Re: [ccp4bb] 3ftt and gremlins
It would be possible for the deposition sites to run a few simple tests to at least find cases where intensities are labelled as amplitudes or vice versa - the truncate plots of moments and cumulative intensities at least would show something was wrong. Eleanor Wladek Minor wrot Dear All, I just received information from Michael Gao (PDB) that updated sf file which is scheduled to be released on March 17, 2009 to replace the current incorrect sf file. Wladek Dr. Wladek Minor Professor of Molecular Physiology and Biological Physics Phone: 434-243-6865 Fax: 434-982-1616 http://krzys.med.virginia.edu/CrystUVa/wladek.htm US-mail address: Department of Molecular Physiology and Biological Physics University of Virginia PO Box 800736, Charlottesville, VA 22908-0736 Fed-Ex address: Department of Molecular Physiology and Biological Physics 1300 Jefferson Park Avenue University of Virginia Charlottesville, VA 22908
Re: [ccp4bb] Could I improve an inconsecutive experimental map?
I presume you have done density modification after calculating the exptl phases? If you use REFMAC to refine your partial model with the exptl/density modified phase restraints your FWT PHWT fourier coefficients already use the combined phase. I am not sure how to choose a damping factor. If you think the exptl/dm phases are good and have realistic weights I guess there shouldnt be one.. SHARP claims to get the weights more or less right; parrot is meant to do a better job of weighting than DM. Eleanor Fengyun Ni wrote: Hi, I have tried SHARP, but no positive results could be obtained. Do you have some articles on how to combine the model phase and experimental phases? I could only seen the consecutive density in mir 8 to 6 A resolution map, so I could only locate roughly the position of helix. After that I use this helix to calculate the structure factor in SFALL. In SIGMAA, what's the DAMP coefficient should I use? After combination, do I need to do density modification? Hope for your help! Regards, Alphar 2009/2/21 Charlie Bond charles.b...@uwa.edu.au Hi Alphar, A while ago I had success with a poor MIR map by building in a few fragments I could identify and then combining phases from this model with the MIR phases using SIGMAA (CCP4 program) and then calculating new maps. A couple of cycles of this resulted in phases in which I had confidence and I was able to build the complete structure. (There's probably a more modern way to do this now ...) Cheers, Charlie Quoting Fengyun Ni alphar...@gmail.com: Thanks, Ezra! I have a native dataset. I'll try what you said, Hope it works in my case. Thanks! Alphar 2009/2/21 Ezra Peisach epeis...@gmail.com Personally, I would try to build into what you see and then do phase recombination. I had a SeMet crystal in which I could only see part of a sheet and helix after DM... Things were not connected - until I improved the phases with my model. Also - do you have a native dataset? You do not mention it. Ezra Fengyun Ni wrote: Hi everyone! I have a question on my poor MIR map. Four datasets (two AU and two HG) were used for phasing upto 3 A resolution in my case. I could locate several heavy atom sites for each dataset with occupancy finally refined to about 0.3 to 0.4, and with B value refined to about 50 to 80. I did not include the anomalous data because once I refine against anomalous data, the anomalous occupancy was only about 0.02, and even smaller as 0.004 for some sites. I guess the anomalous data are not good enough, so I did not use them right now (Could I do this? Or must I include them somehow?). The FOM I got is about 0.6, the Cullis-R factors were about 0.6 for all four data sets, and the phasing power was about 2.5 in each dataset. After I did the density modification, the FOM could increas to about 0.8. My problem is that the protein should form a long helix structure as indicated by other homology protein, but in the map after density modification, the densities are not consecutive though the overall shape seemed to be a long helix. The good thing is that some short helix-like densities could be observed in the current map, but they are not connected to each other. Right now, I am totally lost whether I should believe in the mir-map I have. Could I improve this map with some other method? Or should I re-do the phasing? BTW, the space group for my crystal is R3 or R32 with a=50, b=50, c=380, alpha=90, beta=90 and gamma=120. The c-axis is much longer than a- and b-axis, so the reflection data suffered from the anisotroy effect. Any suggestion on my phasing problem is welcome. -- Alphar Ni Call me alphar~ :) -- Fengyun Ni Call me alphar~ :) -- Charlie Bond Professorial Fellow University of Western Australia School of Biomedical, Biomolecular and Chemical Sciences M310, 35 Stirling Highway Crawley WA 6009, Australia
Re: [ccp4bb] cl.exe
Have you considered gcc under MINGW? It produced more stable code that runs under more versions of windows than CL. = Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 y...@dowling.edu = On Wed, 11 Mar 2009, Bernhard Rupp wrote: Dear All, mysteriously the CL.exe from my MS visual developer studio ancient disappeared and I have no more backup CD. Could someone kindly zip me that program? I think any CL.exe will work. I need to compile/link some C-modules.. Thx!!! Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 b...@qedlife.com bernhardr...@sbcglobal.net http://www.ruppweb.org/
Re: [ccp4bb] cl.exe
Hi Bernhard Did you try this: http://download.corruptedfilerepair.com/post/2008/07/02/clexe-Download-F ile-clexe.aspx (note that after clicking on the Download Link #7: Download CL.EXE link, the actual download link in case it doesn't start automatically, which it didn't for me, is below the ads at the bottom of the page). ... or maybe you don't trust downloads from the net (I wouldn't blame you!). Cheers -- Ian -Original Message- From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of Bernhard Rupp Sent: 12 March 2009 02:59 To: CCP4BB@jiscmail.ac.uk Subject: cl.exe Dear All, mysteriously the CL.exe from my MS visual developer studio ancient disappeared and I have no more backup CD. Could someone kindly zip me that program? I think any CL.exe will work. I need to compile/link some C-modules Thx!!! Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 b...@qedlife.com bernhardr...@sbcglobal.net http://www.ruppweb.org/ Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing i.tic...@astex-therapeutics.com and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
Re: [ccp4bb] 3ftt and gremlins
Dear Eleanor, That is a useful suggestion, but in the case of 3ftt it would not have helped: the amplitudes would have looked as healthy as can be (they were calculated!), and it was the associated Sigmas that had absurd values, being in fact phases in degrees. A sanity check on some (recalculated) I/sig(I) statistics could have detected that something was fishy. Looking forward to the archiving of the REAL data ... i.e. the images. Using any other form of data is like having to eat out of someone else's dirty plate! With best wishes, Gerard. -- On Thu, Mar 12, 2009 at 09:22:26AM +, Eleanor Dodson wrote: It would be possible for the deposition sites to run a few simple tests to at least find cases where intensities are labelled as amplitudes or vice versa - the truncate plots of moments and cumulative intensities at least would show something was wrong. Eleanor -- === * * * Gerard Bricogne g...@globalphasing.com * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * ===
[ccp4bb] Refmac5 and Pseudo-merohedral twinning
Hi, I am currently trying to work with perfectly twinned data and have a starting model that I found through phaser. In trying to refine the model against the data, I noticed that Refmac5 has a twin refinement option that performs some sort of automatic refinement against the found twin laws and refined twin fraction. I couldn't find any documentation on the twin refinement command and was wondering if it could handle pseudo-merohedral twinning. That, in addition to if the twin refinement methods are similar to that of shelxl. CNS is not able to handle pseudo-merohedral twinning and shelxl can - any thoughts on refmac5's ability/preference? Thanks, Walter
Re: [ccp4bb] cl.exe
Just to second this, and point out that with Mingw cross compilers, you can build Windows executables on Linux or OSX that run on all versions of Windows from 95 to Vista... (and might even run on 3.1, but I don't have a 3.1 box to test on). Have you considered gcc under MINGW? It produced more stable code that runs under more versions of windows than CL. = Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 y...@dowling.edu = On Wed, 11 Mar 2009, Bernhard Rupp wrote: Dear All, mysteriously the CL.exe from my MS visual developer studio ancient disappeared and I have no more backup CD. Could someone kindly zip me that program? I think any CL.exe will work. I need to compile/link some C-modules.. Thx!!! Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 b...@qedlife.com bernhardr...@sbcglobal.net http://www.ruppweb.org/
Re: [ccp4bb] Refmac5 and Pseudo-merohedral twinning
Dear Kim, yes, Refmac handles pseudo-merohedral twinning. The procedure is fully automatic and there is not much to change but the documention can be found here: http://www.ccp4.ac.uk/html/refmac5/keywords/keywords_5_5.html#Twin Pavol
[ccp4bb] CALL FOR ESRF SYNCHROTRON BEAM TIME WITH ONLINE DEHUMIDIFIER AT BEAMLINE ID14-2
CALL FOR ESRF SYNCHROTRON BEAM TIME WITH ONLINE DEHUMIDIFIER AT BEAMLINE ID14-2 Proposal Submission Deadline: 31st March 2009 Beamtime will be available from the 14th to the 17th May 2009 at the ESRF for MX data collection (beamline ID14-2) with a device that allows precise control of the humidity of the crystal prior to X-ray diffraction experiments. The device (EMBL HC1b) provides a room temperature humid airflow with adjustable relative humidity [50- 99 %]. Many crystals have been shown to improve their diffraction properties upon dehydration. The machine control software is connected to the host beamline to run dehydration protocols while taking X-ray diffraction images automatically. Users are encouraged to consult the web pages for detailed information (http://www.esrf.eu/UsersAndScience/Experiments/MX/About_our_beamlines/ID14-2/HC1b). Users who are interested in using this beam time (including those who are members of BAG Groups) should use the following mechanism: http://www.esrf.fr/UsersAndScience/UserGuide/Applying/ProposalGuidelines/MXnon-BAGproposal Please specify in the TITLE OF THE PROPOSAL that the dehumidifier is necessary for the project. 24 hours will scheduled for each project. The deadline for this specific application is Tuesday 31st March 2009. *Dates of beam-time: 14th - 17th May 2009 *Storage Ring: 16 bunch (90mA) Beamline: ID14-2 Energy: 13.29 keV Specifications: relative humidity [50- 99 %] Room temperature Data Collection begin:vcard fn:David FLOT n:FLOT;David org:ESRF;Macromolecular Crystallography group adr:6 rue Jules Horowitz;;BP220;Grenoble;;38043;France email;internet:david.f...@esrf.fr title:Beam-Line Operation Manager tel;work:+(33) 4 76 88 17 63 tel;fax:(+33) 4 76 88 26 24 x-mozilla-html:FALSE url:www.esrf.eu version:2.1 end:vcard
Re: [ccp4bb] 3ftt and gremlins
Eleanor, Please note that so far CIF structure factors files were not sent by deposition site for verification to authors. I spoke with Helen and John last Saturday and they promised me to change that policy. Alternatively, one can check his/hers new deposit on every Wednesday morning. Best regards Wladek At 05:22 AM 3/12/2009, Eleanor Dodson wrote: It would be possible for the deposition sites to run a few simple tests to at least find cases where intensities are labelled as amplitudes or vice versa - the truncate plots of moments and cumulative intensities at least would show something was wrong. Eleanor Wladek Minor wrot Dear All, I just received information from Michael Gao (PDB) that updated sf file which is scheduled to be released on March 17, 2009 to replace the current incorrect sf file. Wladek Dr. Wladek Minor Professor of Molecular Physiology and Biological Physics Phone: 434-243-6865 Fax: 434-982-1616 http://krzys.med.virginia.edu/CrystUVa/wladek.htm US-mail address: Department of Molecular Physiology and Biological Physics University of Virginia PO Box 800736, Charlottesville, VA 22908-0736 Fed-Ex address: Department of Molecular Physiology and Biological Physics 1300 Jefferson Park Avenue University of Virginia Charlottesville, VA 22908 Dr. Wladek Minor Professor of Molecular Physiology and Biological Physics Phone: 434-243-6865 Fax: 434-982-1616 http://krzys.med.virginia.edu/CrystUVa/wladek.htm US-mail address: Department of Molecular Physiology and Biological Physics University of Virginia PO Box 800736, Charlottesville, VA 22908-0736 Fed-Ex address: Department of Molecular Physiology and Biological Physics 1300 Jefferson Park Avenue University of Virginia Charlottesville, VA 22908
Re: [ccp4bb] 3ftt and gremlins
Dear Eleanor and Gerard, PDB testing is performed on MTZ file and can not detect conversion errors. Wladek At 10:03 AM 3/12/2009, Gerard Bricogne wrote: Dear Eleanor, That is a useful suggestion, but in the case of 3ftt it would not have helped: the amplitudes would have looked as healthy as can be (they were calculated!), and it was the associated Sigmas that had absurd values, being in fact phases in degrees. A sanity check on some (recalculated) I/sig(I) statistics could have detected that something was fishy. Looking forward to the archiving of the REAL data ... i.e. the images. Using any other form of data is like having to eat out of someone else's dirty plate! With best wishes, Gerard. -- On Thu, Mar 12, 2009 at 09:22:26AM +, Eleanor Dodson wrote: It would be possible for the deposition sites to run a few simple tests to at least find cases where intensities are labelled as amplitudes or vice versa - the truncate plots of moments and cumulative intensities at least would show something was wrong. Eleanor -- === * * * Gerard Bricogne g...@globalphasing.com * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * === Dr. Wladek Minor Professor of Molecular Physiology and Biological Physics Phone: 434-243-6865 Fax: 434-982-1616 http://krzys.med.virginia.edu/CrystUVa/wladek.htm US-mail address: Department of Molecular Physiology and Biological Physics University of Virginia PO Box 800736, Charlottesville, VA 22908-0736 Fed-Ex address: Department of Molecular Physiology and Biological Physics 1300 Jefferson Park Avenue University of Virginia Charlottesville, VA 22908
[ccp4bb] images
Dear Gerard and all MX crystallographers As I see there are two problems. 1) Minor problem: Sanity, semantic and other checks for currently available data. It should not be difficult to do. Things like I/sigma, some statistical analysis expected vs observed statistical behaviour should sort out many of these problems (Eleanor mentioned some and they can be used). I do not think that depositors should be blamed for mistakes. They are doing their best to produce and deposit. There should be a proper mechanism to reduce the number of mistakes. You should agree that situation is now much better than few years. 2) A fundamental problem: What are observed data? I agree with you (Gerard) that images are only true observations. All others (intensities, amplitudes etc) have undergone some processing using some assumptions and they cannot be considered as true observations. The dataprocessing is irreversible process. I hope your effort will be supported by community. I personally get excited with the idea that images may be available. There are exciting possibilities. For example modular crystals, OD, twin in general, space group uncertaintly cannot be truly modeled without images (it does not mean refinement against images). Radiation damage is another example where after processing and merging information is lost and cannot be recovered fully. You can extend the list where images would be very helpful. I do not know any reason (apart from technical one - size of files) why images should not be deposited and archived. I think this problem is very important. regards Garib On 12 Mar 2009, at 14:03, Gerard Bricogne wrote: Dear Eleanor, That is a useful suggestion, but in the case of 3ftt it would not have helped: the amplitudes would have looked as healthy as can be (they were calculated!), and it was the associated Sigmas that had absurd values, being in fact phases in degrees. A sanity check on some (recalculated) I/ sig(I) statistics could have detected that something was fishy. Looking forward to the archiving of the REAL data ... i.e. the images. Using any other form of data is like having to eat out of someone else's dirty plate! With best wishes, Gerard. -- On Thu, Mar 12, 2009 at 09:22:26AM +, Eleanor Dodson wrote: It would be possible for the deposition sites to run a few simple tests to at least find cases where intensities are labelled as amplitudes or vice versa - the truncate plots of moments and cumulative intensities at least would show something was wrong. Eleanor -- === * * * Gerard Bricogne g...@globalphasing.com * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * ===
Re: [ccp4bb] Update X11 in macbook
William G. Scott wrote: On Mar 11, 2009, at 8:49 PM, Raja Dey wrote: Dear Friends, snip 2. If I update X11, whether it will cause any problem to the existing programs? You run the risk of having them work, This risk is marginal. The current 'stable' xquartz 2.3.2 still flickers the hell out of my external screen. Every night I pray to a different god for version 2.4 to actually work. Andreas and thus lowering my blood pressure. In the current economic crisis, this could be enough to cause the collapse of the world's pharmaceutical industries. Thanking you in advance for all the help... Raja Connect with friends all over the world. Get Yahoo! India Messenger at http://in.messenger.yahoo.com/?wm=n/ -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk
Re: [ccp4bb] 3ftt and gremlins
Gerard Bricogne wrote: Looking forward to the archiving of the REAL data ... i.e. the images. Using any other form of data is like having to eat out of someone else's dirty plate! That may be so -- but if I'm hungry now, I just pop it in the sink -- I don't publish a call for tenders on an industrial-scale dish-washer, call up the architects and engineers to redesign the room, re-lay the plumbing, vamp up my electricity transformer and install a new drainage system. Which doesn't mean the industrial-scale washer isn't necessary; but honestly, can't we start by just washing the plate?? phx.
Re: [ccp4bb] 3ftt and gremlins
This thread has evolved into two different topics. Just to clarify: 1) There is a need for additional validation of structure factor depositions. My recollection is that the output of SF Check is available to the depositor via ADIT on the RCSB site. I have found that report to be quite helpful in checking for gross errors in my structure factor files. The Electron Density Server performs similar checks. It shows that the R value for 3ftt is 6.4% with a correlation coefficient between Fo and Fc of 0.996. The EDS flags entries as interesting if the calculated R value is more than 5% higher than the reported R value. Maybe it should also note when the R value is more than 5% lower. The tools for validating structure factors exist but perhaps could be put more in the face of the depositor to more strongly encourage that they be looked at. 2) It would be useful to have a central repository of raw diffraction images. Most of the discussion on this point is the technical difficulty of storing this quantity of data. What has not been mentioned is the much greater difficulty of validating these images. You may think the images for an entry have been deposited only to find out that the investigator's wedding photos were accidentally deposited instead. Validating that the images correspond to the claimed structure will be an enormous task; probably more difficult than coming up with enough hard drives to store them all. Dale Tronrud Frank von Delft wrote: Gerard Bricogne wrote: Looking forward to the archiving of the REAL data ... i.e. the images. Using any other form of data is like having to eat out of someone else's dirty plate! That may be so -- but if I'm hungry now, I just pop it in the sink -- I don't publish a call for tenders on an industrial-scale dish-washer, call up the architects and engineers to redesign the room, re-lay the plumbing, vamp up my electricity transformer and install a new drainage system. Which doesn't mean the industrial-scale washer isn't necessary; but honestly, can't we start by just washing the plate?? phx.
Re: [ccp4bb] 3ftt and gremlins
Dear Frank, Thank you for your answer, as unimitable as ever. We do of course have to wash one plate at a time when we each feel the pinch of hunger; but as we do so we should not forget that the PDB is the Central Planning Office, and that the order for that industrial-scale dishwasher has to be filed and lobbied for if it is ever to be delivered. Otherwise we will continue washing our own plates for ever. Besides, on the serious side of the argument, there are other benefits to the deposition of images, as argued in the paper by Joosten et al. in the recent Acta D volume containing the proceedings of last year's CCP4 Study Weekend. With best wishes, Gerard. -- On Thu, Mar 12, 2009 at 04:07:36PM +, Frank von Delft wrote: Gerard Bricogne wrote: Looking forward to the archiving of the REAL data ... i.e. the images. Using any other form of data is like having to eat out of someone else's dirty plate! That may be so -- but if I'm hungry now, I just pop it in the sink -- I don't publish a call for tenders on an industrial-scale dish-washer, call up the architects and engineers to redesign the room, re-lay the plumbing, vamp up my electricity transformer and install a new drainage system. Which doesn't mean the industrial-scale washer isn't necessary; but honestly, can't we start by just washing the plate?? phx. -- === * * * Gerard Bricogne g...@globalphasing.com * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * ===
Re: [ccp4bb] 3ftt and gremlins
Hi Dale, 1) There is a need for additional validation of structure factor depositions. PHENIX has tools for this: 1) phenix.cif_as_mtz will convert the PDB data file with diffrcation data into MTZ file. It automatically will figure out if the data are X-ray: Iobs or Fobs, or Neutron Fobs or Iobs. 2) The next step will be running phenix.model_vs_data that will take the MTZ from from above and the corresponding PDB file and give a complete statistics, that you can immediately compare with the published value. Note, phenix.model_vs_data can handle: - twinned data; - neutron data; - all unknown ligands dictionaries are generated internally; - PDB files with multiple models (with multiple MODEL records). I run it every month or two, and so I have a nice list of interesting cases. The database of all converted to MTZ data files is used internally by PHENIX developers for various developments etc... In fact, this was used in POLYGON validation tool: Acta Cryst. (2009). D65, 297-300 Pavel.
Re: [ccp4bb] Update X11 in macbook
On Mar 12, 2009, at 9:01 AM, Andreas Förster wrote: Every night I pray to a different god for version 2.4 to actually work. Prayer might be making it worse, depending upon the wrath and vindictiveness of the imaginary deity of choice: http://www.nytimes.com/2006/03/31/health/31pray.html I guess bug reports to Apple might fall into a similar category, but might be worth a try, failing human sacrifice.
Re: [ccp4bb] 3ftt and gremlins
Dear Dale, On Thu, Mar 12, 2009 at 11:07:05AM -0700, Dale Tronrud wrote: This thread has evolved into two different topics. Just to clarify: 1) There is a need for additional validation of structure factor depositions. My recollection is that the output of SF Check is available to the depositor via ADIT on the RCSB site. I have found that report to be quite helpful in checking for gross errors in my structure factor files. The Electron Density Server performs similar checks. It shows that the R value for 3ftt is 6.4% with a correlation coefficient between Fo and Fc of 0.996. The EDS flags entries as interesting if the calculated R value is more than 5% higher than the reported R value. Maybe it should also note when the R value is more than 5% lower. The tools for validating structure factors exist but perhaps could be put more in the face of the depositor to more strongly encourage that they be looked at. 2) It would be useful to have a central repository of raw diffraction images. Most of the discussion on this point is the technical difficulty of storing this quantity of data. What has not been mentioned is the much greater difficulty of validating these images. You may think the images for an entry have been deposited only to find out that the investigator's wedding photos were accidentally deposited instead. My suggestion would be to give the images to (say) XDS: it would run successfully on wedding photographs only in rare cases where the group photograph was taken from a helicopter and the guests were arranged in very peculiar ways ... . Validating that the images correspond to the claimed structure will be an enormous task; probably more difficult than coming up with enough hard drives to store them all. Not necessarily, unless the crystalline specimen is very poor. In ordinary cases, instead of comparing structure factor amplitudes or intensities calculated from the deposited model to those in a file of deposited values, one would run an integration program (or several of them) on the images, check that cell parameters and space group agree, then run TRUNCATE if amplitudes are desired, to get those observed values (up to some re-indexing). For this to be possible automatically one would have to be much stricter with the completeness and accuracy of the information in image headers produced by various detectors, a step that I think many people would welcome. With best wishes, Gerard. Dale Tronrud Frank von Delft wrote: Gerard Bricogne wrote: Looking forward to the archiving of the REAL data ... i.e. the images. Using any other form of data is like having to eat out of someone else's dirty plate! That may be so -- but if I'm hungry now, I just pop it in the sink -- I don't publish a call for tenders on an industrial-scale dish-washer, call up the architects and engineers to redesign the room, re-lay the plumbing, vamp up my electricity transformer and install a new drainage system. Which doesn't mean the industrial-scale washer isn't necessary; but honestly, can't we start by just washing the plate?? phx. -- === * * * Gerard Bricogne g...@globalphasing.com * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * ===
[ccp4bb] Fragment Screening kit
Dear all, We have been trying to crystalize a membrane protein in which the function is unknown. We got some initial crystal hits and we are in the process of optimization. I am looking for a screening kit for identifying the potential ligand/ substrates (small molecule metabolites) of an unknown target by co- crystallization experiments. Any suggestions will be appreciated. Thanks in advance. Cheers Dinesh
[ccp4bb] Please recommend screen kits for membrane proteins
Sorry for the off-topic subject. I am new to membrane proteins. We already have Qiagen MB class I and II, Sigma Membrane, and Membrane Gold kits, but I want to know if there other kits out there you would recommend. Thanks a lot, Joe
Re: [ccp4bb] 3ftt and gremlins
Dear Dale, 1) There is a need for additional validation of structure factor depositions. My recollection is that the output of SF Check is available to the depositor via ADIT on the RCSB site. I have found that report to be quite helpful in checking for gross errors in my structure factor files. The Electron Density Server performs similar checks. It shows that the R value for 3ftt is 6.4% with a correlation coefficient between Fo and Fc of 0.996. The EDS flags entries as interesting if the calculated R value is more than 5% higher than the reported R value. Maybe it should also note when the R value is more than 5% lower. The tools for validating structure factors exist but perhaps could be put more in the face of the depositor to more strongly encourage that they be looked at. Thank you for stressing this again. I had a look at the PDB_REDO results for 3ftt. It uses a procedure similar to that of the EDS, so I wanted to make sure 3ftt was rejected because R(-free) could not be reproduced. However, 3ftt was not in PDB_REDO for a different reason: the R-free set had no information content. That is, all reflection have the same status flag. There are frequent discussions in the CCP4BB about the (un)importance of keeping the R-free set. It would certainly be nice if the PDB would also warn about R-free set problems to the depositor. Funny thing for the status flags of 3ftt: all reflections are marked 'x' (i.e. unmeasured). We should have known that there was something wrong with them. Cheers, Robbie Joosten
Re: [ccp4bb] Refmac5 and Pseudo-merohedral twinning
Hi Pavol, Garib Actually, that bit of doc doesn't answer a few practical questions we keep running into: 1) What spacegroup should you provide the data in? The usual scenario, in practice, is that one merges in too high symmetry, and wants to check whether it is actually lower symmetry with twinning. 2) What spacegroup should the *model* be? The highest symmetry? 3) What exactly is refmac doing: is it expanding the model to the lower symmetries starting from your model? 4) Will it also test for the funny ones (e.g. C222 which is actually P2 twinned). Cheers phx. Pavol wrote: Dear Kim, yes, Refmac handles pseudo-merohedral twinning. The procedure is fully automatic and there is not much to change but the documention can be found here: http://www.ccp4.ac.uk/html/refmac5/keywords/keywords_5_5.html#Twin Pavol
Re: [ccp4bb] Structural biology inside the cell
Dear Mark Stay calm Buzz-words come and very frequently do not stay, they go away with the artifacts they advocate... Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica D, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972 3640 8723 Fax: ++972 3640 9407 Cellular: ++972 547 459 608 On Mar 12, 2009, at 6:14 PM, Mark J. van Raaij wrote: Dear All, a News Views article in Nature 458, pages 37-38 of 5 March 2009 (link below) states: The development of structural biology WAS historically based on the principle of divide and conquer — individual proteins were purified to homogeneity and their atomic structures were solved in vitro by using either X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. This approach WAS tremendously successful, and led to the creation of a protein-structure databank that currently contains more than 50,000 structures. I find the past tense here too much... Greetings, Mark Mark J. van Raaij Dpto de Bioquímica, Facultad de Farmacia Universidad de Santiago 15782 Santiago de Compostela Spain http://web.usc.es/~vanraaij/ http://www.nature.com/nature/journal/v458/n7234/full/458037a.html Structural biology: Inside the living cell
Re: [ccp4bb] Refmac5 and Pseudo-merohedral twinning
Current version does not expand data or model. C222 twinned in P2 will not be handled if data are in C222. Overmerged data are a bit tricky to deal with. And model in higher space group would not fit into the asymmetric unit in general. In short: in the current version space group should be actual space group and model should correspond to it. We are working with on a procedure to deal with overmerged data. Meanwhile ZANUDA from YSBL webserver www.ysbl.york.ac.uk/YSBLPrograms/index.jsp can be used to sort out space group if you have accidentally overmerged and managed to solve structure at higher space group regards Garib On 12 Mar 2009, at 20:49, Frank von Delft wrote: Hi Pavol, Garib Actually, that bit of doc doesn't answer a few practical questions we keep running into: 1) What spacegroup should you provide the data in? The usual scenario, in practice, is that one merges in too high symmetry, and wants to check whether it is actually lower symmetry with twinning. 2) What spacegroup should the *model* be? The highest symmetry? 3) What exactly is refmac doing: is it expanding the model to the lower symmetries starting from your model? 4) Will it also test for the funny ones (e.g. C222 which is actually P2 twinned). Cheers phx. Pavol wrote: Dear Kim, yes, Refmac handles pseudo-merohedral twinning. The procedure is fully automatic and there is not much to change but the documention can be found here: http://www.ccp4.ac.uk/html/refmac5/keywords/keywords_5_5.html#Twin Pavol
[ccp4bb] Beamtime proposal deadline for ALS GU time
The deadline for the may/June cycle of general user time for PX in the ALS is coming up soon (This Sunday). The Berkeley Center for Structural Biology (BCSB) has recently completed a number of upgrades: Sector 8: Recent improvements include: * A high-accuracy microdiffractometer on BL 8.2.1 allows for centering and viewing of very small crystals; * Robot automounters on BL8.2.1 and 8.2.2 are now fully commissioned and the beamlines can be used remotely; * A new large format (315mm active surface area) CCD detector on BL 8.2.1 facilitates data collection on large unit cell crystals. Sector 5: Recent improvements include: * Beamlines (5.0.1 and 5.0.3) now generate 1.5x1011 photons per second at 0.97 Angstrom. This wavelength is slightly above the Se K edge making them ideal for performing Se SAD experiments. * Beamline 5.0.2 (the tunable beamline) generates a peak flux of 8x1011 photons per second, and the energy range of 5.0.2 has been extended to 17 keV, enabling the routine use of shorter wavelengths and anomalously scattering elements such as bromine. * All sector 5 beamlines can be run remotely. The automated sample mounter holds six pucks (96 sample in total). On weekdays, staff is available 22 hours (out of 24) for puck changes and assistance. Please visit http://bcsb.lbl.gov/ for more details about the Center and its beamlines. If you'd like to apply for May/June beamtime at the Advanced Light Source, please submit a General User proposal by March 15, 2009. To find out more, click on: http://www-als.lbl.gov/als/quickguide/independinvest.html We invite you to submit a proposal at: http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PXProposalEntry.shtml/Initialize. If you have any questions or would like to request open beamtime, please e-mail bcsbbeamt...@lbl.gov. [Please note that executed user agreements must be received by LBNL prior to beamtime. Proprietary fees, if applicable, must be received by LBNL at least five working days prior to scheduled beamtime.] -- - P.H. Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CCTBX: http://cctbx.sf.net -
Re: [ccp4bb] Please recommend screen kits for membrane proteins
I like the standard Classics, PEGs 1 and 2, as well as the ProComplex screens. We also use Molecular Dimensions MemStart/MemSys and the Axygen High Probability Peg Screen. Good luck. Franz On Thu, 12 Mar 2009 16:03:10 -0400, JOE CRYSTAL gch...@gmail.com wrote: Sorry for the off-topic subject. I am new to membrane proteins. We already have Qiagen MB class I and II, Sigma Membrane, and Membrane Gold kits, but I want to know if there other kits out there you would recommend. Thanks a lot, Joe
