[ccp4bb] Archiving for fraud detection
One argument for archiving images has been that reprocessing could demonstrate deliberately deceptive structures. In fact, what is needed for this is not necessarily the image. It is the last data file that was produced by a trusted computer. If the structure depends on mtz files produced at the synchrotron, then it is sufficient to authenticate the reduced data. The images are only needed for this purpose if they have been reprocessed. regards, Chris Chris Morris chris.mor...@stfc.ac.uk Tel: +44 (0)1925 603689 Fax: +44 (0)1925 603634 Mobile: 07921-717915 Skype: chrishgmorris http://pims.structuralbiology.eu/ http://www.citeulike.org/blog/chrishmorris Daresbury Lab, Daresbury, Warrington, UK, WA4 4AD
Re: [ccp4bb] MR - small coiled coil, 1.65A = 1.000 solutions, all of them wrong
Dear Napoleão, Thank you for updating everyone on your efforts, and also acknowledging the advice. I wanted to respond to your question regarding maps. I know that many people who try to figure out whether or not their MR solution is the right one would ask the same question. So first of all if you wonder why you actually get very decently looking maps the answer is a classical one: because 'the phases are more important than amplitudes'. The appearance of your map is defined by your model phases, and hence a good match between the model and the map /may not/ be taken as a sign of a correct solution. Once again: /never ever!/ On the contrary, at least in your coil1.jpg image I clearly see that the density exactly follows the model which is almost entirely poly-Ala. Unless your protein is really poly-Ala this should be alarming. If you had a correct solution they you would hope to see the (difference)density for at least some missing side chains. And a second point. Unless your model contains the complete chain (which is rarely the case, especially for the coiled coils, as discussed already) a sign of the correct solution would be the appearance of extra density near the N- and/or C-terminus of the model. If it is not there, it is almost certainly not a solution. And you should not be worried about the R-factors being very high at this stage. If the solution is correct then you should see at least some extra features in the map. Kind regards, Sergei Thank you all for the replies. Sorry for taking so long to reply, I was actually trying some of your interesting ideas (and I'm still trying). I tried using the low resolution data sets for the molecular replacement (thanks to Yuriy Patskovsky), I also improved and increased my coiled coil database and employed it in many approaches using EPRM (interesting program I was not aware of), which I found to produce lots of data, hopefully addressing at some extent the helixes bent (thanks to Bernhard Rupp). I also tried some more tweaking in Phaser, although not sure if did it properly (thanks to Randy Read). There is no twinning as far as I can tell (thanks to Ed Pozharski for the tip). Using a data set with enough completeness (360 degrees @ Brookhaven) and processing in P1 did not help me because in this space group there is most likely 2-3 helixes in the asymmetric unit, which complicates the problem (and it takes a lot of time for Phaser to run). Automated approaches also did not yield a better result (as far as I can tell). I'm convinced that the space group is C2221, but I may be wrong. Thanks to Sergei Strelkov for the numerous useful suggestions on how to approach the problem. One of the big issues for me is to discriminate between a lot of similarly good density maps. For example: http://www.fullonline.org/coils/coil1.jpg http://www.fullonline.org/coils/coil2.jpg I have hundreds of solutions like these and I think they are all wrong. I couldn't manage to run Arcimboldo, could not find a tutorial on it either. It was highly recommended here (and elsewhere), so I'm definitely willing to give it a try (thanks Isabel Uson). You guys opened my eyes about a series of issues that I should learn about and approach, I'm most thankful for that. Best regards, Napo -- Prof. Sergei V. Strelkov Laboratory for Biocrystallography Department of Pharmaceutical Sciences, Katholieke Universiteit Leuven O&N2, Campus Gasthuisberg, Herestraat 49 bus 822, 3000 Leuven, Belgium Work phone: +32 16 330845 Fax: +32 16 323469 OR +32 16 323460 Mobile: +32 486 294132 Lab pages: http://pharm.kuleuven.be/anafar
Re: [ccp4bb] MR - small coiled coil, 1.65A = 1.000 solutions, all of them wrong
We have unintentionally discovered a very simple way of telling whether an MR solution is correct or not, provided that (as in this case) native data have been measured to about 2.1A or better. This uses the current beta-test of SHELXE that does autotracing (available on email request). First rename the PDB file from MR to name.pda and generate a SHELX format file name.hkl, e.g. using Tim Gruene's mtz2hkl, where 'name' may be chosen freely but should be the same for both input files. Then run SHELXE with a large number of autotracing cycles (here 50), e.g. shelxe name.pda -a50 -s0.5 -y2 -s sets the solvent content and -y a resolution limit for generating starting phases. If the .hkl file contains F rather than intensity the -f switch is also required. If the model is wrong the CC value for the trace will gradually decrease as the model disintegrates. If the model is good the CC will increase, and if it reaches 30% or better the structure is solved. In cases with a poor but not entirely wrong starting fragment, the CC may vary erratically for 10-30 cycles before it locks in to the correct solution and the CC increases over three or four cycles to the value for a solved structure (25 to 50%). The solution with the best CC is written to name.pdb and its phases to name.phs for input to e.g. Coot. George On Fri, Nov 04, 2011 at 10:42:27AM +0100, Sergei Strelkov wrote: > Dear Napoleão, > > Thank you for updating everyone on your > efforts, and also acknowledging the advice. > > I wanted to respond to your question regarding maps. > I know that many people who try to figure out > whether or not their MR solution is the right one > would ask the same question. > > So first of all if you wonder why you actually get very > decently looking maps the answer is a classical one: > because 'the phases are more important than amplitudes'. > The appearance of your map is defined by > your model phases, and hence a good match between the > model and the map may not be taken as > a sign of a correct solution. Once again: never ever! > > On the contrary, at least in your coil1.jpg > image I clearly see that the density exactly follows > the model which is almost entirely poly-Ala. > Unless your protein is really poly-Ala this should be > alarming. If you had a correct solution they you > would hope to see the (difference)density for > at least some missing side chains. > > And a second point. Unless your model contains > the complete chain (which is rarely the case, especially > for the coiled coils, as discussed already) > a sign of the correct solution would be the appearance > of extra density near the N- and/or C-terminus of > the model. If it is not there, it is almost certainly not > a solution. > > And you should not be worried about the R-factors being > very high at this stage. If the solution is correct then > you should see at least some extra features in the map. > > Kind regards, > Sergei > > > > Thank you all for the replies. > > Sorry for taking so long to reply, I was actually trying some of your > interesting ideas (and I'm still trying). > > I tried using the low resolution data sets for the molecular replacement > (thanks to Yuriy Patskovsky), I also improved and increased my coiled > coil database and employed it in many approaches using EPRM (interesting > program I was not aware of), which I found to produce lots of data, > hopefully addressing at some extent the helixes bent (thanks to Bernhard > Rupp). I also tried some more tweaking in Phaser, although not sure if > did it properly (thanks to Randy Read). > > There is no twinning as far as I can tell (thanks to Ed Pozharski for > the tip). Using a data set with enough completeness (360 degrees @ > Brookhaven) and processing in P1 did not help me because in this space > group there is most likely 2-3 helixes in the asymmetric unit, which > complicates the problem (and it takes a lot of time for Phaser to run). > Automated approaches also did not yield a better result (as far as I can > tell). I'm convinced that the space group is C2221, but I may be wrong. > > Thanks to Sergei Strelkov for the numerous useful suggestions on how to > approach the problem. > > One of the big issues for me is to discriminate between a lot of > similarly good density maps. For example: > > http://www.fullonline.org/coils/coil1.jpg > http://www.fullonline.org/coils/coil2.jpg > > I have hundreds of solutions like these and I think they are all wrong. > > I couldn't manage to run Arcimboldo, could not find a tutorial on it > either. It was highly recommended here (and elsewhere), so I'm > definitely willing to give it a try (thanks Isabel Uson). > > You guys opened my eyes about a series of issues that I should learn > about and approach, I'm most thankful for that. > Best regards, > Napo > > > > -- > Prof
Re: [ccp4bb] Archiving for fraud detection
If the data files generated from trusted computers carry digital signatures it would be more trustworthy. Otherwise, a person with proper knowledge can still manipulate the data files, even if it is in binary. If the image processing software routinely incorporate encrypted key information of the original data to the final data files, then data from any computer can be trusted. This would be best considering that in real life we often have to combat the ice rings, splitting reflections, etc., at home. For example, if the frames used for indexing the dataset are encrypted and saved with or within the final data file as "proof of experiment", in a universal format that can be used by the structure deposition servers to verify the reported space group, resolution, and, to some degree, the structure itself, it would probably serve the purpose. Zhijie -- From: "Chris Morris" Sent: Friday, November 04, 2011 4:09 AM To: Subject: [ccp4bb] Archiving for fraud detection One argument for archiving images has been that reprocessing could demonstrate deliberately deceptive structures. In fact, what is needed for this is not necessarily the image. It is the last data file that was produced by a trusted computer. If the structure depends on mtz files produced at the synchrotron, then it is sufficient to authenticate the reduced data. The images are only needed for this purpose if they have been reprocessed. regards, Chris Chris Morris chris.mor...@stfc.ac.uk Tel: +44 (0)1925 603689 Fax: +44 (0)1925 603634 Mobile: 07921-717915 Skype: chrishgmorris http://pims.structuralbiology.eu/ http://www.citeulike.org/blog/chrishmorris Daresbury Lab, Daresbury, Warrington, UK, WA4 4AD
Re: [ccp4bb] Archiving for fraud detection
On Nov 4, 2011, at 2:09 AM, Chris Morris wrote: > One argument for archiving images has been that reprocessing could > demonstrate deliberately deceptive structures. > > In fact, what is needed for this is not necessarily the image. It is the last > data file that was produced by a trusted computer. Although this is a good idea from the perspective of storage, it is difficult to implement. For this idea to work, you need a (1) certificate system, (2) certificate authority. The certification is necessary to verify that the data file was indeed generated by a trusted computer. The chosen file needs to be certified by the authority and the certification archived on a trusted system. None of these requirements are terribly problematic. The infrastructure for a certificate system is free in the form of openSSL. Almost any lab or institution could easily become a certificate authority. The storage requirements for the certificates are trivial. For example, if a certificate were 2 KB, then, for the 8,000 structures per year, the storage requirements would be 1.6 MB. After 1000 years, we would fill up my $14.95 2 GB thumb drive. The difficulty is that certification should be done on the file before it is transferred from the trusted computer. This requires inserting the certification process somewhere in the transfer pipeline, which is difficult because it requires all the synchrotrons to actually implement it. Allowing the user to produce the certificate after transfer is as useful as having no certificate system at all. Then there is the issue of data collection on a home source. James
[ccp4bb] Call for submissions to Computational Crystallography Newsletter
Calling for articles and short communications of interest tostructural biologists. The deadline for publication in the January2012 issue is 1st Dec, 2011. The Computational Crystallography Newsletter (CCN) is an electronicnewsletter for structural biologists, and is published online every 6months. Feature articles, meeting announcements and reports can besubmitted to me at any time for consideration. Submission of text byemail or word-processing files using the CCN templates is requested.Past newsletters and the template are available atwww.phenix-online.org/newsletter. Cheers Nigel -- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : nwmoria...@lbl.gov Fax : 510-486-5909 Web : CCI.LBL.gov
Re: [ccp4bb] atomic scattering factors in REFMAC
Im very grateful to the community for supporting me with so interesting information! Now my understanding of the subject is much better! With best regards, Ivan Shabalin
[ccp4bb] Xenon Derivatization
Hi everyone, My name is Brennan Bonnet and I am doing my Master’s project on SAD phasing of proteins using xenon gas. I plan on doing several proteins but first I am trying to get everything working smoothly on lysozyme since it is easy to grow, diffracts well, and is already known to bind xenon atoms (PDB entry 1C10, 3 sites @ 8bar pressure). Put simply, my method involves growing the crystals, mounting them in cryoloops, cryoprotection (if required), pressurization by xenon gas using the Hampton Xenon Chamber and quickly freezing them using liquid nitrogen with only a couple of seconds between depressurization and freezing. I have chosen pressures and durations of pressurization based on previous work which indicates that suitable derivatives may be produced using pressures between 1-100 bar and that binding should be complete within minutes. (see Use of Noble Gases Xenon and Krypton as Heavy Atoms in Protein Structure Determination by M. Schiltz, R. Fourme, and Thierry Prangé for a summary). Therefore I have chosen to use pressures between 7-28bar (100-400psi) for a duration of 15 minutes. After processing using XDS and solving with Phenix, the results show occupancies <0.1 which indicate no xenon binding or at least nothing that “sticks out”. The general trend is that increased xenon pressure results in a stronger anomalous signal and I have attached a table below with some processed data from XDS. I plan on trying a couple of other things. I have been collecting at 7keV but plan to try 6keV in order to get closer to the xenon L-edges and get a better anomalous signal. I also plan on trying longer pressurization times up to an hour to hopefully get better occupancy. Has anyone had any success with this method or any sort of “Aha!” moment? Help in the matter would be much appreciated. Set Pressure Energy Anom MaxAnom Total Anom Max / Anom Total Rmeas Resolution Last shell I/σ(I) (psi)(keV) (%) (Å) Sep7100 7 2.111 1.352 1.56139053342.03 13.9 Sep7160 7 1.935 1.244 1.5554662384.7 2.03 12.17 Sep7200 7 2.454 1.293 1.8979118333.4 2.03 11.01 Jul28 200 7 3.13 1.7491.7895940542.2 2.03 17.6 Sep7280 7 2.375 1.54 1.5422077923.1 2.03 14.33 Jul28 400 7 3.082 1.649 1.8690115223.5 2.03 14.29 Thanks, ~Brennan~
