the stock. In a nutshell, Whether a particular source of error contributes to accuracy or precision of an experiment depends on how experiment is conducted. And one more thing. No need to waste precious protein on evaluating error of pipetting. I can determine that from a separate calibration experiment using lysozyme solution of comparable concentration/surface tension. Technically, a single measurement has accuracy of said 4% (padded by whatever is error in extinction coefficient). But one can also project that with actual dilution repeats, the precision would be this same 4% (assuming that this is a dominant source of error). So, is there anything wrong with this? Naturally, the question really is not about extinction coefficients, but rather about semantics of what is accuracy and what is precision and whether certain source of experimental error is rigidly assigned to one of the two categories. There is, of course, the wikipedia article on accuracy vs precision, and section 3.1 from Ian's paper (ActaD 68:454) can be used as a point of reference. Cheers, Ed. - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFRPhm5UxlJ7aRr7hoRAuoSAJwN9zAJj2qbZBNMlF0cJ0goszaqWQCg2hFp 9u+slrVyYEYbCf2D2/SOVTg= =UACi -END PGP SIGNATURE-
Re: [ccp4bb] statistical or systematic? bias or noise?
On 11 March 2013 15:46, Ed Pozharski epozh...@umaryland.edu wrote: Notice that I only prepared one sample, so if on that particular instance I picked up 4.8ul and not 5.0ul, this will translate into systematically underestimating protein concentration, even though it could have equally likely been 5.2ul Ed, surely the point is that you don't know that you only picked up 4.8ul - as you say what you actually picked up for all you know could equally well have been 5.2ul (I'm assuming that you don't conduct a separate more accurate experiment to measure what was actually picked up by each pipetting). Statistics is about expectation as distinct from actuality, and the expected error is 0.2ul (or whatever: you would have to repeat the pipetting several times to estimate the standard deviation), regardless of what the actual error is. This expected error then feeds into the expected error of the measured concentration which results from performing the experiment in its entirety, using the usual rules of error propagation. Again the actual error in the concentration from a single experiment is unrelated to its expected error, except insofar that you would normally expect it to fall within (say) a +- 3 sigma envelope. Personally I tend to avoid the systematic vs random error distinction and think instead in terms of controllable and uncontrollable errors: systematic errors are potentially under your control (given a particular experimental setup), whereas random errors aren't. Cheers -- Ian
Re: [ccp4bb] statistical or systematic? bias or noise?
Hi Ed, Ed Pozharski wrote: An interesting thing happens when I do that. What used to be a systematic error of pipetting now becomes statistical error, because my experiment now includes reproducing dilution of the stock. In a nutshell, Whether a particular source of error contributes to accuracy or precision of an experiment depends on how experiment is conducted. My take on it is slightly different - the difference seems to be more on how the source of error is modeled (although that may dictate changes to the experiment) rather than essentially depending on how the experiment was conducted. Or (possibly) more clearly, systematic error is a result of the model of the experiment incorrectly reflecting the actual experiment; measurement error is due to living in a non-deterministic universe. Of course, there could be better ways of looking at it that I'm missing. Pete
Re: [ccp4bb] statistical or systematic? bias or noise?
Tim, On Mon, 2013-03-11 at 18:51 +0100, Tim Gruene wrote: I don't share your opinion about a single measurement translating into a systematic error. I would call it a poorly designed experiment in case you were actually iterested in how accurately you determined the protein concentration. OK. As I said, this is not about protein concentration, but let's say I only have about 6ul of protein sample, so that I can only have *one* dilution. Would pipetting uncertainty then be considered systematic error or statistical error? I am afraid this is a matter of unsettled definitions. By the way, it wasn't an opinion, more of an option in interpretation. I can say that whatever is not sampled in a particular experimental setup is systematic error. Or I can say that (as you seem to suggest, and I like this option better) that whenever there is a theoretical possibility of sampling something, it is statistical error even though the particular setup does not allow accounting for it. Ed. -- Hurry up before we all come back to our senses! Julian, King of Lemurs
Re: [ccp4bb] statistical or systematic? bias or noise?
Ian, thanks for the quick suggestion. On Mon, 2013-03-11 at 18:34 +, Ian Tickle wrote: Personally I tend to avoid the systematic vs random error distinction and think instead in terms of controllable and uncontrollable errors: systematic errors are potentially under your control (given a particular experimental setup), whereas random errors aren't. Should you make a distinction then between controllable (cycling cuvette in and out of the holder) and potentially controllable errors (dilution)? And the latter may then become controllable with a different experimental setup? Cheers, Ed. -- I don't know why the sacrifice thing didn't work. Science behind it seemed so solid. Julian, King of Lemurs
Re: [ccp4bb] statistical or systematic? bias or noise?
Pete, On Mon, 2013-03-11 at 13:42 -0500, Pete Meyer wrote: My take on it is slightly different - the difference seems to be more on how the source of error is modeled (although that may dictate changes to the experiment) rather than essentially depending on how the experiment was conducted. Or (possibly) more clearly, systematic error is a result of the model of the experiment incorrectly reflecting the actual experiment; measurement error is due to living in a non-deterministic universe. I see your point. I want to clarify that reproducing an experiment as far back as possible is best. Of course it's possible to design an experiment better and account for pipetting errors. The question is not whether it has to be done (certainly yes) but whether pipetting error should be considered as inaccuracy or imprecision when the experiment is not repeated. One can say it's inaccuracy when it is not estimated and imprecision when it is. Or one can accept Ian's suggestion and notice that there is no fundamental difference between things you can control and things you can potentially control. IIUC, you are saying that nature of the error should be independent of my decision to model it or not. Other words, if I can potentially sample some additional random variable in my experiment, it contributes to precision whether I do it or not. When it's not sampled, the precision is simply underestimated. Does that make more sense? Cheers, Ed. -- After much deep and profound brain things inside my head, I have decided to thank you for bringing peace to our home. Julian, King of Lemurs
Re: [ccp4bb] [Err] Re: [ccp4bb] statistical or systematic? bias or noise?
By the way, am I the only one who gets this thing with every post? If anyone can ask Jin Kwang (liebe...@korea.ac.kr) to either clean up his mailbox or unsubscribe, that would be truly appreciated. Delete button is easy and fun to use, but this has been going on for quite some time. On Tue, 2013-03-12 at 04:16 +0900, spam_mas...@korea.ac.kr wrote: ransmit Report: liebe...@korea.ac.kr ; 5 õ Ͽ4ϴ. ( / : 554 Transaction failed. 402 Local User Inbox Full (liebe...@korea.ac.kr) 4,61440,370609(163.152.6.98)) / User unknown :; ڰ x = Socket connect fail: DATA write fail: ۽ DATA reponse fail : κ -- Bullseye! Excellent shot, Maurice. Julian, King of Lemurs.
Re: [ccp4bb] qtrview command line options
Hi Ed Thank you for the suggestion. We are looking into this and hopefully will provide a solution soon. Regards Andrey On 11 Mar 2013, at 14:26, Ed Pozharski wrote: Is there some way of opening a log file (specifically, the pointandscale.log that imosflm bridge to scala generates) with qtrview from command line? I tried, of course, this qtrview pointandscale.log but it opens empty, no log-file. I tried qtrview -h and qtrview --help and man qtrview but there is seemingly no documentation. I found the source code (yes, I can google) and can deduce that available options at startup are --log-file --report-xml --report-xrt --inp-file The only thing that works is qrtview --log-file pointandscale.log but that only shows me the log-file itself, i.e. no graphs etc. I understand that the program was designed primarily for ccp4 gui and I know loggraph (and it works). By the way, checkout instructions for the qtrview repository at https://fg.oisin.rc-harwell.ac.uk/projects/qtrview/ don't work throwing this error bzr: ERROR: Connection error: curl connection error (server certificate verification failed. CAfile: /etc/ssl/certs/ca-certificates.crt CRLfile: none) on https://fg.oisin.rc-harwell.ac.uk/anonscm/bzr/qtrview/.bzr/smart Cheers, Ed. -- Hurry up before we all come back to our senses! Julian, King of Lemurs -- Scanned by iCritical.
[ccp4bb] Opportunity for a Staff Scientist - Membrane Protein Chemistry @ Takeda California (San Diego)
Takeda California is looking for a Staff Scientist, Membrane Protein Chemistry who will purify, characterize and assist crystallization of integral membrane proteins including GPCRs to support structure based drug design or assay development and compound screening for drug discovery programs. The successful candidate will have a Ph.D. in a life science with post doctorate and 0-3 years of relevant experience in membrane protein chemistry for structural biology studies and strong hands-on experience and method development skills in membrane protein expression, purification and characterization. Experience in membrane protein X-ray crystallography is a plus. Regards, David Marshman Senior Recruiter Takeda California 10410 Science Center Drive San Diego, CA 92121 858-731-3694 858-550-9571 (fax) david.marsh...@takeda.commailto:che...@takedasd.com
Re: [ccp4bb] [Err] Re: [ccp4bb] statistical or systematic? bias or noise?
I've just have the same thing. I'll write to Jin Kwang and remove him from the bb-list if he will not respond by tomorrow evening Andrey On 11 Mar 2013, at 19:27, Ed Pozharski wrote: By the way, am I the only one who gets this thing with every post? If anyone can ask Jin Kwang (liebe...@korea.ac.kr) to either clean up his mailbox or unsubscribe, that would be truly appreciated. Delete button is easy and fun to use, but this has been going on for quite some time. On Tue, 2013-03-12 at 04:16 +0900, spam_mas...@korea.ac.kr wrote: ransmit Report: liebe...@korea.ac.kr ; 5 õ Ͽ4ϴ. ( / : 554 Transaction failed. 402 Local User Inbox Full (liebe...@korea.ac.kr) 4,61440,370609(163.152.6.98)) / User unknown :; ڰ x = Socket connect fail: DATA write fail: ۽ DATA reponse fail : κ -- Bullseye! Excellent shot, Maurice. Julian, King of Lemurs.
[ccp4bb] validating ligand density
Hello all, We co-crystallized an inactive variant of our enzyme in the presence of substrate and have determined the structure at 1.85A. Now, we want to validate the fitting of the ligand into the electron density. We tried validating using the difference map (2Fo-Fc) after refining the structure without the ligand. But, it is still a bit inconclusive if the density fits the ligand. It would be very kind to know if there are tools for validating this electron density. We were excited about twilight but turns out it can only be used with deposited structure. We will appreciate your help and suggestions. Many thanks, Srinivasan
Re: [ccp4bb] [Err] Re: [ccp4bb] statistical or systematic? bias or noise?
It should stop. I'll see after sending this message. On 11 Mar 2013, at 19:27, Ed Pozharski wrote: By the way, am I the only one who gets this thing with every post? If anyone can ask Jin Kwang (liebe...@korea.ac.kr) to either clean up his mailbox or unsubscribe, that would be truly appreciated. Delete button is easy and fun to use, but this has been going on for quite some time. On Tue, 2013-03-12 at 04:16 +0900, spam_mas...@korea.ac.kr wrote: ransmit Report: liebe...@korea.ac.kr ; 5 õ Ͽ4ϴ. ( / : 554 Transaction failed. 402 Local User Inbox Full (liebe...@korea.ac.kr) 4,61440,370609(163.152.6.98)) / User unknown :; ڰ x = Socket connect fail: DATA write fail: ۽ DATA reponse fail : κ -- Bullseye! Excellent shot, Maurice. Julian, King of Lemurs.
[ccp4bb] [Final Call] The International Symposium on Diffraction Structural Biology 2013
Dear all, This is the final call for the International Symposium on Diffraction Structural Biology 2013. The deadline for abstract submission is March 15. Dear Colleagues, We are pleased to announce the Scientific Programme for the 4th International Symposium on Diffraction Structural Biology (ISDSB2013) to be held May 26th to 29th 2013 at NAGOYA TRADE INDUSTRY CENTER in Nagoya, Japan. This conference is the Fourth in the series of ISDSBs initiated in 2003 by the Japan Society for the Promotion of Science (JSPS). The University-Industry Cooperative Research Committee (#169) of JSPS, is Chaired by Professor Noriyoshi Sakabe. See:- http://www.sbsp.jp/ISDSB2013/homepage/index.html The scientific topics covered in ISDSB2013 will include the following sessions:- S1. Synchrotron and Free Electron Lasers S2. New Methodology and instrumentation S3. Drug design S4. Tomography and imaging S5. Membrane Proteins S6. Neutron diffraction and hydration structure S7. Membrane proteins and macromolecular complexes S8. Protein structure and dynamics We have confirmed speakers as advertised at the website above including two Nobelists Lectures by Professor Thomas Steitz and Professor Brian Kobilka, 3 Plenary Lecturers and 32 Session Lecturers. There will be Poster sessions and also a Commercial and Industrial Companies Exhibition as well as a visit to the NUSR：Nagoya University Synchrotron Radiation Research Center. In co-operation with the Journal of Synchrotron Radiation, we plan on publishing the manuscripts presented in a special issue of JSR. Both invited and contributed manuscripts will be subjected to the usual refereeing process of JSR. The concept of this Series of Symposia is to bring structural biologists using diffraction and the scientists using a wide range of other advanced technologies closer together as well as interlace where possible basic research with industrial applications. The 169th Committee was the first to propound the concept of the need for a Symposium on Diffraction Structural Biology and thus led the way by convening the first International Symposium on Diffraction Structural Biology held in 2003. This, the detailed planning of the fourth in the Series, again confirms its worth and value to this extensive, global, research community. The immediately previous 3rd International Symposium on Diffraction Structural Biology (ISDSB2010) was the first to be convened outside Japan and took place in Paris and was successful in number and range of countries and scientific fields represented. It again showed that the continuing organization of these Symposia aims to present the state-of-the-art frontiers of diffraction structural biology and its cognate fields especially the microscopies and imaging. Structural Biology has again progressed rapidly after ISDSB2010 and is making clear the reaction mechanisms of molecular machineries which preside within life processes. In terms of technologies and experimental techniques an equally vital set of developments is underway. Of particular note are the arrival of the 'ultimate storage ring' synchrotron radiation sources, the results from the first X-ray Free Electron Lasers and the newer, more intense, spallation neutron sources. We are again planning to discuss the integration of all kinds of structure determination methods so as to understand more systematically the biological function of macromolecules, and which are closely related to medical care or drug discoveries. We will also intensively discuss a broad range of the latest discoveries in the understanding of life processes at all length scales, from molecular to cellular. These results and developments will firmly, wherever possible, be with respect to the potential and/or actual applications to industrial uses. These discoveries are based on the structures determined by X-rays, electrons and neutrons as the core probes of matter, and by the other novel techniques encouraging the broad development of structural biology. Given the intense excitement in this field there is a very fruitful potential to invite internationally eminent authorities. This upcoming Symposium will again be identified as supplying the interface between academic and industrial researchers, and also the interface between diffraction technologies and the other active fields to discuss the research breakthroughs. We look forward to seeing you in Nagoya at ISDSB2013! Yours sincerely, Takashi Yamane, Chairperson of ISDSB2013 Noriyoshi Sakabe, Chairperson of #169 committee of JSPS Local Organizing Committee of ISDSB2013
Re: [ccp4bb] statistical or systematic? bias or noise?
Ed, Ed Pozharski wrote: IIUC, you are saying that nature of the error should be independent of my decision to model it or not. Other words, if I can potentially sample some additional random variable in my experiment, it contributes to precision whether I do it or not. When it's not sampled, the precision is simply underestimated. Does that make more sense? Actually, I was trying to say the opposite - that the decision to include something in the model (or not) could change the nature of the error. Too bad that what I was thinking doesn't apply to the situation you described - my intuition was assuming that there was some time of optimization/refinement/fitting going on. By analogy to profile fitting, modeling a spot as a circle or ellipsoid will have an effect on the standard deviation attributed to that spot. But that wasn't the situation you were describing. Pete PS - IIUC := ?
