Re: [ccp4bb] self-rotation interpretation, 5 minutes
Yanming Zhang a écrit : Hi, Would some experts help me to interpretate the attached self rotation function ps graph? The cell: 84.847 84.847 172.485 P4 indexing. In perticular, I was puzzled by: 1,Does the peak (90 45 180) a crystallographic 2-fold or non-crystallographic 2-fold? 2,Why there is no crystallographic peak on the section kappa=90? Giving P4 space group, there should be some high crystallographic 4-fold peaks appear on the section. It probably takes you only 5 minutes. Your help is greatly appreciated. Yanming Deqr Yanming The north pole of the diagramm corresponds to the direction of the z axis. There is well a crystallographic 4-fold (and automatically 2- fold) peak in this direction. Then there are non-crystallographic 2-fold axes in the x,y plane, spaced by 45 degrees, as all the peaks appear to have the same height. Greetings Wim Burmeister -- *** Wim Burmeister Professeur, Membre de l'Institut Universitaire de France Unit of Virus Host Cell Interactions (UVHCI) UMR5233 UJF-EMBL-CNRS 6 rue Jules Horowitz B.P. 181, F-38042 Grenoble Cedex 9 FRANCE E-mail: [EMAIL PROTECTED] Tel:+33 (0) 476 20 72 82 Fax: +33 (0) 476 20 94 00 http://www2.ujf-grenoble.fr/pharmacie/laboratoires/gdrviro ***
Re: [ccp4bb] self-rotation interpretation, 5 minutes
Unless there is pseudo-symmetry, I would say that the self-rotation indicates that crystal point group is 422... Did the indexing program suggested something with this symmetry? Cheers, Miguel 2007/8/20, Wim Burmeister [EMAIL PROTECTED]: Yanming Zhang a écrit : Hi, Would some experts help me to interpretate the attached self rotation function ps graph? The cell: 84.847 84.847 172.485 P4 indexing. In perticular, I was puzzled by: 1,Does the peak (90 45 180) a crystallographic 2-fold or non-crystallographic 2-fold? 2,Why there is no crystallographic peak on the section kappa=90? Giving P4 space group, there should be some high crystallographic 4-fold peaks appear on the section. It probably takes you only 5 minutes. Your help is greatly appreciated. Yanming Deqr Yanming The north pole of the diagramm corresponds to the direction of the z axis. There is well a crystallographic 4-fold (and automatically 2- fold) peak in this direction. Then there are non-crystallographic 2-fold axes in the x,y plane, spaced by 45 degrees, as all the peaks appear to have the same height. Greetings Wim Burmeister -- *** Wim Burmeister Professeur, Membre de l'Institut Universitaire de France Unit of Virus Host Cell Interactions (UVHCI) UMR5233 UJF-EMBL-CNRS 6 rue Jules Horowitz B.P. 181, F-38042 Grenoble Cedex 9 FRANCE E-mail: [EMAIL PROTECTED] Tel:+33 (0) 476 20 72 82 Fax: +33 (0) 476 20 94 00 http://www2.ujf-grenoble.fr/pharmacie/laboratoires/gdrviro *** -- correo-e: [EMAIL PROTECTED] ~~~ Je suis de la mauvaise herbe, Braves gens, braves gens, Je pousse en liberté Dans les jardins mal fréquentés! Georges Brassens
Re: [ccp4bb] The importance of USING our validation tools
Dear Alex, Of course a simplified one page summary would not be the last word, but I think that it would be a big step in the right direction. For example a value of Rfree that is 'too good' because the reflection set for it has been chosen wrongly can be detected statistically (Tickle et al., Acta D56 (2000) 443-450). And it would be not be too difficult to distinguish between three possible causes of incomplete data: (a) there is a dead cone of data because it was a single scan of a low symmetry crystal, (b) a large number of 'overloads' were rejected (they would all have fairly low resolution and high Fc values) or (c) the missing reflections are fairly randomly distributed because they have been removed by hand to improve the R-values. I think that there is a very good case for making this Rinformation available to referees in an easily comprehensible form. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-2582 On Sun, 19 Aug 2007, Alexander Aleshin wrote: I do not think the small molecule approach proposed by George Sheldrick is sufficient for validation of protein structures, as misrepresentation of experimental statistics/resolution is hard to detect with it, and these factors appear to play crucial role in defining the fate of many hot structures. The bad statistics hurts publication more than mistakes in a model, and improving the experiment is often too hard. I know my structure is right. Why should I spend another year growing better crystals only to make the statistics look right? - sounds as a strong argument for a desperate researcher. Making up an artificial data set overkills the task. There are easier and less amoral ways such as rejection of outliers and incorrect assignment of the Rfree test set. Ironically, an undereducated crystallographer may not recognize wrongdoing in such data treatment, which makes it even more likely to occur. Do I sound paranoid? And please do not suggest that I have shared personal experiences. Alex Aleshin On Sat, 18 Aug 2007, George M. Sheldrick wrote: There are good reasons for preserving frames, but most of all for the crystals that appeared to diffract but did not lead to a successful structure solution, publication, and PDB deposition. Maybe in the future there will be improved data processing software (for example to integrate non-merohedral twins) that will enable good structures to be obtained from such data. At the moment most such data is thrown away. However, forcing everyone to deposit their frames each time they deposit a structure with the PDB would be a thorough nuisance and major logistic hassle. It is also a complete illusion to believe that the reviewers for Nature etc. would process or even look at frames, even if they could download them with the manuscript. For small molecules, many journals require an 'ORTEP plot' to be submitted with the paper. As older readers who have experienced Dick Harlow's 'ORTEP of the year' competition at ACA Meetings will remember, even a viewer with little experience of small-molecule crystallography can see from the ORTEP plot within seconds if something is seriously wrong, and many non-crystallographic referees for e.g. the journal Inorganic Chemistry can even make a good guess as to what is wrong (e.g wrong element assigned to an atom). It would be nice if we could find something similar for macromolecules that the author would have to submit with the paper. One immediate bonus is that the authors would look at it carefully themselves before submitting, which could lead to an improvement of the quality of structures being submitted. My suggestion is that the wwPDB might provide say a one-page diagnostic summary when they allocate each PDB ID that could be used for this purpose. A good first pass at this would be the output that the MolProbity server http://molprobity.biochem.duke.edu/ sends when is given a PDB file. It starts with a few lines of summary in which bad things are marked red and the structure is assigned to a pecentile: a percentile of 6% means that 93% of the sturcture in the PDB with a similar resolution are 'better' and 5% are 'worse'. This summary can be understood with very little crystallographic background and a similar summary can of course be produced for NMR structures. The summary is followed by diagnostics for each residue, normally if the summary looks good it would not be necessary for the editor or referee to look at the rest. Although this server was intended to help us to improve our structures rather than detect manipulated or fabricated data, I asked it for a report on 2HR0 to see what it would do (probably many other people were trying to do exactly the
Re: [ccp4bb] diffraction images images/jpeg2000
Hi, I looked at jpeg2000 as a compression for diffraction images for archiving purposes - it works well but is *SLOW*. It's designed with the idea in mind of compressing a single image, not the several hundred typical for our work. There is also no place to put the header. Bzip2 works pretty much as well and is standard, but again slow. This is what people mostly seem to use for putting diffraction images on the web, particularly the JCSG. The ccp4 pack format which has been around for a very long time works very well and is jolly quick, and is supported in a number of data processing packages natively (Mosflm, XDS). Likewise there is a new compression being used for the Pilatus detector which is quicker again. These two have the advantage of being designed for diffraction images and with speed in mind. So there are plenty of good compression schemes out there - and if you use CBF these can be supported natively in the image standard... So you don't even need to know or care... Just my 2c on this one. Cheers, Graeme -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Maneesh Yadav Sent: 18 August 2007 00:02 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] diffraction images images/jpeg2000 FWIW, I don't agree with storing image data, I don't think they justify the cost of storage even remotely (some people debate the value of the structures themselves)...but if you want to do it anyway, maybe we should use a format like jpeg2000. Last time I checked, none of the major image processing suites used it, but it is a very impressive and mature format that (I think) would be suitable for diffraction images. If anyone is up for experimenting, you can get a nice suite of tools from kakadu (just google kakdu + jpeg2000).
Re: [ccp4bb] The importance of USING our validation tools
I worry a bit about some of this discussion, in that I wouldn't like the free-R-factor police to get too powerful. I imagine that many of us have struggled with datasets which are sub-optimal for all sorts of reasons (all crystals are multiple/split/twinned; substantial disordered regions; low resolution, etc) - and it is not possible to get better data. I have certainly fought hard to get free-R below (the magic) 30%, when I know the structure is _essentially_ right, but the details are a little blurred in places, even when I have done the best I can. Anyway the important things are not the statistics, but the maps. Does this make the structure unpublishable? No, provided that we remember a basic tenet of science, that the conclusions drawn should be supported by the evidence available. With limited data, the conclusions may be more limited, but still often illuminate the biology, which is the reason for solving the structure in the first place. The evidence should be available to readers referees, so deposition at least structure factors should be compulsory (why isn't it already?). Unmerged data or images would be nice, but I doubt that many people would use them (great for developers though) Phil On 20 Aug 2007, at 08:24, George M. Sheldrick wrote: Dear Alex, Of course a simplified one page summary would not be the last word, but I think that it would be a big step in the right direction. For example a value of Rfree that is 'too good' because the reflection set for it has been chosen wrongly can be detected statistically (Tickle et al., Acta D56 (2000) 443-450). And it would be not be too difficult to distinguish between three possible causes of incomplete data: (a) there is a dead cone of data because it was a single scan of a low symmetry crystal, (b) a large number of 'overloads' were rejected (they would all have fairly low resolution and high Fc values) or (c) the missing reflections are fairly randomly distributed because they have been removed by hand to improve the R-values. I think that there is a very good case for making this Rinformation available to referees in an easily comprehensible form. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-2582 On Sun, 19 Aug 2007, Alexander Aleshin wrote: I do not think the small molecule approach proposed by George Sheldrick is sufficient for validation of protein structures, as misrepresentation of experimental statistics/resolution is hard to detect with it, and these factors appear to play crucial role in defining the fate of many hot structures. The bad statistics hurts publication more than mistakes in a model, and improving the experiment is often too hard. I know my structure is right. Why should I spend another year growing better crystals only to make the statistics look right? - sounds as a strong argument for a desperate researcher. Making up an artificial data set overkills the task. There are easier and less amoral ways such as rejection of outliers and incorrect assignment of the Rfree test set. Ironically, an undereducated crystallographer may not recognize wrongdoing in such data treatment, which makes it even more likely to occur. Do I sound paranoid? And please do not suggest that I have shared personal experiences. Alex Aleshin On Sat, 18 Aug 2007, George M. Sheldrick wrote: There are good reasons for preserving frames, but most of all for the crystals that appeared to diffract but did not lead to a successful structure solution, publication, and PDB deposition. Maybe in the future there will be improved data processing software (for example to integrate non-merohedral twins) that will enable good structures to be obtained from such data. At the moment most such data is thrown away. However, forcing everyone to deposit their frames each time they deposit a structure with the PDB would be a thorough nuisance and major logistic hassle. It is also a complete illusion to believe that the reviewers for Nature etc. would process or even look at frames, even if they could download them with the manuscript. For small molecules, many journals require an 'ORTEP plot' to be submitted with the paper. As older readers who have experienced Dick Harlow's 'ORTEP of the year' competition at ACA Meetings will remember, even a viewer with little experience of small-molecule crystallography can see from the ORTEP plot within seconds if something is seriously wrong, and many non-crystallographic referees for e.g. the journal Inorganic Chemistry can even make a good guess as to what is wrong (e.g wrong element assigned to an atom). It would be nice if we could find something similar for macromolecules that the author would have to submit with the paper. One immediate bonus is that the authors
Re: [ccp4bb] Posting again: Is the H-bond length in CYS.cif library correct?
I think Garib or Alexei must answer this and they are both on holiday till the end of August Eleanor juergen J. Mueller wrote: Dear all, using refmac5 to provide H-atoms for a known protein structure the distance between CYS-CG and HG is defined to 1.34 Ang. in CYS.cif. This distance has been critisiced by a non-CCP4 program by * Poor covalent bond length of 1.33954 for hydrogen atom HG. In an other library-file CSH.cif the same distance is defined to 1.1 Ang. WHATIF uses 1.0 Ang. What is the most correct one? Could the CCP4-people comment on this? (Of course I know hydrogens will not be refined but they are neccessary for some modeling programs). Thank you, Juergen
[ccp4bb] AW: [ccp4bb] Posting again: Is the H-bond length in CYS.cif library correct?
Dear Juergen, I did a quick check in the CSD and found SG-H bondlengths between 0.587 and 1.338 Ang. for various cysteine derivatives. The most common values where around 1.33 Ang. but the average may be around 1.1 or 1.2 Ang. I did not work out any statistics. It seems that the SG-H distance is either experimentally not very well defined (there were quite a few entries with this hydrogen missing) or it might be very sensitive to e.g. (ionization). I hope this helps. Best regards, Herman -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:[EMAIL PROTECTED] Im Auftrag von Juergen J. Mueller Gesendet: Montag, 20. August 2007 15:31 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Posting again: Is the H-bond length in CYS.cif library correct? Dear all, using refmac5 to provide H-atoms for a known protein structure the distance between CYS-CG and HG is defined to 1.34 Ang. in CYS.cif. This distance has been critisiced by a non-CCP4 program by * Poor covalent bond length of 1.33954 for hydrogen atom HG. In an other library-file CSH.cif the same distance is defined to 1.1 Ang. WHATIF uses 1.0 Ang. What is the most correct one? Could the CCP4-people comment on this? (Of course I know hydrogens will not be refined but they are neccessary for some modeling programs). Thank you, Juergen
Re: [ccp4bb] Posting again: Is the H-bond length in CYS.cif library correct?
For what it is worth, SHELXL sets the S-H distance to 1.20A. As with other bonds to hydrogen, this allows for apparent shortening to fit the electron distribution and also librational effects. An S-H distance determined by neutron diffraction would be longer. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-2582 On Mon, 20 Aug 2007, Juergen J. Mueller wrote: Dear all, using refmac5 to provide H-atoms for a known protein structure the distance between CYS-CG and HG is defined to 1.34 Ang. in CYS.cif. This distance has been critisiced by a non-CCP4 program by * Poor covalent bond length of 1.33954 for hydrogen atom HG. In an other library-file CSH.cif the same distance is defined to 1.1 Ang. WHATIF uses 1.0 Ang. What is the most correct one? Could the CCP4-people comment on this? (Of course I know hydrogens will not be refined but they are neccessary for some modeling programs). Thank you, Juergen
Re: [ccp4bb] self-rotation interpretation, 5 minutes
I'd rather agree with Miguel. You certainly have evidence telling your 4-fold is crystallographic (indexing, cell, ), and you do see it on your k=90 section (of course also on your 180). You need to check your k=180 peak heights to compare with the 4-fold axis: they seem to be so perfectly at 90deg to the 4-fold (and apparently strong enough...), really suggesting a 422 point group. They could of course be the result of a 2-fold NCS, accidentally at 90deg of the single 4-fold , but then they should show a significantly lower height wrt the xtallographic axis; how many mols/ASU are you expecting? (if the heights are equivalent, you shouldn't automatically rule out a twinning phenomenon in this PG (twinning law would be kh-l): look at intensity distribution statistics (CCP4 TRUNCATE gives you several), at regular solvent fractions they are usually quite revealing...) hth ale Miguel Ortiz-Lombardía wrote: Unless there is pseudo-symmetry, I would say that the self-rotation indicates that crystal point group is 422... Did the indexing program suggested something with this symmetry? Cheers, Miguel 2007/8/20, Wim Burmeister [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]: Yanming Zhang a écrit : Hi, Would some experts help me to interpretate the attached self rotation function ps graph? The cell: 84.847 84.847 172.485 P4 indexing. In perticular, I was puzzled by: 1,Does the peak (90 45 180) a crystallographic 2-fold or non-crystallographic 2-fold? 2,Why there is no crystallographic peak on the section kappa=90? Giving P4 space group, there should be some high crystallographic 4-fold peaks appear on the section. It probably takes you only 5 minutes. Your help is greatly appreciated. Yanming Deqr Yanming The north pole of the diagramm corresponds to the direction of the z axis. There is well a crystallographic 4-fold (and automatically 2- fold) peak in this direction. Then there are non-crystallographic 2-fold axes in the x,y plane, spaced by 45 degrees, as all the peaks appear to have the same height. Greetings Wim Burmeister -- *** Wim Burmeister Professeur, Membre de l'Institut Universitaire de France Unit of Virus Host Cell Interactions (UVHCI) UMR5233 UJF-EMBL-CNRS 6 rue Jules Horowitz B.P. 181, F-38042 Grenoble Cedex 9 FRANCE E-mail: [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] Tel:+33 (0) 476 20 72 82 Fax: +33 (0) 476 20 94 00 http://www2.ujf-grenoble.fr/pharmacie/laboratoires/gdrviro *** -- correo-e: [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] ~~~ Je suis de la mauvaise herbe, Braves gens, braves gens, Je pousse en liberté Dans les jardins mal fréquentés! Georges Brassens -- Alejandro Buschiazzo, PhD Research Scientist Laboratory of Structural Biology Pasteur Institute of Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +5982 5220910 int. 120 Fax: +5982 5220910 int. 111
[ccp4bb] Scientist or Senior Scientist position available in Plexxikon Inc.
Department: Structural Biology Location: Berkeley, California URL: www.plexxikon.com Start Date: ASAP Duration: Perminant Description: Located in Berkeley, California, Plexxikon is a leader in the discovery and development of novel small molecule pharmaceuticals to treat human disease. Since operations commenced June 2001, Plexxikon has applied its proprietary platform technology to identify and build a portfolio of product opportunities for therapeutic indications in metabolic disorders, cardiovascular disease, inflammation and oncology. We are seeking a highly motivated and experienced X-ray protein crystallographer in our Structural Biology Department at the level of Scientist or Senior Scientist depending on qualifications. The successful candidate will participate in our scaffold-based drug discovery effort on many exciting therapeutic targets by carrying out high throughput co-crystal structure determination, co-crystallization and synchrotron data collection. The incumbent will also participate in specific drug target project teams and collaborate closely with scientists from Molecular Biology, Protein Chemistry, Assay Development, Informatics and Chemistry in shaping the direction of our drug discovery effort. This position requires a PhD and, for Sr. Scientist, a minimum of five years of industry experience in drug discovery. Postdoctoral research experience in related areas will be considered, however preference will be given to candidates with relevant industrial experience. Qualified candidates must possess excellent communication skills and the ability to work in a highly collaborative and team oriented environment. The ideal candidate will have a track record of accomplishments demonstrating technical proficiency, independent thinking, and scientific creativity. Extensive experience with high throughput co-crystal structure determination and high throughput co-crystallization are required. Experience with script writing and programming that facilitates automatic crystallographic structure determination and related tasks would be a plus. If you are interested in applying for this opportunity, please submit your resume or CV, a cover letter and salary requirements to the address below. All submissions will be evaluated and interviews will be conducted for those applicants who most strongly fit our needs. If you are not contacted for an interview, your resume will remain on file and active for available positions for a period of one year. Other details: Plexxikon is an equal opportunity employer. Please submit: CV, 3 references Person to contact: Human Resources Surface mail address: Plexxikon Inc., 91 Bolivar Dr., Berkeley, CA 94710, USA. Email address: [EMAIL PROTECTED] Phone number: (510)647-4000 Fax number: (510)647-4090 Job Posted: 08/20/07 Job ID Number: 1179788911
Re: [ccp4bb] Release of Mosflm version 7.0.1 iMosflm 0.5.3
Hi folks a sharp-eyed user has noticed a bug in the Windows version of iMosflm 0.5.3; this does not affect any other version. If you have already downloaded the Windows version, you should replace the file imosflm.tcl in the top-level imosflm folder with this file - http://www.mrc-lmb.cam.ac.uk/harry/imosflm/downloads/imosflm.tcl NOTE that this is _not_ the file of the same name in the src folder. I've fixed this in the imosflm.zip file so any further downloads will not display this bug. Sorry about this! Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 2QH
[ccp4bb] water water everywhere
While we're still on the subject of good model-building habits and reviewing pitfalls, I've been shocked to download a couple of structures recently that seem to have solvent channels chock full of allegedly ordered water (many layers deep, and not exactly at 0.5A resolution). To any new students out there: making Rfree go down a bit by putting a water in every unexplained blob is NOT the same as building a good model! I'm afraid I reviewed one of these (sans coordinates) ... so sorry to the community ... it wasn't obvious from table 1. Phoebe --- Phoebe A. Rice Assoc. Prof., Dept. of Biochemistry Molecular Biology The University of Chicago phone 773 834 1723 fax 773 702 0439 http://bmb.bsd.uchicago.edu/index.html http://www.nasa.gov/mission_pages/cassini/multimedia/pia06064.html
Re: [ccp4bb] water water everywhere
I've often wondered whether it would be more fair to report R-factors with and without waters, since waters can be used to beautify statistics. I also think providing pdb coordinates and Fobs with experimental phases as supplementary information in a standard format to be supplied automatically to all the reviewers should be required by the journals. I actually tried to force Cell to do this in 2006, or at least provide a link to our password-protected website, but they balked. I did manage to sneak in a pymol saved session with the MAD and composite omit maps, and at least one of the referees thanked us for that. [EMAIL PROTECTED] wrote: While we're still on the subject of good model-building habits and reviewing pitfalls, I've been shocked to download a couple of structures recently that seem to have solvent channels chock full of allegedly ordered water (many layers deep, and not exactly at 0.5A resolution). To any new students out there: making Rfree go down a bit by putting a water in every unexplained blob is NOT the same as building a good model! I'm afraid I reviewed one of these (sans coordinates) ... so sorry to the community ... it wasn't obvious from table 1. Phoebe --- Phoebe A. Rice Assoc. Prof., Dept. of Biochemistry Molecular Biology The University of Chicago phone 773 834 1723 fax 773 702 0439 http://bmb.bsd.uchicago.edu/index.html http://www.nasa.gov/mission_pages/cassini/multimedia/pia06064.html
