[ccp4bb] Pisa application
Dear ccp4ers I just wonder whether anybody knows if the PISA software could be used/modified to detect potential interfaces of interaction of different proteins? This would be very useful as a tool to validate protein-protein interactions detected by in vivo methods such as yeast 2 hybrid screens. If PISA is not quite there yet, does anyone know of other software that could do a similar thing? Best Careina
Re: [ccp4bb] Process multiple data sets
Before any further attempts you must check that the crystals have the same unit cell volume. I usually do this using matthewscoeff from the GUI ( By the way why isn't the volume automatically written into the mtz header asap!!!) If the cell volumes differ by as much as 5% no reindexing or any other trick will be able to get those data sets to scale together. However if the cell volumes are similar then you may well be able to get a different indexing scheme which will match them. pointless will try to do this, or if all else fails you can run the old MR program almn, with two data sets as input and it will suggest how they mitt be related.. Eleanor PS Phil is too despondent about output from scale pack into aimless. (use the scale pack option NOMERGE to get an unmerged but scaled set of intensities.) SCALEPACK will already have done the internal scaling so you only need aimless to get scales between the different passes. Eleanor On 2 Aug 2012, at 15:53, Uma Ratu wrote: Hi, Micheal: Thank you for your comments. I am getting to know where is the problem. Sorry that I did not give the information of my datasets in details. Here are the answears of the some of the concerns: 1) putative space group? P2 or P21. 2) observed resolution 50 - 1.5 A 3) how big was the crystal and what was its shape? Was the crystal split? Crystals is abot 100 um x 20 um x 20 um. Thesy are thin rods. The crystal is not split. 4) were the data sets taken at different points on the crystal? Is radiation damage a factor? The data sets were taken at different points on the crystal. Radiation damage is not a facotr. 5) did you just rotate around phi (or omega) to collect the different data sets or did you change the other angular settings? Collections were taken at one direction along the long side of the crystal, at diffrent spots. 6) are all your data sets indexed in exactly the same way Yes, each can be index and intergrate individually without any probelm using HKL. But I can not combine them togehter using just one standard. I notice that the cell deminsions are diffrent from these sets. As you and other suggested, non-uniformity in a large crystal may be the cause. I will try to use other program as suggested by many of you. Thank you very much for all your inputs Uma On Thu, Aug 2, 2012 at 9:04 AM, R. M. Garavito rmgarav...@gmail.com wrote: Uma, Before this discussion goes much further, you need to provide more details: 1) putative space group? 2) observed resolution and diffraction anisotropy? 3) how big was the crystal and what was its shape? Was the crystal split? 4) were the data sets taken at different points on the crystal? Is radiation damage a factor? 5) did you just rotate around phi (or omega) to collect the different data sets or did you change the other angular settings? 6) are all your data sets indexed in exactly the same way (a tricky and non-obvious factor for a novice to appreciate). Using pointless on unmerged data sets helps with this. You have a number of unknowns here, and your problem in merging the data sets may be due to radiation damage, non-uniformity in a large crystal, index refinement problems due to diffraction anisotropy, etc. We routinely merge different data sets from a single crystal, which has been translated and rotated about one axis only. We try to index and process the data sets using a common setting matrix (which is easy with XDS). However, sometimes it just does work, but merging pairs of data sets often allowed us to discard the worst offender(s). Good luck, Michael R. Michael Garavito, Ph.D. Professor of Biochemistry Molecular Biology 603 Wilson Rd., Rm. 513 Michigan State University East Lansing, MI 48824-1319 Office: (517) 355-9724 Lab: (517) 353-9125 FAX: (517) 353-9334Email: rmgarav...@gmail.com On Aug 1, 2012, at 4:37 PM, Uma Ratu wrote: I notice one thing with my data sets. The unit cells is slightly different from each other. For example, one has a/b/c @ 79/126/83. The other has a/b/c @ 84/127/90. Although they are collected from the same crystal. Is this the reason that I can't index both with same parameter in HKL? And subsequently, can't integrate and scala together. If so, is there a way that I can fix it? Thank you for your advice Uma On Wed, Aug 1, 2012 at 8:50 AM, Uma Ratu rosiso2...@gmail.com wrote: Dear All: I collected 5 data sets from one crystal and would like to process them together. Here is how I did: In HKL2000, load the all data sets. Index each set. When I try Intergrate, the program automatically go through the whole data sets there, and do not go through. I then
Re: [ccp4bb] CC1/2, XDS and resolution cut off
A technical remark in relation to the CC1/2, XDS issue: Refmac currently reports Rfactors vs. resolution shells (i.e. Rw/Rf in each resolution shell). That is useful for one aspect of the analysis, however, in the K D paper, it's the change in overall Rfactors vs. resolution that is reported. In the cases analyzed in this paper this is the value which was used as criterion for justifying adding higher resolution shells according to the CC1/2. Perhaps reporting of the overall Rfactors vs. resolution can be added to Refmac (at least as an option for interested users)? Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Eleanor Dodson [eleanor.dod...@york.ac.uk] Sent: Wednesday, August 08, 2012 12:10 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] CC1/2, XDS and resolution cut off Like Ian, I tend to use as much data as is reasonable - but it is useful to look at the Rfactors plot again resolution in REFMAC output. If this shoots sky high at the limit, the data is probably not very useful in refinement or map calculation (and will automatically be down-weghted by the ML weighting) . So all it does is make your Rfactors look worse! Eleanor On 6 Aug 2012, at 12:21, Marcus Fislage wrote: Dear all, We have in our lab a data set collected and are discussing where to cut the resolution for refinement. According to the work of Kai Diederichs and Andy Karplus one should use CC 1/2 of 12.5% (in case it is significant) to determine the highest resolution independent of the I/sigI and R factor rules used earlier. But I would like to know if this also counts for low completeness data? The problem is that we have in the highest resolution shell an I/sigI of 4, a good cc1/2 but only a completeness of 30%. Which I guess means we measured the high resolution data very accurate but not complete. Would you still use the low complete data in the highest resolution shell or should that be still a valid argument to cut your data towards lower resolution? My guess would be to use the data still even if the completeness drops, since the data we measured is good and according to CC1/2 significant. Are we right to do so or would you disagree? Thanks for any input Marcus -- Marcus Fislage Structural Biology Brussels Vrije Universiteit Brussel Department of Structural Biology, VIB Oefenplein, Gebouw E Pleinlaan 2, 1050 Brussel Belgium Tel: +32-2-629 18 51 Email : marcus.fisl...@vib-vub.be Url: http://www.verseeslab.structuralbiology.be
Re: [ccp4bb] CC1/2, XDS and resolution cut off
Eleanor But is the R factor a good way to assess this? - in fact who cares if R looks worse, the goal of structure refinement after all is certainly not to get a better R factor! The R factor if it's anything is a measure of comparative model quality, not comparative data quality. What I mean is that whereas it's valid to use it (and other statistics such as likelihood) to compare models while keeping the same data, it's not valid to use it compare different subsets of the data, whether the model is kept fixed or not. Likelihood is a function of the model with fixed data, i.e. L(model | data) not L(data | model) - that's the probability. The problem with the standard R is that it's unweighted so that weak data will have a disproportionately big effect on it, much more so in fact that in ML refinement where as you say data with low signal/noise will be severely weighted down and will have minimal effect on the refined structure and the maps. The weighted (aka Hamilton) R would surely be a better way to assess the optimal resolution cut-off. If the outer shell average (I / sigma(I)) is say 2 then the Wilson distribution implies that in order to get that average there must be present in the shell a significant proportion of useful data with (I / sigma(I)) 3. As several people have already pointed out the important thing is surely not to throw away useful data! Cheers -- Ian On 8 August 2012 10:10, Eleanor Dodson eleanor.dod...@york.ac.uk wrote: Like Ian, I tend to use as much data as is reasonable - but it is useful to look at the Rfactors plot again resolution in REFMAC output. If this shoots sky high at the limit, the data is probably not very useful in refinement or map calculation (and will automatically be down-weghted by the ML weighting) . So all it does is make your Rfactors look worse! Eleanor On 6 Aug 2012, at 12:21, Marcus Fislage wrote: Dear all, We have in our lab a data set collected and are discussing where to cut the resolution for refinement. According to the work of Kai Diederichs and Andy Karplus one should use CC 1/2 of 12.5% (in case it is significant) to determine the highest resolution independent of the I/sigI and R factor rules used earlier. But I would like to know if this also counts for low completeness data? The problem is that we have in the highest resolution shell an I/sigI of 4, a good cc1/2 but only a completeness of 30%. Which I guess means we measured the high resolution data very accurate but not complete. Would you still use the low complete data in the highest resolution shell or should that be still a valid argument to cut your data towards lower resolution? My guess would be to use the data still even if the completeness drops, since the data we measured is good and according to CC1/2 significant. Are we right to do so or would you disagree? Thanks for any input Marcus -- Marcus Fislage Structural Biology Brussels Vrije Universiteit Brussel Department of Structural Biology, VIB Oefenplein, Gebouw E Pleinlaan 2, 1050 Brussel Belgium Tel: +32-2-629 18 51 Email : marcus.fisl...@vib-vub.be Url: http://www.verseeslab.structuralbiology.be
[ccp4bb] Fwd: [ccp4bb] CC1/2, XDS and resolution cut off
Begin forwarded message: From: Eleanor Dodson eleanor.dod...@york.ac.uk Subject: Re: [ccp4bb] CC1/2, XDS and resolution cut off Date: 8 August 2012 10:10:55 GMT+01:00 To: Marcus Fislage marcus.fisl...@vib-vub.be Cc: CCP4BB@JISCMAIL.AC.UK Like Ian, I tend to use as much data as is reasonable - but it is useful to look at the Rfactors plot again resolution in REFMAC output. If this shoots sky high at the limit, the data is probably not very useful in refinement or map calculation (and will automatically be down-weghted by the ML weighting) . So all it does is make your Rfactors look worse! Eleanor On 6 Aug 2012, at 12:21, Marcus Fislage wrote: Dear all, We have in our lab a data set collected and are discussing where to cut the resolution for refinement. According to the work of Kai Diederichs and Andy Karplus one should use CC 1/2 of 12.5% (in case it is significant) to determine the highest resolution independent of the I/sigI and R factor rules used earlier. But I would like to know if this also counts for low completeness data? The problem is that we have in the highest resolution shell an I/sigI of 4, a good cc1/2 but only a completeness of 30%. Which I guess means we measured the high resolution data very accurate but not complete. Would you still use the low complete data in the highest resolution shell or should that be still a valid argument to cut your data towards lower resolution? My guess would be to use the data still even if the completeness drops, since the data we measured is good and according to CC1/2 significant. Are we right to do so or would you disagree? Thanks for any input Marcus -- Marcus Fislage Structural Biology Brussels Vrije Universiteit Brussel Department of Structural Biology, VIB Oefenplein, Gebouw E Pleinlaan 2, 1050 Brussel Belgium Tel: +32-2-629 18 51 Email : marcus.fisl...@vib-vub.be Url: http://www.verseeslab.structuralbiology.be
[ccp4bb] XRD pattern of CC
Hi I would like to know whether it is possible to get to know the number of molecules (helices) present in a coiled coil based on its XRD pattern. I only know that for coiled coil there will be a meridian arc around 5.1 A (corresponding to helical repeat) and an equatorial arc around 10 A (corresponding to mean distance between helical axes). I am actually curious to know whether it is possible to distinguish double from triple stranded coiled coil from its XRD pattern. Thank you Uday
[ccp4bb] Unexplainable Density
While building our crystal structure model we encountered density which we weren't able to assign. The unknown molecule/molecules seems to coordinate a Ni^2+ -ion. This ion is also coordinated by a histidin and probably one H_2 O-molecule. The crystals have been grown from a protein-complex including the carotinoid peridinin, the lipid DGDG and Chlorophyll. Besides this the solution in which they have been grown contains Tris pH 8.5, NiCl_2 and PEG 2000 MME. The linked images show a rotation around the density in 90°-steps (1.1A, 1.2sigma contour level). The above mentioned H_2 O-molecule has been removed. It is supposed to fill the density that is below the Ni^2+ -Ion in the first picture. Images: http://www.bioxtal.rub.de/myst.html.en Any hints are welcome =) Mario
Re: [ccp4bb] Pisa application
Maybe Nat Protoc.http://www.ncbi.nlm.nih.gov/pubmed?term=Predicting%20protein-protein%20interactions%20on%20a%20proteome%20scale%20by%20matching%20evolutionary%20and%20structural%20similarities%20at%20interfaces%20using%20PRISM# 2011 Aug 11;6(9):1341-54. doi: 10.1038/nprot.2011.367. Predicting protein-protein interactions on a proteome scale by matching evolutionary and structuralsimilarities at interfaces using PRISM. Tuncbag Nhttp://www.ncbi.nlm.nih.gov/pubmed?term=Tuncbag%20N%5BAuthor%5Dcauthor=truecauthor_uid=21886100, Gursoy Ahttp://www.ncbi.nlm.nih.gov/pubmed?term=Gursoy%20A%5BAuthor%5Dcauthor=truecauthor_uid=21886100, Nussinov Rhttp://www.ncbi.nlm.nih.gov/pubmed?term=Nussinov%20R%5BAuthor%5Dcauthor=truecauthor_uid=21886100, Keskin Ohttp://www.ncbi.nlm.nih.gov/pubmed?term=Keskin%20O%5BAuthor%5Dcauthor=truecauthor_uid=21886100. Source Center for Computational Biology and Bioinformatics, College of Engineering, Koc University, Rumelifeneri Yolu, Sariyer Istanbul, Turkey. Abstract Prediction of protein-protein interactions at the structural level on the proteome scale is important because it allows prediction of protein function, helps drug discovery and takes steps toward genome-wide structural systems biology. We provide a protocol (termed PRISM, protein interactions bystructural matching) for large-scale prediction of protein-protein interactions and assembly of protein complex structures. The method consists of two components: rigid-body structural comparisons of target proteins to known template protein-protein interfaces and flexible refinement using a docking energy function. The PRISM rationale follows our observation that globally different protein structures can interact via similar architectural motifs.PRISM predicts binding residues by using structural similarity and evolutionary conservation of putative binding residue 'hot spots'. Ultimately,PRISM could help to construct cellular pathways and functional, proteome-scale annotation. PRISM is implemented in Python and runs in a UNIX environment. The program accepts Protein Data Bank-formatted protein structures and is available at http://prism.ccbb.ku.edu.tr/prism_protocol/. On 8 Aug 2012, at 07:33, Careina Edgooms wrote: Dear ccp4ers I just wonder whether anybody knows if the PISA software could be used/modified to detect potential interfaces of interaction of different proteins? This would be very useful as a tool to validate protein-protein interactions detected by in vivo methods such as yeast 2 hybrid screens. If PISA is not quite there yet, does anyone know of other software that could do a similar thing? Best Careina Roberto Steiner Randall Division of Cell and Molecular Biophysics King's College London Room 3.10A New Hunt's House Guy's Campus SE1 1UL, London, UK Tel 0044-20-78488216 Fax 0044-20-78486435 roberto.stei...@kcl.ac.ukmailto:roberto.stei...@kcl.ac.uk
Re: [ccp4bb] dumb software question
All: Joel's attempt to post an interesting article somehow got concatenated 3 times. The URL should be: http://www.rdmag.com/News/2012/08/Life-Science-Biology-Microscopy-Virtual-nanoscop-Like-Google-Earth-for-cell-biologists/?et_cid=2784615et_rid=54732139 Also in an off-board conversation, Joel pointed out some work done by his group that looks interesting and useful: proteopedia.orghttp://proteopedia.org Steven This message (including any attachments) may contain confidential, proprietary, privileged and/or private information. The information is intended to be for the use of the individual or entity designated above. If you are not the intended recipient of this message, please notify the sender immediately, and delete the message and any attachments. Any disclosure, reproduction, distribution or other use of this message or any attachments by an individual or entity other than the intended recipient is prohibited.
Re: [ccp4bb] Pisa application
Hi Careina To my knowledge PISA by itself is not able to do interface prediction. In any case there are a few methods available for protein-protein interface prediction. See for example this nice compilation: http://rosettadesigngroup.com/blog/58/10-protein-protein-interface-prediction-servers/ Hope it helps Jose On 08/08/2012 08:33 AM, Careina Edgooms wrote: Dear ccp4ers I just wonder whether anybody knows if the PISA software could be used/modified to detect potential interfaces of interaction of different proteins? This would be very useful as a tool to validate protein-protein interactions detected by in vivo methods such as yeast 2 hybrid screens. If PISA is not quite there yet, does anyone know of other software that could do a similar thing? Best Careina
[ccp4bb] 3 x Postdoctoral Research Fellow positions at the University of Sussex ( DNA Damage Repair and Signalling)
3 (Three) Cancer Research UK-funded Postdoctoral Research Fellow positions are available immediately in the laboratory of Professor Laurence Pearl FRS and Dr Antony Oliver, to study the structural basis for the assembly and specificity of multi-protein complexes involved in the recognition and repair of DNA damage, and DNA damage signalling. Additional information, plus full details of how to apply for each of the posts can be found on the University of Sussex website at the following URL: http://www.sussex.ac.uk/aboutus/jobs/768 The formal closing date for applications is the 28th September 2012. - - - The internationally renowned MRC Genome Damage and Stability Centre and the School of Life Sciences are very well equipped for all aspects of modern structural biology, with state-of-the-art laboratories for molecular biology, recombinant expression in bacterial and eukaryotic hosts, biochemistry, biophysics and X-ray crystallography. Excellent synchrotron access (~ 2 days/month) is also available through rolling beam-allocation programmes at both the Diamond Light Source and ESRF. Applicants must have a PhD, and extensive experience in recombinant expression and protein purification. Previous experience of crystallization and X-ray crystallography would be a distinct advantage. The post-holder will be responsible for expression, purification, crystallization and structure determination of protein-protein and protein-DNA complexes, plus downstream biochemical and biophysical characterisation. ** Informal enquiries only ** may be made to either Professor Pearl [ laurence.pe...@sussex.ac.uk ], or Dr Oliver [ antony.oli...@sussex.ac.uk ]. - - - --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ email: antony.oli...@sussex.ac.uk tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512
Re: [ccp4bb] Pisa application
Perhaps IBIS does what you want? http://www.ncbi.nlm.nih.gov/Structure/ibis/ibis.cgi IBIS ... infers/predicts interacting partners and binding sites by homology -- David On 8 August 2012 07:33, Careina Edgooms careinaedgo...@yahoo.com wrote: Dear ccp4ers I just wonder whether anybody knows if the PISA software could be used/modified to detect potential interfaces of interaction of different proteins? This would be very useful as a tool to validate protein-protein interactions detected by in vivo methods such as yeast 2 hybrid screens. If PISA is not quite there yet, does anyone know of other software that could do a similar thing? Best Careina
Re: [ccp4bb] Pisa application
Hi Careina, I asked the exactly same question in this year's CCP4 summer school @APS, and the answer I got was no ... PISA is not for predicting Cheers, Xun Sent from my iPad On Aug 8, 2012, at 2:33 AM, Careina Edgooms careinaedgo...@yahoo.com wrote: Dear ccp4ers I just wonder whether anybody knows if the PISA software could be used/modified to detect potential interfaces of interaction of different proteins? This would be very useful as a tool to validate protein-protein interactions detected by in vivo methods such as yeast 2 hybrid screens. If PISA is not quite there yet, does anyone know of other software that could do a similar thing? Best Careina
[ccp4bb] The 70th Pittsburgh Diffraction Conference September 30th - October 2nd, 2012 Stanford, CA
Dear Colleagues, I would like to draw your attention on behalf of Dr. Guillermo Calero that the 70th Annual Pittsburgh diffraction conference will be held in the beautiful state of California this coming September. This meeting will bring together many great speakers in the field of structural biology of biomacromolecules. Please follow this link ( http://www.pittdifsoc.org/PDC_2012/) for more information and registration. Below is the details. The Pittsburgh Diffraction Conference September 30th - October 2nd, 2012 SLAC National Accelerator Laboratory Menlo Park, CA The 70th Annual Pittsburgh Diffraction Conference is a three day event featuring lecture and poster presentations covering a wide range of subject matter of interest to researchers in chemistry, physics and structural biology. The goal of the conference is to bring together researchers in all areas of fundamental and applied diffraction and crystallographic research to present current topics. The program of the 2012 conference includes nanocrystallography, femtosecond diffraction methods, hybrid methods for structural biology research, new ideas in crystallography and exciting macromolecular structures. Conference social events include an opening reception on September 30th and a banquet on October 1st. The conference will preceed the 2012 SSRL/LCLS Users'Meeting and Workshops October 3rd - 6th. Student poster abstracts may be considered for an oral presentation and are eligible for the Chung Soo Yoo Award. For more information and a list of invited speakers please visit our website at: http://www.pittdifsoc.org/PDC_2012/ The PDS is also accepting nomination for the 2013 Sidhu Award. The Sidhu Award, in memory of Professor Surhain Sidhu, honors significant contributions to the science of crystallography and/or diffraction by an outstanding scientist who is within six (6) years of having earned the Ph.D. or its equivalent. The award carries a cash prize of $2000. --- Hilary Stevenson Graduate Student, Department of Pharmacology Chemical Biology University of Pittsburgh School of Medicine (740) 405-3044 h...@pitt.edu
Re: [ccp4bb] Unexplainable Density
You might be interested in some work done on NikA, which binds a nickel complex with a small organic ligand. They tentatively identified the ligand as butane-1,2,4-tricarboxylate. http://www.rcsb.org/pdb/explore.do?structureId=3e3k Good luck, Arthur On Aug 8, 2012, at 4:56 AM, Mario Sniady wrote: While building our crystal structure model we encountered density which we weren't able to assign. The unknown molecule/molecules seems to coordinate a Ni2+-ion. This ion is also coordinated by a histidin and probably one H2O-molecule. The crystals have been grown from a protein-complex including the carotinoid peridinin, the lipid DGDG and Chlorophyll. Besides this the solution in which they have been grown contains Tris pH 8.5, NiCl2 and PEG 2000 MME. The linked images show a rotation around the density in 90°-steps (1.1A, 1.2sigma contour level). The above mentioned H2O-molecule has been removed. It is supposed to fill the density that is below the Ni2+-Ion in the first picture. Images: http://www.bioxtal.rub.de/myst.html.en Any hints are welcome =) Mario
Re: [ccp4bb] Unexplainable Density
From: Mario Sniady [mailto:mario.sni...@bph.rub.de] Sent: Wednesday, August 08, 2012 7:56 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Unexplainable Density It looks like it could be citrate. Is there any possibility of that? John Andersen While building our crystal structure model we encountered density which we weren't able to assign. The unknown molecule/molecules seems to coordinate a Ni2+-ion. This ion is also coordinated by a histidin and probably one H2O-molecule. The crystals have been grown from a protein-complex including the carotinoid peridinin, the lipid DGDG and Chlorophyll. Besides this the solution in which they have been grown contains Tris pH 8.5, NiCl2 and PEG 2000 MME. The linked images show a rotation around the density in 90°-steps (1.1A, 1.2sigma contour level). The above mentioned H2O-molecule has been removed. It is supposed to fill the density that is below the Ni2+-Ion in the first picture. Images: http://www.bioxtal.rub.de/myst.html.en Any hints are welcome =) Mario
Re: [ccp4bb] Unexplainable Density
It is hard for me to visualize density with just screenshots - I like to rotate the image to see the 3d. This is really clear density, however, and you should be able to figure out what it is. As far as I can tell from your images it looks like half of an EDTA with the other half trailing off into the space above. Was your protein exposed to that compound somewhere along the way? Dale Tronrud On 08/08/12 04:56, Mario Sniady wrote: While building our crystal structure model we encountered density which we weren't able to assign. The unknown molecule/molecules seems to coordinate a Ni^2+ -ion. This ion is also coordinated by a histidin and probably one H_2 O-molecule. The crystals have been grown from a protein-complex including the carotinoid peridinin, the lipid DGDG and Chlorophyll. Besides this the solution in which they have been grown contains Tris pH 8.5, NiCl_2 and PEG 2000 MME. The linked images show a rotation around the density in 90°-steps (1.1A, 1.2sigma contour level). The above mentioned H_2 O-molecule has been removed. It is supposed to fill the density that is below the Ni^2+ -Ion in the first picture. Images: http://www.bioxtal.rub.de/myst.html.en Any hints are welcome =) Mario
[ccp4bb] loading maps in coot using EDS
Hi all, I was trying to get maps using the *fetch PDB and Map using EDS option* in coot, however the map would not open I am using coot version 0.6.2 was wondering if anybody else had similar problems and how to fix this, the following is the error message I get. It used to work fine with a previous version of coot. CCP4MTZfile: open_read - File missing or corrupted: coot-download/3tvn_sigmaa.mtz INFO:: not an mtz file: coot-download/3tvn_sigmaa.mtz ERROR: no f_cols! ERROR: no phi_cols! valid_labels(coot-download/3tvn_sigmaa.mtz,FOFCWT,PHFOFCWT,,0) returns 0 CCP4 library signal library_file:End of File (Error) raised in ccp4_file_raw_read System signal 0:Success (Error) raised in ccp4_file_rarch CCP4 library signal library_file:End of File (Error) raised in ccp4_file_raw_read System signal 0:Success (Error) raised in ccp4_file_readchar CCP4 library signal mtz:Read failed (Error) raised in MtzGet CCP4MTZfile: open_read - File missing or corrupted: coot-download/3tvn_sigmaa.mtz INFO:: not an mtz file: coot-download/3tvn_sigmaa.mtz ERROR: no f_cols! ERROR: no phi_cols! WARNING:: label(s) not found in mtz file coot-download/3tvn_sigmaa.mtz FOFCWT PHFOFCWT WARNING:: -1 is not a valid molecule in set_scrollable_map thanks, Shya
Re: [ccp4bb] loading maps in coot using EDS
It appears that the Electron Density Server could not calculate a map for 3TVN. These cryptic messages are what you get from Coot when there is no map on the server. I can see from the RCSB web page that there is no EDS link in the Experimental Details section, which also happens when the EDS comes up empty. When the EDS fails to calculate a reasonable map for an entry they do not tell us why. If they knew what the problem was they would fix it themselves. They remain silent hoping that the authors of the entry will contact them and give them some help. It is absolutely amazing that they can calculate as many maps as they do. Dale Tronrud On 08/08/12 13:39, Shya Biswas wrote: Hi all, I was trying to get maps using the *fetch PDB and Map using EDS option* in coot, however the map would not open I am using coot version 0.6.2 was wondering if anybody else had similar problems and how to fix this, the following is the error message I get. It used to work fine with a previous version of coot. CCP4MTZfile: open_read - File missing or corrupted: coot-download/3tvn_sigmaa.mtz INFO:: not an mtz file: coot-download/3tvn_sigmaa.mtz ERROR: no f_cols! ERROR: no phi_cols! valid_labels(coot-download/3tvn_sigmaa.mtz,FOFCWT,PHFOFCWT,,0) returns 0 CCP4 library signal library_file:End of File (Error) raised in ccp4_file_raw_read System signal 0:Success (Error) raised in ccp4_file_rarch CCP4 library signal library_file:End of File (Error) raised in ccp4_file_raw_read System signal 0:Success (Error) raised in ccp4_file_readchar CCP4 library signal mtz:Read failed (Error) raised in MtzGet CCP4MTZfile: open_read - File missing or corrupted: coot-download/3tvn_sigmaa.mtz INFO:: not an mtz file: coot-download/3tvn_sigmaa.mtz ERROR: no f_cols! ERROR: no phi_cols! WARNING:: label(s) not found in mtz file coot-download/3tvn_sigmaa.mtz FOFCWT PHFOFCWT WARNING:: -1 is not a valid molecule in set_scrollable_map thanks, Shya
Re: [ccp4bb] loading maps in coot using EDS
The 3tvn coordinates/SF were released today. I'm not sure what the lag time is between the PDB and EDS but you'd probably need to download the structure factors and generate the map yourself. If you're not in a super rush I know the person who refined that specific PDB and I may be able to get you a copy of her final maps to send you off-board once she gets back from vacation. Cheers, Katherine On Wed, Aug 8, 2012 at 3:39 PM, Shya Biswas shyabis...@gmail.com wrote: Hi all, I was trying to get maps using the *fetch PDB and Map using EDS option*in coot, however the map would not open I am using coot version 0.6.2 was wondering if anybody else had similar problems and how to fix this, the following is the error message I get. It used to work fine with a previous version of coot. CCP4MTZfile: open_read - File missing or corrupted: coot-download/3tvn_sigmaa.mtz INFO:: not an mtz file: coot-download/3tvn_sigmaa.mtz ERROR: no f_cols! ERROR: no phi_cols! valid_labels(coot-download/3tvn_sigmaa.mtz,FOFCWT,PHFOFCWT,,0) returns 0 CCP4 library signal library_file:End of File (Error) raised in ccp4_file_raw_read System signal 0:Success (Error) raised in ccp4_file_rarch CCP4 library signal library_file:End of File (Error) raised in ccp4_file_raw_read System signal 0:Success (Error) raised in ccp4_file_readchar CCP4 library signal mtz:Read failed (Error) raised in MtzGet CCP4MTZfile: open_read - File missing or corrupted: coot-download/3tvn_sigmaa.mtz INFO:: not an mtz file: coot-download/3tvn_sigmaa.mtz ERROR: no f_cols! ERROR: no phi_cols! WARNING:: label(s) not found in mtz file coot-download/3tvn_sigmaa.mtz FOFCWT PHFOFCWT WARNING:: -1 is not a valid molecule in set_scrollable_map thanks, Shya
Re: [ccp4bb] loading maps in coot using EDS
On 08/08/12 14:31, Katherine Sippel wrote: The 3tvn coordinates/SF were released today. I'm not sure what the lag time is between the PDB and EDS but you'd probably need to download the structure factors and generate the map yourself. A very good point. I saw the deposition date of 2011 but didn't read down to the release date. The EDS does not get an advanced look at entries in the PDB. The data has to be released to the public before it can begin the calculations. This can take a couple weeks. In addition, the server, itself, appears to be down at the moment. I don't think you could download the map even if it existed. Dale Tronrud If you're not in a super rush I know the person who refined that specific PDB and I may be able to get you a copy of her final maps to send you off-board once she gets back from vacation. Cheers, Katherine On Wed, Aug 8, 2012 at 3:39 PM, Shya Biswas shyabis...@gmail.com mailto:shyabis...@gmail.com wrote: Hi all, I was trying to get maps using the *fetch PDB and Map using EDS option* in coot, however the map would not open I am using coot version 0.6.2 was wondering if anybody else had similar problems and how to fix this, the following is the error message I get. It used to work fine with a previous version of coot. CCP4MTZfile: open_read - File missing or corrupted: coot-download/3tvn_sigmaa.mtz INFO:: not an mtz file: coot-download/3tvn_sigmaa.mtz ERROR: no f_cols! ERROR: no phi_cols! valid_labels(coot-download/3tvn_sigmaa.mtz,FOFCWT,PHFOFCWT,,0) returns 0 CCP4 library signal library_file:End of File (Error) raised in ccp4_file_raw_read System signal 0:Success (Error) raised in ccp4_file_rarch CCP4 library signal library_file:End of File (Error) raised in ccp4_file_raw_read System signal 0:Success (Error) raised in ccp4_file_readchar CCP4 library signal mtz:Read failed (Error) raised in MtzGet CCP4MTZfile: open_read - File missing or corrupted: coot-download/3tvn_sigmaa.mtz INFO:: not an mtz file: coot-download/3tvn_sigmaa.mtz ERROR: no f_cols! ERROR: no phi_cols! WARNING:: label(s) not found in mtz file coot-download/3tvn_sigmaa.mtz FOFCWT PHFOFCWT WARNING:: -1 is not a valid molecule in set_scrollable_map thanks, Shya
Re: [ccp4bb] loading maps in coot using EDS
On 08/08/12 21:39, Shya Biswas wrote: Hi all, I was trying to get maps using the *fetch PDB and Map using EDS option* in coot, however the map would not open I am using coot version 0.6.2 was wondering if anybody else had similar problems and how to fix this, the following is the error message I get. It used to work fine with a previous version of coot. If you have 0.7-pre Extensions - Get from PDBe (I like to keep my refmac pretty up to date). On 08/08/12 22:28, Dale Tronrud wrote: It appears that the Electron Density Server could not calculate a map for 3TVN. The EDS doesn't speak to me at all. Maybe I am asking in the wrong places... These cryptic messages are what you get from Coot when there is no map on the server. ... no mtz file on the server (which probably amounts to the same thing). I can see from the RCSB web page that there is no EDS link in the Experimental Details section, which also happens when the EDS comes up empty. When the EDS fails to calculate a reasonable map for an entry they do not tell us why. Coot downloads the web page too and parses it for message referring to the non-existence of a reliable map. It lets you know if it finds such a thing. If they knew what the problem was they would fix it themselves. They remain silent hoping that the authors of the entry will contact them and give them some help. It is absolutely amazing that they can calculate as many maps as they do. wwPDBs are better at making parsable/convertible data these days (in my experience). Paul.
Re: [ccp4bb] loading maps in coot using EDS
Hi, Thanks, I think the problem is with the EDS server as I tried numerous pdb files (not just the 3TVN) and none of them worked so far. Shya On Wed, Aug 8, 2012 at 5:47 PM, Paul Emsley paul.ems...@bioch.ox.ac.ukwrote: On 08/08/12 21:39, Shya Biswas wrote: Hi all, I was trying to get maps using the *fetch PDB and Map using EDS option* in coot, however the map would not open I am using coot version 0.6.2 was wondering if anybody else had similar problems and how to fix this, the following is the error message I get. It used to work fine with a previous version of coot. If you have 0.7-pre Extensions - Get from PDBe (I like to keep my refmac pretty up to date). On 08/08/12 22:28, Dale Tronrud wrote: It appears that the Electron Density Server could not calculate a map for 3TVN. The EDS doesn't speak to me at all. Maybe I am asking in the wrong places... These cryptic messages are what you get from Coot when there is no map on the server. ... no mtz file on the server (which probably amounts to the same thing). I can see from the RCSB web page that there is no EDS link in the Experimental Details section, which also happens when the EDS comes up empty. When the EDS fails to calculate a reasonable map for an entry they do not tell us why. Coot downloads the web page too and parses it for message referring to the non-existence of a reliable map. It lets you know if it finds such a thing. If they knew what the problem was they would fix it themselves. They remain silent hoping that the authors of the entry will contact them and give them some help. It is absolutely amazing that they can calculate as many maps as they do. wwPDBs are better at making parsable/convertible data these days (in my experience). Paul.
Re: [ccp4bb] Problem with Coot on Mountain Lion
I'm unable to reproduce the error. Can you try it in a temporary new account that doesn't have anything modified, and see if it works? William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA On Aug 8, 2012, at 4:50 PM, Jinyi Zhu jinyi.c...@gmail.com wrote: Hi, I recently upgrade to Mountain Lion and update fink following the official instructions. After that, CCP4, Phenix and pymol all run well without problems. However, I could not start Coot. The error message is as following: DEBUG:: stating pydirectory /sw/share/coot/python INFO:: importing coot.py from /sw/share/coot/python/coot.py Importing python module coot using command from coot import * INFO:: coot.py imported Fatal Python error: PyThreadState_Get: no current thread /sw/bin/coot: line 6: 66155 Abort trap: 6 /sw/bin/coot-real $@ I have update all fink packages up to date and tried to re-install Coot by compiling after removing Coot completely. Does anyone have some good suggestion to make Coot work? Thanks! Best, Jinyi
Re: [ccp4bb] loading maps in coot using EDS
Shya Biswas wrote: Hi, Thanks, I think the problem is with the EDS server as I tried numerous pdb files (not just the 3TVN) and none of them worked so far. Shya I suppose that when the first message in this thread came out yesterday morning, it was a signal for hundreds of thousands of WW crystallographers to take aim with their coots and their browsers at the EDS and kept hitting the refresh button, creating a sustained denial of service attack that brought down the server for the duration. Maybe we need to take up a collection and buy the folks at BMC a faster server and network upgrade.
