Re: [ccp4bb] examples of applied struct bio?
Dear Frank, I would only add to Randy's excellent suggestions a commendation of Max Perutz's book Is Science necessary http://www.amazon.com/Is-Science-Necessary-Essays-Scientists/dp/0192861182 It includes global longevity and food production issues and improvements. Of course these are wider contexts than structural biology, but marshalled by Max Perutz himself. Greetings, John Prof John R Helliwell DSc On 16 Sep 2013, at 14:23, Frank von Delft frank.vonde...@sgc.ox.ac.uk wrote: Hello, I need stuff for a lecture, so I figured I'd best crowd-source it from the best forum on the intertubes: Anybody know some examples of where structural biology threw up insight(s) that led to very significant practical improvements in some public health approach or industrial process or other non-research application -- ideally in the context of a developing nation/economy/society. If they made someone rich, even better. Of particular interest are examples about: communicable diseases: not only the big ones (TB, HIV, malaria), but also immunization, livestock, etc. food security: better diet, food shelf life, crop yields, etc. green energy: [preferably excluding so-called biofuels, but I won't be picky] water reclamation: purification, sewage treatment, etc. Specifically NOT of interest is structure-guided medicinal chemistry. (I have some examples, but presumably there are better ones.) Any scraps of info welcome: journal reference, name of researcher/group, URL, news release, etc. [Links to actual slides would be an unexpected bonus.] Thanks! phx
[ccp4bb] 3D graphics linux compatibility question
Dear BB, We are still a bit confused about compatibility of graphics cards with 3D Coot/PyMol in Linux: (a) In previous CCP4bb discussions, it was stated that only Quadro cards are compatible with Linux setups. But could someone tell me what the minimum standard really is: is it Quadro FX380, 2000, 3800 or something else ? The nVidia site lists Quadro 3700 and 3800 as the two lowest (cheapest) options compatible with Linux 3D. However, different CCP4ers have in the past mentioned the other two options as working perfectly or with little trouble. (b) If a monitor such as the ASUS VG278H , which has an in-built nVidia 3D vision emitter which takes its stereo synch from a DVI cable is used, can we even use the simpler GeForce GTX670 or 680 ? As you might imagine, we are on a rather tight budget. Any info would be greatly appreciated! Emmanuel Saridakis N.C.S.R. DEMOKRITOS Athens 15 310 Greece esari...@chem.demokritos.gr tel. +30-210-6503793
Re: [ccp4bb] 3D graphics linux compatibility question
(a) In previous CCP4bb discussions, it was stated that only Quadro cards are compatible with Linux setups. But could someone tell me what the minimum standard really is: is it Quadro FX380, 2000, 3800 or something else ? The nVidia site lists Quadro 3700 and 3800 as the two lowest (cheapest) options compatible with Linux 3D. However, different CCP4ers have in the past mentioned the other two options as working perfectly or with little trouble. Use the 3700 with the external nvidia emitters (these require the 3 pin mini din connection from the emitter into the video card) and 120Hz LCD's that don't have built-in nvidia emitters. (b) If a monitor such as the ASUS VG278Hhttp://www.asus.com/Monitors_Projectors/VG278H/#overview , which has an in-built nVidia 3D vision emitter which takes its stereo synch from a DVI cable is used, can we even use the simpler GeForce GTX670 or 680 ? No, I've tried this with a GTX680. You cannot use a GeForce in Linux with monitors such as the Asus VG278H with built in nvidia emitters and the official nvidia drivers to get 3D. You have to have a quadro card with a G8x GPU or better. In this case the cheapest card that would work is the Quadro FX 370 (not a typo, this is a different card from the 3700). We use a Quadro 600 or K600 with our Asus VG278H to get 3D. As you might imagine, we are on a rather tight budget. Any info would be greatly appreciated! which require the 3 pin mini din port on the video card. The VG278H is not a cheap monitor. You may be able to get nvidia 3d vision kit (make sure the model # comes with the 2.5mm vesa to 3 pin mini din cable since some don't, esp. the ones bundled with 120Hz monitors) + quadro 3700 + regular 120Hz monitor for slightly less than the price of the VG278H + quadro.
Re: [ccp4bb] What kind of reflection data to deposit to PDB
Sorry to contradict, But the mmCIF data model certainly does not seem to require hkl unique within the reflection data. Like CIF the mmCIF formalism has been developed to allow a complete description of a diffraction experiment and the data arising from it. There is a full description at http://mmcif.pdb.org/dictionaries/mmcif_pdbx_v40.dic/Categories/diffrn_refln.html (I am grateful to Rachel Kramer Green at the RCSB for pointing out these links to the dictionary and the papers describing its development). Having chosen mmCIF for the archive and then not using its flexibility seems a bit like having your cake and NOT eating it. It is strange to hear on a discussion board that recently considered the advantages of depositing complete image data, that a case will have to be made for allowing the deposition of full unmerged datasets. ++Martyn On 16/09/2013 14:03, Gerard DVD Kleywegt wrote: Dear all, At present, unmerged data cannot be handled properly as part of a PDB deposition. One reason for this is that changes to the mmCIF/PDBx data model will be required (at the moment, hkl must be unique within the reflection data, which is logical for merged data but precludes handling of unmerged data). There are other (easier to resolve) issues to work out, e.g. having to do with file naming and distribution via the wwPDB ftp archive. The wwPDB partners are presently focusing all efforts on rolling out the new joint deposition and annotation system. Once this system is reasonably stable we will look into accepting/validating/distributing new kinds of data. This concerns not only unmerged Is for X-ray but also unassigned NOE peak lists for NMR. We will seek the advice of the corresponding wwPDB VTFs (Validation Task Forces) to help define the data items that need to be captured, how the data should be processed by wwPDB, and what kind(s) of validation is/are required. --Gerard --- Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK ger...@ebi.ac.uk . pdbe.org Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk On Thu, 5 Sep 2013, Raji Edayathumangalam wrote: Hi Folks, Sorry for the non-ccp4 post. I am trying to determine what is the best form of unmerged reflection data to deposit to the PDB. I have single wavelength anomalous data for my structure and I have two flavors of scaled files from the same exact set of diffraction images: (1) data indexed and scaled in p1, and (2) data indexed in p222, scaled in Scalepack using the no merge original index option and converted to .mtz since the unit cell in the header of the output .sca file was missing. The space group for the dataset is p212121. Please could you let me know what might be the best approach. Many thanks and cheers, Raji -- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and Women's Hospital Visiting Research Scholar, Brandeis University Best wishes, --Gerard ** Gerard J. Kleywegt http://xray.bmc.uu.se/gerard mailto:ger...@xray.bmc.uu.se ** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. ** Little known gastromathematical curiosity: let z be the radius and a the thickness of a pizza. Then the volume of that pizza is equal to pi*z*z*a ! **
Re: [ccp4bb] 3D graphics linux compatibility question
Hi Emmanuel Here we have tried the nvidia Quadro 2000 with two different monitors (both with the built-in IR emitter, thus with synching through DVI): ASUS VG278HR and BenQ XL2420TX. The setup works perfectly well in Linux, both pymol and coot work without issues. Unfortunately we have no experience with other nvidia cards, so can't comment on that. Hope it helps Jose --- Jose Duarte Laboratory of Biomolecular Research Paul Scherrer Institute 5232 Villigen PSI Switzerland On 09/17/2013 12:09 PM, Emmanuel Saridakis wrote: Dear BB, We are still a bit confused about compatibility of graphics cards with 3D Coot/PyMol in Linux: (a) In previous CCP4bb discussions, it was stated that only Quadro cards are compatible with Linux setups. But could someone tell me what the minimum standard really is: is it Quadro FX380, 2000, 3800 or something else ? The nVidia site lists Quadro 3700 and 3800 as the two lowest (cheapest) options compatible with Linux 3D. However, different CCP4ers have in the past mentioned the other two options as working perfectly or with little trouble. (b) If a monitor such as the ASUS VG278H http://www.asus.com/Monitors_Projectors/VG278H/#overview , which has an in-built nVidia 3D vision emitter which takes its stereo synch from a DVI cable is used, can we even use the simpler GeForce GTX670 or 680 ? As you might imagine, we are on a rather tight budget. Any info would be greatly appreciated! Emmanuel Saridakis N.C.S.R. DEMOKRITOS Athens 15 310 Greece esari...@chem.demokritos.gr mailto:esari...@chem.demokritos.gr tel. +30-210-6503793
Re: [ccp4bb] What kind of reflection data to deposit to PDB
Hi Martyn, I too was puzzled by the statement that unmerged data cannot be handled properly as part of a PDB deposition. We have deposited the unmerged original index intensities for the refinement wavelength (and for additional wavelengths used for phasing in the case of MAD) since 2005. This was based on recommendation #2 from the Report of Task Force on Numerical Criteria in Structural Genomics from the 2001 Airlie meeting (2nd Intl. Struct. Genomics Mtg.). http://www.nigms.nih.gov/NR/rdonlyres/14937E88-B916-4503-A29E-FA11E4B3D445/0/numerical.doc http://www.isgo.org/organization/members07/010410.html Which states that For X-ray data, unmerged integrated intensities (omitting outliers but including systematically-absent axial reflections) should be deposited along with the final, merged intensities and amplitudes for all wavelengths and/or derivatives. We worked the RCSB staff to refine the format of the mmCIF formatted reflection containing multiple data loops for our depositions and this has been used for more than 1300 JCSG depositions and the data is retrievable from all wwPDB partner sites. Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Martyn Symmons Sent: Tuesday, September 17, 2013 3:44 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] What kind of reflection data to deposit to PDB Sorry to contradict, But the mmCIF data model certainly does not seem to require hkl unique within the reflection data. Like CIF the mmCIF formalism has been developed to allow a complete description of a diffraction experiment and the data arising from it. There is a full description at http://mmcif.pdb.org/dictionaries/mmcif_pdbx_v40.dic/Categories/diffrn_refln.html (I am grateful to Rachel Kramer Green at the RCSB for pointing out these links to the dictionary and the papers describing its development). Having chosen mmCIF for the archive and then not using its flexibility seems a bit like having your cake and NOT eating it. It is strange to hear on a discussion board that recently considered the advantages of depositing complete image data, that a case will have to be made for allowing the deposition of full unmerged datasets. ++Martyn On 16/09/2013 14:03, Gerard DVD Kleywegt wrote: Dear all, At present, unmerged data cannot be handled properly as part of a PDB deposition. One reason for this is that changes to the mmCIF/PDBx data model will be required (at the moment, hkl must be unique within the reflection data, which is logical for merged data but precludes handling of unmerged data). There are other (easier to resolve) issues to work out, e.g. having to do with file naming and distribution via the wwPDB ftp archive. The wwPDB partners are presently focusing all efforts on rolling out the new joint deposition and annotation system. Once this system is reasonably stable we will look into accepting/validating/distributing new kinds of data. This concerns not only unmerged Is for X-ray but also unassigned NOE peak lists for NMR. We will seek the advice of the corresponding wwPDB VTFs (Validation Task Forces) to help define the data items that need to be captured, how the data should be processed by wwPDB, and what kind(s) of validation is/are required. --Gerard --- Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK ger...@ebi.ac.uk . pdbe.org Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk On Thu, 5 Sep 2013, Raji Edayathumangalam wrote: Hi Folks, Sorry for the non-ccp4 post. I am trying to determine what is the best form of unmerged reflection data to deposit to the PDB. I have single wavelength anomalous data for my structure and I have two flavors of scaled files from the same exact set of diffraction images: (1) data indexed and scaled in p1, and (2) data indexed in p222, scaled in Scalepack using the no merge original index option and converted to .mtz since the unit cell in the header of the output .sca file was missing. The space group for the dataset is p212121. Please could you let me know what might be the best approach. Many thanks and cheers, Raji -- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and Women's Hospital Visiting Research Scholar, Brandeis University Best wishes, --Gerard ** Gerard J. Kleywegt http://xray.bmc.uu.se/gerard mailto:ger...@xray.bmc.uu.se ** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. ** Little known gastromathematical curiosity: let z be the radius and a the thickness of a pizza. Then the volume
Re: [ccp4bb] What kind of reflection data to deposit to PDB
Hi all, Sorry for contributing to the noise as well as the signal in the discussion. To clarify: It is not an issue of not having a place to put the data as we certainly have definitions for this and for intermediate phasing data sets. You cannot simply put the data into the current REFLN category which is where we presently collect reflection data. At present, there is no official wwPDB policy in place describing how this data is to be processed, validated and distributed. Stuffing it into the structure factor files, as has been done informally by some depositors, is not a good long term solution as there is no way for people to easily find the information. What we'll likely end up doing is store these data in separate files (just like for NMR the raw NOE peak lists and distance restraints are likely to be archived and distributed as separate files). As I tried to explain yesterday, the case for both unmerged Is and unassigned NOE peak lists has been made, and this will get implemented. It will just take a bit of time. --Gerard --- Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK ger...@ebi.ac.uk . pdbe.org Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk On Tue, 17 Sep 2013, Miller, Mitchell D. wrote: Hi Martyn, I too was puzzled by the statement that unmerged data cannot be handled properly as part of a PDB deposition. We have deposited the unmerged original index intensities for the refinement wavelength (and for additional wavelengths used for phasing in the case of MAD) since 2005. This was based on recommendation #2 from the Report of Task Force on Numerical Criteria in Structural Genomics from the 2001 Airlie meeting (2nd Intl. Struct. Genomics Mtg.). http://www.nigms.nih.gov/NR/rdonlyres/14937E88-B916-4503-A29E-FA11E4B3D445/0/numerical.doc http://www.isgo.org/organization/members07/010410.html Which states that For X-ray data, unmerged integrated intensities (omitting outliers but including systematically-absent axial reflections) should be deposited along with the final, merged intensities and amplitudes for all wavelengths and/or derivatives. We worked the RCSB staff to refine the format of the mmCIF formatted reflection containing multiple data loops for our depositions and this has been used for more than 1300 JCSG depositions and the data is retrievable from all wwPDB partner sites. Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Martyn Symmons Sent: Tuesday, September 17, 2013 3:44 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] What kind of reflection data to deposit to PDB Sorry to contradict, But the mmCIF data model certainly does not seem to require hkl unique within the reflection data. Like CIF the mmCIF formalism has been developed to allow a complete description of a diffraction experiment and the data arising from it. There is a full description at http://mmcif.pdb.org/dictionaries/mmcif_pdbx_v40.dic/Categories/diffrn_refln.html (I am grateful to Rachel Kramer Green at the RCSB for pointing out these links to the dictionary and the papers describing its development). Having chosen mmCIF for the archive and then not using its flexibility seems a bit like having your cake and NOT eating it. It is strange to hear on a discussion board that recently considered the advantages of depositing complete image data, that a case will have to be made for allowing the deposition of full unmerged datasets. ++Martyn On 16/09/2013 14:03, Gerard DVD Kleywegt wrote: Dear all, At present, unmerged data cannot be handled properly as part of a PDB deposition. One reason for this is that changes to the mmCIF/PDBx data model will be required (at the moment, hkl must be unique within the reflection data, which is logical for merged data but precludes handling of unmerged data). There are other (easier to resolve) issues to work out, e.g. having to do with file naming and distribution via the wwPDB ftp archive. The wwPDB partners are presently focusing all efforts on rolling out the new joint deposition and annotation system. Once this system is reasonably stable we will look into accepting/validating/distributing new kinds of data. This concerns not only unmerged Is for X-ray but also unassigned NOE peak lists for NMR. We will seek the advice of the corresponding wwPDB VTFs (Validation Task Forces) to help define the data items that need to be captured, how the data should be processed by wwPDB, and what kind(s) of validation is/are required. --Gerard --- Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK ger...@ebi.ac.uk . pdbe.org Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk On Thu, 5 Sep 2013, Raji Edayathumangalam wrote: Hi Folks, Sorry for the non-ccp4 post. I am trying to determine what is the best form of unmerged reflection data to deposit to the PDB. I have single wavelength anomalous data for my structure and I have two flavors of
[ccp4bb] Code to handle the syntax of (mm)CIF data correctly.
Dear all, At Global Phasing, we have seen that there are still issues with the way that different applications deal with mmCIF-format data, and this continues to cause problems for users. I believe that part of the reason for this is that the underlying syntax (the STAR format) is not universally understood, and that a common and complete understanding of the full STAR syntax amongst programmers who deal with the format will help with some of the existing problems. I wrote some code for low-level handling of the STAR format a while ago that I have been meaning to release for over a year. Garry Battle's announcement on 23 August about the mmCIF/PDBx workshop at the EBI has prompted me into action: I have written a short article that discusses some examples of the issues that we have encountered, and made my code available for download. The references in the article are given primarily as web links: more conventional citations can usually be found in the pages that I link to. This code has not been used in any released products, but it has had some internal use at Global Phasing. There is an MX bias in the article's discussion, but the issues are not restricted to MX. As I explain in the article, the handling of the input data is based on an enourmous regular expression that matches STAR data, with only a little logic in the code itself. The regular expression should be usable with a variety of other languages, not only in Java (which I have used in this case). The code, or the regular expression on its own, may be freely used in other projects: see the included licencing for details, but basically you should: (i) give credit for using it, and (ii) if you choose to modify the regular expression, state that you have done so in that credit. The article, which contains links to a tar file containing the code, and the documentation, is here: http://www.globalphasing.com/startools/ Hoping that others will find this useful and/or help to resolve or clarify outstanding questions, Peter. -- Peter Keller Tel.: +44 (0)1223 353033 Global Phasing Ltd., Fax.: +44 (0)1223 366889 Sheraton House, Castle Park, Cambridge CB3 0AX United Kingdom
[ccp4bb] Postdoctoral Fellow Position Available
Postdoctoral Fellow Position in Biochemistry/Structural Biology The research group of Demet Arac-Ozkan, Ph.D. at the University of Chicago is seeking a postdoctoral fellow with expertise in protein biochemistry. The laboratory is housed in the Department of Biochemistry and Molecular Biology. The overarching goal of our group is to understand the structure/function relationship of cell surface proteins involved in cellular adhesion at the central nervous system. We are particularly interested in understanding the mechanism by which adhesion-type G-protein coupled receptors function in the brain. Postdoctoral fellows will have the opportunity to learn the newest methods in biochemistry and biophysics, in addition to complementary functional methods. We use various approaches, including X-ray crystallography, molecular biology, protein biochemistry, and eukaryotic cell-based studies. For more information, please refer to the lab website: arac.uchicago.edu Candidates must have a Ph.D. degree and a strong background in molecular biology and protein expression/purification. Those with experience in x-ray crystallography and baculovirus expression are preferred. Interested individuals must submit a CV including contact information for three references and a cover letter as a single pdf file to: arac at uchicago dot edu Demet Arac-Ozkan
Re: [ccp4bb] weekend puzzle
Thanks to all who engaged with my little puzzle. The weekend is over and I'm not exactly closer to fitting the right pieces into the density. Benzamidine was a good suggestion for the first bit of density. However, I didn't use that inhibitor during purification. The second set of blobs doesn't sit on a twofold. It might just remain undefined. Thanks anyway for all replies. Andreas On 13/09/13 17:50, Andreas Förster wrote: Dear all, a structure I'm refining is enjoying a free R factor of 18 but still suffers from mystery density that nothing in the crystallization condition could explain. I can't explain it either. Maybe you like to venture some guesses? The missing ligand is derivatized benzoic acid, nitrobenzene or benzamide. I didn't find anything obvious in the PDB. Any suggestions? http://www.msf.bio.ic.ac.uk/images/puzzle/puzzle1.png The second ligand is a longer shot, two blobs connected by a substantial bridge. The two views are slightly rotated, and a bit of peptide is shown to give an idea of the size. http://www.msf.bio.ic.ac.uk/images/puzzle/puzzle2.png http://www.msf.bio.ic.ac.uk/images/puzzle/puzzle3.png Happy guessing! -- Andreas Förster Crystallization and Xray Facility Manager Centre for Structural Biology Imperial College London
