[ccp4bb] refmac failed message
Dear all, I am refining a structure in Refmac at 2.2 A in win OS. However, Refmac failed and send this message: forrtl: error (72): floating overflow Thank you in advance for your any helpful suggestions. Best, Elad Elad Binshtein Ph.D student Department of Life Science Ben Gurion University of the Negev Ph: 972-8-6461325
Re: [ccp4bb] refmac failed message
Hi Elad You don't say which version of Refmac you are using but I think the first thing to do would be to try the latest version (5.5.0102). You can pick this up from ftp://ftp.ccp4.ac.uk/nds/windows/refmac_5.5.0102/refmac5.exe Copy this exe file to the bin subdirectory of your CCP4 installation. (Probably wise to make a backup copy of the existing refmac5.exe first). Best wishes Norman Stein CCP4 From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Elad Binshtien Sent: 30 July 2009 11:50 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] refmac failed message Dear all, I am refining a structure in Refmac at 2.2 A in win OS. However, Refmac failed and send this message:forrtl: error (72): floating overflow Thank you in advance for your any helpful suggestions. Best, Elad Elad Binshtein Ph.D student Department of Life Science Ben Gurion University of the Negev Ph: 972-8-6461325 -- Scanned by iCritical.
[ccp4bb] question of extra high B factor
Dear All, I am refining a structure of a complex between of 50kD protein and a 20kD glycosylated protien. The data is of 2.9 A resolution. The wilson B factor is as high as 86.3 A^2. The refinement seems well with R/Rf of 0.21/0.25. But the B-factor is extra high. For the 50kD part, the average B factor is 76.5 A^2. But the B factor of the 20 kD glycosylated protein is as high as 133.3 A^2. Although the electron density looks fine, even the sugar chain is seen clearly. My question is: 1. How to reduce the B factor to a reasonable level? 2. If it can not be redueced, when I published it, is this value acceptable? 3. In the same of similar resolutionIs, is there some other structures like this situation? A component or a subunit of the protein has a extra high B factor as high as 130. Thanks and best wishes. -- Jiamu Du, Ph.D. State Key Laboratory of Molecular Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 320 Yue-Yang Road Shanghai 200031 P. R. China Tel: +86-21-5492-1117 E-mail: jiam...@gmail.com
Re: [ccp4bb] question of extra high B factor
Hi Jiamu, My question is: 1. How to reduce the B factor to a reasonable level? 3. In the same of similar resolutionIs, is there some other structures like this situation? POLYGON tool is (one of) your friend(s) to answer this question (apart from debatable one about a reasonable level): Acta Cryst. D65, 297-300 (2009). Now it is available in PHENIX (from the latest nightly builds): http://www.phenix-online.org/ Please let me know if you have any questions about it. Pavel.
Re: [ccp4bb] question of extra high B factor
Dear Jiamu, On Fri, Jul 31, 2009 at 12:00:25AM +0800, Jiamu Du wrote: I am refining a structure of a complex between of 50kD protein and a 20kD glycosylated protien. The data is of 2.9 A resolution. The wilson B factor is as high as 86.3 A^2. The refinement seems well with R/Rf of 0.21/0.25. But the B-factor is extra high. For the 50kD part, the average B factor is 76.5 A^2. But the B factor of the 20 kD glycosylated protein is as high as 133.3 A^2. Although the electron density looks fine, even the sugar chain is seen clearly. My question is: 1. How to reduce the B factor to a reasonable level? How do you define 'reasonable'? And why would you want to reduce this anyway? ( 50*76.5 + 20*133.3 ) / 70 = 92.7 which seems fairly close to the Wilson B of 86.3, right? 2. If it can not be redueced, when I published it, is this value acceptable? Better question: is it the right value? Remember it is results - publish and not publish - results ;-) If they're correct than they are acceptable (I would accept those values). 3. In the same of similar resolutionIs, is there some other structures like this situation? A component or a subunit of the protein has a extra high B factor as high as 130. I'm sure hundreds of them ... but I'm sure you want your structure to stand on its own, so don't look too close at other structures and repeat the various mistakes we've all made and that are now set in stone in some old PDB file. Cheers Clemens -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-- * BUSTER Development Group (http://www.globalphasing.com) ***
Re: [ccp4bb] question of extra high B factor
I am using TLS refinement with Phenix for the structure refinement. On Fri, Jul 31, 2009 at 12:00 AM, Jiamu Du jiam...@gmail.com wrote: Dear All, I am refining a structure of a complex between of 50kD protein and a 20kD glycosylated protien. The data is of 2.9 A resolution. The wilson B factor is as high as 86.3 A^2. The refinement seems well with R/Rf of 0.21/0.25. But the B-factor is extra high. For the 50kD part, the average B factor is 76.5 A^2. But the B factor of the 20 kD glycosylated protein is as high as 133.3 A^2. Although the electron density looks fine, even the sugar chain is seen clearly. My question is: 1. How to reduce the B factor to a reasonable level? 2. If it can not be redueced, when I published it, is this value acceptable? 3. In the same of similar resolutionIs, is there some other structures like this situation? A component or a subunit of the protein has a extra high B factor as high as 130. Thanks and best wishes. -- Jiamu Du, Ph.D. State Key Laboratory of Molecular Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 320 Yue-Yang Road Shanghai 200031 P. R. China Tel: +86-21-5492-1117 E-mail: jiam...@gmail.com -- Jiamu Du, Ph.D. State Key Laboratory of Molecular Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 320 Yue-Yang Road Shanghai 200031 P. R. China Tel: +86-21-5492-1117 E-mail: jiam...@gmail.com
[ccp4bb] Coot:findwaters in REFMAC
I used Coot:findwaters facility in REFMAC (CCP4 6.1.1) to add waters to the refined structure. Often for the well ordered water sites the routine added two water molecules in single water site, with their distance (~1 Angs) way shorter than allowed hydrogen bonding distance. I have to remove the extra water molecules manually. Is this a intended feature? It seems to only create extra work to the user. What is the purpose of having different chain IDs for waters output from this routine? Huiying Li, Ph. D Department of Molecular Biology and Biochemistry Natural Sciences I, Rm 2443 University of California at Irvine Irvine, CA 92697, USA Tel: 949-824-4322(or -1953); Fax: 949-824-3280 email: h...@uci.edu
Re: [ccp4bb] Coot:findwaters in REFMAC
Huiying Li wrote: I used Coot:findwaters facility in REFMAC (CCP4 6.1.1) to add waters to the refined structure. Often for the well ordered water sites the routine added two water molecules in single water site, with their distance (~1 Angs) way shorter than allowed hydrogen bonding distance. I have to remove the extra water molecules manually. Sounds like an old version. Things have improved. Is this a intended feature? It seems to only create extra work to the user. :-( What is the purpose of having different chain IDs for waters output from this routine? I thought (at the time) that it was sensible to add waters to a different chain ID to the protein atoms (I still do, in fact). There are others (somewhat less involved in model-building I suspect) that think otherwise. Paul.
Re: [ccp4bb] question of extra high B factor
Jiamu Du schrieb: Dear All, I am refining a structure of a complex between of 50kD protein and a 20kD glycosylated protien. The data is of 2.9 A resolution. The wilson B factor is as high as 86.3 A^2. The refinement seems well with R/Rf of 0.21/0.25. But the B-factor is extra high. For the 50kD part, the average B factor is 76.5 A^2. But the B factor of the 20 kD glycosylated protein is as high as 133.3 A^2. Although the electron density looks fine, even the sugar chain is seen clearly. My question is: 1. How to reduce the B factor to a reasonable level? Please check out http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Refinement#help.2C_my_protein_has_high_B-factors.21 2. If it can not be redueced, when I published it, is this value acceptable? As there's nothing wrong with it, it can be published. 3. In the same of similar resolutionIs, is there some other structures like this situation? A component or a subunit of the protein has a extra high B factor as high as 130. Just look at the B-factors of new PDB entries which have a a resolution worse than 3 A (e.g., membrane proteins) - there are quite a few of those. HTH, Kay -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: kay.diederi...@uni-konstanz.de Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universitaet Konstanz, Box M647, D-78457 Konstanz smime.p7s Description: S/MIME Cryptographic Signature
[ccp4bb] Postdoctoral position in protein crystallography at Karolinska Institutet
POSTDOCTORAL FELLOWSHIP IN PROTEIN CRYSTALLOGRAPHY AT KAROLINSKA INSTITUTET As part of a collaboration between the laboratories of Rune Toftgård and Luca Jovine at the KI Department of Biosciences and Nutrition and the Center for Biosciences, a postdoctoral position is immediately available on structural studies of key players in the Hedgehog signaling pathway. The Department of Biosciences and Nutrition has state-of-the-art equipment for protein expression, purification and in house X-ray data collection; frequent access to synchrotron sites and excellent computational facilities are also available. With their close integration of academic, clinical and industrial research, KI and the Center for Biosciences offer a highly international and collaborative environment for biomedical studies. Highly motivated candidates with experience in protein expression (particularly in insect and/or mammalian cells), purification, crystallization and structure determination, are encouraged to apply by e-mailing a curriculum vitae, summary of research experience and interests, and names and contact information for two references to Luca Jovine (luca.jov...@ki.se). Please note that, in order to be eligible for this scholarship, candidates should be non-Swedish citizens who have obtained a doctorate or the equivalent outside Sweden. Deadline for application is 1 October 2009. Luca Jovine, Ph.D. Group Leader, Protein Crystallography Unit Karolinska Institutet Department of Biosciences and Nutrition Hälsovägen 7, SE-141 57 Huddinge, Sweden Voice: +46.(0)8.6083-301 FAX: +46.(0)8.6089-290 E-mail: luca.jov...@ki.se W3: http://jovinelab.org
Re: [ccp4bb] question of extra high B factor
On 00:00 Fri 31 Jul , Jiamu Du wrote: Dear All, I am refining a structure of a complex between of 50kD protein and a 20kD glycosylated protien. The data is of 2.9 A resolution. The wilson B factor is as high as 86.3 A^2. The refinement seems well with R/Rf of 0.21/0.25. But the B-factor is extra high. For the 50kD part, the average B factor is 76.5 A^2. But the B factor of the 20 kD glycosylated protein is as high as 133.3 A^2. Although the electron density looks fine, even the sugar chain is seen clearly. My question is: 1. How to reduce the B factor to a reasonable level? 2. If it can not be redueced, when I published it, is this value acceptable? 3. In the same of similar resolutionIs, is there some other structures like this situation? A component or a subunit of the protein has a extra high B factor as high as 130. Our group published a paper a few years ago with an average B of 80 A^2 (JMB 328:893 (2003)). One referee had some objections to this, so we performed analyses of the whole Protein Data Bank for proteins at 2.5-3.0 A (see Fig. 2D in the paper). You may find this figure useful if you need to convince anyone. -- Thanks, Donnie Donnie Berkholz P. Andrew Karplus lab Oregon State University pgprRgbk0YHdz.pgp Description: PGP signature
Re: [ccp4bb] OpenGL Stereo 3D on 120 Hz LCDs, at last!
Just got this working on a machine with a Quadro FX 3800. Stereo looks great on both Pymol (v1.1) and the latest build of WinCoot (v0.6 build 2172). On Fri, Jul 17, 2009 at 1:20 AM, Warren DeLano war...@delsci.com wrote: FYI, for folks not subscribed to pymol-users: nVidia today released beta drivers which at last enable OpenGL-based stereo 3D visualization on 120 Hz LCDs using Quadro graphics cards. So long as you are willing to put up with Windows, you can finally abandon those old CRTs without spending a fortune and without sacrificing quality of the stereo 3D effect. Details posted at http://www.pymol.org Cheers, Warren -- Jim Fairman Graduate Research Assistant Department of Biochemistry, Cellular, and Molecular Biology (BCMB) University of Tennessee -- Knoxville 216-368-3337 jfair...@utk.edu james.fair...@case.edu
Re: [ccp4bb] Foils for energy calibration
At ALS, we have a box of foils from EXAFS Materials that seems to get passed around from beamline to beamline. I ran absorption scans on 17 edges from the metals in the box one day, and found that there was considerable scatter in the expected vs observed edge positions: http://bl831.als.lbl.gov/~jamesh/pickup/mono_calib.png Here I have plotted the correct position of each edge as determined by Bearden Burr (1967), against the edge I determined using the criterion recommended in the Reference Spectra document in the exafsmaterials.com website: the first inflection point in the derivative spectrum. I think a large amount of the scatter is because my mono (like many PX/MX beamlines) is Si(111) and not Si(220) like the one used to determine the reference spectra. It is not hard to imagine how blurring the spectrum with a wider energy spread of the incident beam will shift the position of the edge. One could try to use the electron binding energy tabulated in the little orange book: http://xdb.lbl.gov/Section1/Sec_1-1.html but these do not always take into account the near edge features (like the white line from SeMet) which change depending on the chemical environment around the metal, radiation damage, etc. It would be nice if someone could calibrate some standard reference materials using a Si(111) monochromator, but I don't know of anyone who has done this. However, another way to get your x-ray wavelength is using Bragg's law: lambda = 2*d*sin(theta) and the d-spacing of silicon is known to be 5.43159 ± 0.00020 A, and NIST will sell you certified Si powder: https://www-s.nist.gov/srmors/view_detail.cfm?srm=640d The problem here is that although you know d very accurately, the error in lambda is dominated by sin(theta), or rather the uncertainty in your detector distance. The pixel field on most detectors is actually quite accurate, as a NIST-traceable calibration is used to make the pinhole calibration mask, and the encoder on most detector distance stages is very accurate for relative moves (counting ticks on the encoder). But there is always an offset from the zero position predicted by the encoder to the true center of rotation that is hard to know. Nevertheless, all you really want is for the d-spacing of silicon powder rings to be right at all detector distances. You can use the program FIT2D to refine the wavelength, distance, detector tilt, etc. or any combination thereof for a given image, but you will find that the repeatability of such a fit (using different starting parameters) is not great because the distance and wavelength are highly correlated. However, there is a way around this: Since we know that a relative move of the distance will be accurate, there should be one and only one offset that you can add to the recorded value of distance of each image to make it the right distance. You can define the right offset as the one where FIXing the resulting right distance in FIT2D and refining everything else gives you the same refined value for the wavelength from every image. You need to manually refine this offset for a few rounds. What you will generally see is that the graph of fitted wavelength vs the distance is a straight line, and you want to make the slope of this line to be zero. Eventually, you will arrive at some offset that gives you the smallest spread in refined wavelength values. The average refined wavelength is then the true wavelength. Should be able to get it within one or two eV. Perhaps more if you take a lot of silicon powder images. At ALS beamlines 8.3.1 and 12.3.1 I have done both kinds of calibration, and I am fairly certain I get the wavelength accurate to within 1 eV by calibrating the half-way-up point of an absorption scan of a ~122 micron thick copper metal foil to 8979.0 eV. -James Holton MAD Scientist Richard Gillilan wrote: In the past we've used elemental foils from exafsmaterials.com for energy calibration of our MAD beamline. These standards are for EXAFS and XANES. Most are thin (5 micron) metal foils. Has anyone had experience with other sources of standards or other forms (such as compounds rather than pure elements)? I notice that a number of companies offer XRF standard kits. Richard Gillilan MacCHESS
[ccp4bb] mosflm and hkl2000
We have a little internal project where we want to compare the quality of data reduced with HKL2000 and IMOSFLM (mosflm) to 1.3 A. Unfortunately, imosflm with its standard settings crashes always even at lower resolution whereas HKL2000 is rock stable. Why is that so? Any experience with that? Data collected at a synchrotron, axis set to reversephi in imosflm (newest release). Suse Linux, Swap space 2 GB. Anyway, even if (i)mosflm looses orientation, it should complain and not crash. Thanks, Marius Dr.habil. Marius Schmidt Asst. Professor University of Wisconsin-Milwaukee Department of Physics Room 454 1900 E. Kenwood Blvd. Milwaukee, WI 53211 phone: +1-414-229-4338 email: m-schm...@uwm.edu http://users.physik.tu-muenchen.de/marius/
Re: [ccp4bb] question of extra high B factor
Dear Ewa, I can model a 3 residues sugar chain in the glycosylated protein. The structure was build with an identical 2.3 A resolution structure as model. The final structure is nearly identical with its model. So I think the model is not wrong. The data was collected at 100K. During the refinement, the TLS analysis was included using the program Phenix. By analysis the structure, I found that only the 50 kD protein (the one with lower B factor of 70) contributed to the crystal packing., while the glycosylated 20 kD protein do not paticipate the crystal packing. It is only stablized by the interaction with the large one. I think this will probably explain the extra high B factor of the glycosylated 20 kD protein. Am I right? Thanks and best wishes. On Fri, Jul 31, 2009 at 12:29 AM, Skrzypczak-Jankun, Ewa ewa.skrzypczak-jan...@utoledo.edu wrote: all the errors go into B and so you can get decent R with wrong structure. Glycosylated proteins have a large component totally disordered - do you see any sugars? with B~133 you uj is 3.7A which means that atom is all over the place and meaningless As a reviewer I would certainly question the interpretation of such structure. If the data collection was at 100K (or any cryo condition) one expects B~20 for a good structure and higher only on the outskirts of the molecule exposed to solvent where you expect more flexibility and thus disorder, also in case for flexible loops. But if you have high B for something like a helice I would suspect a libration movement for the entire helice and you may refine it with partial occupancy for two positions for example. Have you done TLS analysis for your complex? Just a suggestion - TLS is worth looking at and consider including into refmac for refinement. E. Dr. Ewa Skrzypczak-Jankun Associate Professor University of Toledoe-mail: ewa.skrzypczak-jan...@utoledo.edu Health Science Campus Mail Stop#1091 http://golemxiv.dh.meduohio.edu/~ewahttp://golemxiv.dh.meduohio.edu/%7Eewa Department of UrologyDowling Hall r. 2257 3000 Arlington Ave.phone 419 383 5414 Toledo OH 43614 fax 419 383 3785 _ -- *From:* Jiamu Du [mailto:jiam...@gmail.com] *Sent:* Thu 7/30/2009 12:15 PM *To:* Skrzypczak-Jankun, Ewa *Subject:* Re: [ccp4bb] question of extra high B factor Dear Dr. Ewa, I have checked the data with Phenix. It is not a twin. I think the spacegroup is right, or else the R/Rf factor should not be so low. Best wishes. On Fri, Jul 31, 2009 at 12:05 AM, Skrzypczak-Jankun, Ewa ewa.skrzypczak-jan...@utoledo.edu wrote: have you check for twinning? or if the choice of the space group is correct? take a look at 1LOX and 2P0M in PDB - this is an excellent example of simple errors Good luck - E. Dr. Ewa Skrzypczak-Jankun Associate Professor University of Toledoe-mail: ewa.skrzypczak-jan...@utoledo.edu Health Science Campus Mail Stop#1091 http://golemxiv.dh.meduohio.edu/~ewahttp://golemxiv.dh.meduohio.edu/%7Eewa Department of UrologyDowling Hall r. 2257 3000 Arlington Ave.phone 419 383 5414 Toledo OH 43614 fax 419 383 3785 _ -- *From:* CCP4 bulletin board on behalf of Jiamu Du *Sent:* Thu 7/30/2009 12:00 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] question of extra high B factor Dear All, I am refining a structure of a complex between of 50kD protein and a 20kD glycosylated protien. The data is of 2.9 A resolution. The wilson B factor is as high as 86.3 A^2. The refinement seems well with R/Rf of 0.21/0.25. But the B-factor is extra high. For the 50kD part, the average B factor is 76.5 A^2. But the B factor of the 20 kD glycosylated protein is as high as 133.3 A^2. Although the electron density looks fine, even the sugar chain is seen clearly. My question is: 1. How to reduce the B factor to a reasonable level? 2. If it can not be redueced, when I published it, is this value acceptable? 3. In the same of similar resolutionIs, is there some other structures like this situation? A component or a subunit of the protein has a extra high B factor as high as 130. Thanks and best wishes. -- Jiamu Du, Ph.D. State Key Laboratory of Molecular Biology Institute of
Re: [ccp4bb] question of extra high B factor
Dear Vonrhein, On Fri, Jul 31, 2009 at 12:47 AM, Clemens Vonrhein vonrh...@globalphasing.com wrote: Dear Jiamu, On Fri, Jul 31, 2009 at 12:00:25AM +0800, Jiamu Du wrote: I am refining a structure of a complex between of 50kD protein and a 20kD glycosylated protien. The data is of 2.9 A resolution. The wilson B factor is as high as 86.3 A^2. The refinement seems well with R/Rf of 0.21/0.25. But the B-factor is extra high. For the 50kD part, the average B factor is 76.5 A^2. But the B factor of the 20 kD glycosylated protein is as high as 133.3 A^2. Although the electron density looks fine, even the sugar chain is seen clearly. My question is: 1. How to reduce the B factor to a reasonable level? How do you define 'reasonable'? And why would you want to reduce this anyway? ( 50*76.5 + 20*133.3 ) / 70 = 92.7 which seems fairly close to the Wilson B of 86.3, right? SO, the B value is right. 2. If it can not be redueced, when I published it, is this value acceptable? Better question: is it the right value? Remember it is results - publish and not publish - results ;-) If they're correct than they are acceptable (I would accept those values). You can accept these values. But I am not sure that you will be my reviewer certainly. Someone else can not accept. This is the key point. 3. In the same of similar resolutionIs, is there some other structures like this situation? A component or a subunit of the protein has a extra high B factor as high as 130. I'm sure hundreds of them ... but I'm sure you want your structure to stand on its own, so don't look too close at other structures and repeat the various mistakes we've all made and that are now set in stone in some old PDB file. Thanks for your comments and best wishes. This is a great sustainment for me. Cheers Clemens -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-- * BUSTER Development Group (http://www.globalphasing.com) *** -- Jiamu Du, Ph.D. State Key Laboratory of Molecular Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 320 Yue-Yang Road Shanghai 200031 P. R. China Tel: +86-21-5492-1117 E-mail: jiam...@gmail.com
Re: [ccp4bb] mosflm and hkl2000
Dear Marius, 'crash' is a very general term. Maybe you could describe at what stage imosflm crashes? Is it reproducible or does it crash at random stages? When you start imosflm from a terminal, what are the last words printed to the terminal? Are there any log-files that might give a hint as to what went wrong? Sincerely, Tim B.T.W.: I've seen cases where hkl2000 gets stuck, too... -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Fri, 31 Jul 2009, Marius Schmidt wrote: We have a little internal project where we want to compare the quality of data reduced with HKL2000 and IMOSFLM (mosflm) to 1.3 A. Unfortunately, imosflm with its standard settings crashes always even at lower resolution whereas HKL2000 is rock stable. Why is that so? Any experience with that? Data collected at a synchrotron, axis set to reversephi in imosflm (newest release). Suse Linux, Swap space 2 GB. Anyway, even if (i)mosflm looses orientation, it should complain and not crash. Thanks, Marius Dr.habil. Marius Schmidt Asst. Professor University of Wisconsin-Milwaukee Department of Physics Room 454 1900 E. Kenwood Blvd. Milwaukee, WI 53211 phone: +1-414-229-4338 email: m-schm...@uwm.edu http://users.physik.tu-muenchen.de/marius/
Re: [ccp4bb] mosflm and hkl2000
Is it the gui or mosflm itself that crashes? The new gui is dependent upon a number of external dependencies, so you are at the mercy of the stability of those. The old gui still works fine, at least last time I checked. On Thu, July 30, 2009 4:40 pm, Marius Schmidt wrote: We have a little internal project where we want to compare the quality of data reduced with HKL2000 and IMOSFLM (mosflm) to 1.3 A. Unfortunately, imosflm with its standard settings crashes always even at lower resolution whereas HKL2000 is rock stable. Why is that so? Any experience with that? Data collected at a synchrotron, axis set to reversephi in imosflm (newest release). Suse Linux, Swap space 2 GB. Anyway, even if (i)mosflm looses orientation, it should complain and not crash. Thanks, Marius Dr.habil. Marius Schmidt Asst. Professor University of Wisconsin-Milwaukee Department of Physics Room 454 1900 E. Kenwood Blvd. Milwaukee, WI 53211 phone: +1-414-229-4338 email: m-schm...@uwm.edu http://users.physik.tu-muenchen.de/marius/ William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/
Re: [ccp4bb] question of extra high B factor
Hi, all the errors go into B and so you can get decent R with wrong structure. Glycosylated proteins have a large component totally disordered - do you see any sugars? with B~133 you uj is 3.7A which means that atom is all over the place and meaningless As a reviewer I would certainly question the interpretation of such structure. If the data collection was at 100K (or any cryo condition) one expects B~20 for a good structure I wouldn't interpret it that literally. The distribution of mean B-factors computed for structures in PDB at resolutions between 2.8 and 3..2A is: Mean B-factor value Number of structures in PDB 1.000 - 21.000 : 137 21.000 - 41.000 : 430 41.000 - 61.000 : 612 61.000 - 81.000 : 390 81.000 - 101.000: 172 101.000 - 121.000: 36 121.000 - 141.000: 12 141.000 - 161.000: 8 161.000 - 181.000: 0 181.000 - 201.000: 1 There is good amount of models with mean B-factors well higher than 70. I doubt that PDB would accept a structure where atoms are all over the place -:) And I wouldn't claim that those models are all bad simply because they don't have B-factors~20. There is a number of publications that discuss this and show similar histograms, so there is no point to repeat it. So, Jiamu, *if* the high B-factors is the only issue with this part of your structure, then make sure that the domain in question is properly modeled, and keep the above histogram just in case should you run into a picky reviewer -:) Pavel. PS Same histogram as above, but computed for all models in resolution range from 3 to 4A: Mean B-factor value Number of structures in PDB 0.000 - 22.720 : 90 22.720 - 45.440 : 250 45.440 - 68.160 : 295 68.160 - 90.880 : 271 90.880 - 113.600: 131 113.600 - 136.320: 73 136.320 - 159.040: 32 159.040 - 181.760: 13 181.760 - 204.480: 8 204.480 - 227.200: 5 and finally, for high resolution models in 0.0 to 1.0A: Mean B-factor value Number of structures in PDB 1.800 - 4.190 : 3 4.190 - 6.580 : 4 6.580 - 8.970 : 18 8.970 - 11.360 : 41 11.360 - 13.750 : 50 13.750 - 16.140 : 34 16.140 - 18.530 : 9 18.530 - 20.920 : 3 20.920 - 23.310 : 3 23.310 - 25.700 : 5
