[ccp4bb] AW: [ccp4bb] insertion code problem
Dear Rain, Insertion codes are still a sore point for many CCP4 programs and one of the reasons I prefer Buster over Refmac. Refmac5 does not remove insertion codes so I suspect the problem was with autoMR. The easiest is to superimpose your search model with insertion codes onto the pdb file which came out of the autoMR procedure. You could use lsqkab, but I think you can also do it in Coot. Then you continue refinement with this superimposed model. However, when I refined some structure with insertion codes in Refmac last week, Refmac created LINKR gap records for the inserted residues, cutting all peptide links. With an editor I had to change the gap to TRANS and then it worked. Good luck! Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von MAGGIE Gesendet: Mittwoch, 26. Juni 2013 04:07 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] insertion code problem Dear group, I have a insertion code question. I used molecular replacement (CCP4, autoMR) to solve two structures: one is monomer, and another one is tetramer. The model I used is one chain of a dimer and the model has insertion code. After molecular replacement and refinement using refmac5 in CCP4, the new structures lost the insertion code, and the residues were numbered consecutively. Can anyone tell me how to keep the insertion code in the new structures? Thank you, Rain
Re: [ccp4bb] AW: [ccp4bb] insertion code problem
I think pdbset from CCP4 can renumber a PDB and hence get rid of the uggly insertion codes. On 06/26/2013 03:33 PM, herman.schreu...@sanofi.com wrote: Dear Rain, Insertion codes are still a sore point for many CCP4 programs and one of the reasons I prefer Buster over Refmac. Refmac5 does not remove insertion codes so I suspect the problem was with autoMR. The easiest is to superimpose your search model with insertion codes onto the pdb file which came out of the autoMR procedure. You could use lsqkab, but I think you can also do it in Coot. Then you continue refinement with this superimposed model. However, when I refined some structure with insertion codes in Refmac last week, Refmac created LINKR gap records for the inserted residues, cutting all peptide links. With an editor I had to change the gap to TRANS and then it worked. Good luck! Herman *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von *MAGGIE *Gesendet:* Mittwoch, 26. Juni 2013 04:07 *An:* CCP4BB@JISCMAIL.AC.UK *Betreff:* [ccp4bb] insertion code problem Dear group, I have a insertion code question. I used molecular replacement (CCP4, autoMR) to solve two structures: one is monomer, and another one is tetramer. The model I used is one chain of a dimer and the model has insertion code. After molecular replacement and refinement using refmac5 in CCP4, the new structures lost the insertion code, and the residues were numbered consecutively. Can anyone tell me how to keep the insertion code in the new structures? Thank you, Rain
[ccp4bb] AW: [ccp4bb] AW: [ccp4bb] insertion code problem
Dear Francois, I also prefer not to use insertion codes. However, for certain protein families (serine proteases, antibodies), vast amounts of literature exist using amino acid numbering schemes with insertion codes. By creating a new numbering scheme without insertion codes, one would create a lot of confusion. Also, nowhere in the PDB definitions it is mentioned that insertion codes are not allowed or that amino acids should be numbered consecutively. It is only due to poor programming that programs are not able to handle insertion codes correctly. Best regards, Herman -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Francois Berenger Gesendet: Mittwoch, 26. Juni 2013 08:42 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] AW: [ccp4bb] insertion code problem I think pdbset from CCP4 can renumber a PDB and hence get rid of the uggly insertion codes. On 06/26/2013 03:33 PM, herman.schreu...@sanofi.com wrote: Dear Rain, Insertion codes are still a sore point for many CCP4 programs and one of the reasons I prefer Buster over Refmac. Refmac5 does not remove insertion codes so I suspect the problem was with autoMR. The easiest is to superimpose your search model with insertion codes onto the pdb file which came out of the autoMR procedure. You could use lsqkab, but I think you can also do it in Coot. Then you continue refinement with this superimposed model. However, when I refined some structure with insertion codes in Refmac last week, Refmac created LINKR gap records for the inserted residues, cutting all peptide links. With an editor I had to change the gap to TRANS and then it worked. Good luck! Herman *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von *MAGGIE *Gesendet:* Mittwoch, 26. Juni 2013 04:07 *An:* CCP4BB@JISCMAIL.AC.UK *Betreff:* [ccp4bb] insertion code problem Dear group, I have a insertion code question. I used molecular replacement (CCP4, autoMR) to solve two structures: one is monomer, and another one is tetramer. The model I used is one chain of a dimer and the model has insertion code. After molecular replacement and refinement using refmac5 in CCP4, the new structures lost the insertion code, and the residues were numbered consecutively. Can anyone tell me how to keep the insertion code in the new structures? Thank you, Rain
[ccp4bb] AW: [ccp4bb] Rfree is 20%,why still green and red density?
Dear Jiang Yan, The Matthews function is based on an average protein crystal with 50% solvent. However, crystals do exist with as little as 25% solvent or as much as 75% solvent, so if your structure refines to an Rfree of 20%, your structure is solved and you have a crystal with a high percentage of solvent (which may explain your low Rfree). Maps are usually contoured at sigma levels, based on the variation in the electron density map. So with an Rfree of 20%, your difference map will be very flat with and the sigma will be very low. Also the 3 sigma level usually used for difference maps will be very low and statistically, there are always some peaks at plus or minus 3 sigma, but they are nothing to worry about. Best, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von ?? Gesendet: Mittwoch, 26. Juni 2013 06:05 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Rfree is 20%,why still green and red density? Hi everyone, I now meet some problems when trying to solve structure.Space group is P6422, and Mathews function shows there are 4 molecules in one asymmetry unit. However, Phenix-autobuild shows only 2 molecules in on one asymmetry unit, after refinement, Rfree=20%,(resolution is 2.8A). Although AA fit the map well, there are still some green and red density. I wonder if anyone met this problem before? Any suggestion is welcome. Best, Jiang Yan
Re: [ccp4bb] AW: [ccp4bb] Rfree is 20%,why still green and red density?
The Matthews function is based on an average protein crystal with 50% solvent. Not sure what that a 'Matthews function' exactly would be - and that an assumption of 50 solvent content is made anywhere in the Vm calculation is new to me. The only defensible prior that goes into the calculation of Vm is a fixed protein specific volume, for details see Quillin Matthews 2000 Acta D56 791. The Matthews Probability calculator in addition considers the actual resolution and provides a probability distribution, i.e. the probability for each of the possible numbers of molecules in the unit cell. The more molecules are possible, the more indiscriminate the possible solutions become, i.e. the actual number needs to be determined by other, supplemental information. http://www.ruppweb.org/mattprob/ Best, BR
[ccp4bb] FW: [ccp4bb] PIMS XtalView Help
Hi Dwayne, Please send me a copy of your stack traces. I have just release PiMS4.4. I would like to review the errors that have affected you before building a release of xtalPiMS. Regards, Chris Morris From: McCully, Dwayne (NIH/NIAMS) [C] dmccu...@mail.nih.govmailto:dmccu...@mail.nih.gov Date: 21 June 2013 11:17:47 GMT+01:00 To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] PIMS XtalView Help Reply-To: McCully, Dwayne (NIH/NIAMS) [C] dmccu...@mail.nih.govmailto:dmccu...@mail.nih.gov Hello Everyone, I'm looking for a group/person that has PIMS and Xtailpims installed which does not throw Java errors while using the program. I've been struggling to get the program to work without error trying different versions of the below programs. I believe PIMS and Xtalpims has potential for my group so I looking for outside help. I need to know the following, with no errors, to make sure my setup is correct: Java Version Tomcat Version Windows or Linux version Apache Version Thanks in advance. Dwayne Dwayne McCully Structural Biology Section, NIAID, NIH Contractor -- Scanned by iCritical.
Re: [ccp4bb] Rfree is 20%,why still green and red density?
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Jiang Yan, how many reflections to you have in the free-set. At P6422 with a resolution of 2.8 you may have only a few hundred and thus not get a reliable Rfree value. Its low value may be due to overfitting. What does the cyrstal packing look like: Do you have the impression there is room for one or two extra residues? If not and if your model looks pleasing than you may not have a problem but a well refined structure. Best, Tim On 06/26/2013 06:05 AM, 姜艳 wrote: Hi everyone, I now meet some problems when trying to solve structure.Space group is P6422, and Mathews function shows there are 4 molecules in one asymmetry unit. However, Phenix-autobuild shows only 2 molecules in on one asymmetry unit, after refinement, Rfree=20%,(resolution is 2.8A). Although AA fit the map well, there are still some green and red density. I wonder if anyone met this problem before? Any suggestion is welcome. Best, Jiang Yan - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFRyr28UxlJ7aRr7hoRAvNFAJ9wv2Yharh75/Eo5lfMeboViVuJ8wCgljS8 dh1VqqeriYb6uM9F5hCa77M= =+0kN -END PGP SIGNATURE-
Re: [ccp4bb] iMosflm bug? - SOLVED
Hi I've just installed a Plain vanilla copy of Ubuntu 13.0.4 (aka rastafarian reefer or somesuch) with iMosflm 1.0.7 and CCP4 6.3.0 and found that Roger's suggestions were all that was needed (but I did log out and in again to use them) - sudo apt-get install ttf-mscorefonts-installer # installs microsoft fonts sudo apt-get install xfs xfstt xfonts-75dpi xfonts-100dpi # installs xfonts and xfont server Curiously, although Thomas found that the mscorefonts were installed by default, they weren't on my system. For those of you with time to spare, the Unity desktop that comes with Ubuntu is interesting and may reward further investigation... On 26 Jun 2013, at Wed26 Jun 06:21, Thomas Cleveland wrote: Hi everyone, Thanks again for the help. As several people suggested, it seems to have been a fonts package that was needed. I'm not sure if there is a single particular package that would have solved the problem, but I installed the following combination: t1-xfree86-nonfree ttf-xfree86-nonfree ttf-xfree86-nonfree-syriac xfonts-75dpi xfonts-100dpi xfs xfstt (ttf-mscorefonts-installer was already installed by default) Everything is working fine now. Thanks again. -Thomas On Tue, Jun 25, 2013 at 10:23 AM, Thomas Cleveland thomas.clevel...@gmail.com wrote: Hi everyone, Thanks for all your responses. I will try working on the fonts when I get back to my computer and report back when I find a working solution. I'm using a fresh installation of Ubuntu 13.04 amd64, so hopefully it will be relevant to other users of newer Ubuntu releases. Harry, I could drag the lower right corner to make the window *smaller*, but it would not let me make it any bigger. Reginald, I'll take a look at that. Thanks, Thomas On Mon, Jun 24, 2013 at 10:46 PM, Thomas Cleveland thomas.clevel...@gmail.com wrote: Has anyone else encountered this? When I go to processing options in iMosflm 1.0.7, many of the parameters on the right hand side of the window are cut off, and there is no way to scroll over so that I can enter them. I've attached link to a picture of what it looks like. https://www.dropbox.com/s/muwblcgohhxu94c/iMosflm-cut-off.png Thanks, Thomas Cleveland Harry -- ** note change of address ** Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH Chairman of European Crystallographic Association SIG9 (Crystallographic Computing)
Re: [ccp4bb] Rfree is 20%,why still green and red density?
you may have only a few hundred and thus not get a reliable Rfree value. The estimate for the error in R free as a function of the number of reflections is as follows: Brunger initially estimated^35 that the uncertainty in R-free is proportional to (Nref )^-1/2, which is reasonable to assume because this is how uncertainties vary with sample size. Tickle et al. finally showed^38 that the relative uncertainty in Rfree is exactly equal to (2Nref )^-1/2 confirming Brunger's initial estimate, with constant of proportionality as 2^-1/2. Following this proportionality, ~1000 reflections are sufficient to obtain a better than 1% precision for an overall R-free in the 20-30% range, i.e. 'a few hundred' is still not too bad. Best, BR
Re: [ccp4bb] Rfree is 20%,why still green and red density?
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Sure, but in P6422 with 2.8A I'd say that 5% of reflections are more likely near 40-50 than 'a few hundreds' if the cell too small. And most people simply flag 5% of their reflections without checking how many these really are. Splitting these up into resolution ranges makes the situation even worse, and as far as I understand this is what most ML-programs do for proper Maximum Likelihood refinement. A proper k-fold cross validation (eg. 50-fold) would, in my point of view, give a more realistic R value. Best, Tim On 06/26/2013 01:30 PM, Bernhard Rupp wrote: you may have only a few hundred and thus not get a reliable Rfree value. The estimate for the error in R free as a function of the number of reflections is as follows: Brunger initially estimated^35 that the uncertainty in R-free is proportional to (Nref )^-1/2, which is reasonable to assume because this is how uncertainties vary with sample size. Tickle et al. finally showed^38 that the relative uncertainty in Rfree is exactly equal to (2Nref )^-1/2 confirming Brunger's initial estimate, with constant of proportionality as 2^-1/2. Following this proportionality, ~1000 reflections are sufficient to obtain a better than 1% precision for an overall R-free in the 20-30% range, i.e. 'a few hundred' is still not too bad. Best, BR - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFRytS9UxlJ7aRr7hoRAllOAJ0VfeYdyrkQV422etZ5y+8v1N7lbQCg5ejR NwLiN2StqANxSKPB3yhjUqE= =A266 -END PGP SIGNATURE-
Re: [ccp4bb] announcement: (another) GUI for XDS
Hi Kay, hi all, sorry to bother again, but I was wondering if people is experiencing the same problem I am. With the nice new XDS graphical interface, I cannot manage to have the show frame with predicted spots script to work. It looks like all the steps are performed correctly, but then XDS-viewer does not display the frame (here you can see what happens: https://dl.dropboxusercontent.com/u/4914553/Screen%20Shot%202013-06-26%20at%204.44.40%20PM.png). Is anybody else experiencing this? Any hint on how to make XDS-viewer to work in this case? Thanks in advance, Sebastiano On Jun 15, 2013, at 9:49 AM, Kay Diederichs kay.diederi...@uni-konstanz.de wrote: Hi everybody, I developed a GUI for academic users of XDS which is documented at http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/XDSgui . This XDSwiki article also has the links to binaries of xdsGUI (or XDSgui or xds-gui; this has not been decided yet ...), for Linux 32 and 64 bit (compiled on a RHEL 6 clone), and Mac OS X (compiled on 10.7). The 'added value' of the GUI is that it produces informative plots which should greatly help to make decisions in data processing. The GUI is simple, tries to be self-explanatory and should be straightforward to operate. Noteworthy may be the TOOLS tab which offers a means to run commandline scripts upon a click with the mouse. This tab accepts user modifications which should make it attractive also for expert users - they can run their own scripts. This is the first version made publicly available. There are probaby bugs and I would like to learn about these. In particular, Mac experts please tell me how to solve the problems explained at the bottom of the Wiki article ... thanks, Kay -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: kay.diederi...@uni-konstanz.de Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box 647, D-78457 Konstanz -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990
Re: [ccp4bb] announcement: (another) GUI for XDS
Hi Sebastiano, sorry, I don't see immediately what's wrong. The console seems to show the XDS output of an INTEGRATE job that only looked at a single (judging from the small number of reflections ...) frame (number 10, I'd guess; you could check this if you scroll up a bit). Could you please check the contents of the temp directory? It should have a file FRAME_10.cbf . If you use the console window, cd to that directory and run xds-viewer FRAME_10.cbf then you should be able to see what you want to see. If that works, then I do not understand why the script fails. If the file is _not_ there or xds-viewer FRAME_10.cbf does _not_ show it, then we'll have to sort this out. I suggest to move the debugging to private email, though, and to only post the solution. But maybe someone else has the solution already? By the way, a newer version of xdsGUI is available for download, and there's also versions that run on older Linux systems. best, Kay
Re: [ccp4bb] announcement: (another) GUI for XDS
Hi Sebastiano, Yes, you have to put the xds-viewer executable in your PATH. In the Mac and assuming /usr/local/bin is in your PATH: cd /usr/local/bin ln -s /Applications/Sci/Struct/XDS-Viewer.app/Contents/MacOS/xds-viewer-bin . Cheers, Miguel Ortiz Lombardía Architecture et Fonction des Macromolécules Biologiques (UMR7257) CNRS, Aix-Marseille Université Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 86 44 Fax: +33(0) 491 26 67 20 mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia Le 26/06/13 16:50, Sebastiano Pasqualato a écrit : Hi Kay, hi all, sorry to bother again, but I was wondering if people is experiencing the same problem I am. With the nice new XDS graphical interface, I cannot manage to have the show frame with predicted spots script to work. It looks like all the steps are performed correctly, but then XDS-viewer does not display the frame (here you can see what happens: https://dl.dropboxusercontent.com/u/4914553/Screen%20Shot%202013-06-26%20at%204.44.40%20PM.png). Is anybody else experiencing this? Any hint on how to make XDS-viewer to work in this case? Thanks in advance, Sebastiano On Jun 15, 2013, at 9:49 AM, Kay Diederichs kay.diederi...@uni-konstanz.de mailto:kay.diederi...@uni-konstanz.de wrote: Hi everybody, I developed a GUI for academic users of XDS which is documented at http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/XDSgui . This XDSwiki article also has the links to binaries of xdsGUI (or XDSgui or xds-gui; this has not been decided yet ...), for Linux 32 and 64 bit (compiled on a RHEL 6 clone), and Mac OS X (compiled on 10.7). The 'added value' of the GUI is that it produces informative plots which should greatly help to make decisions in data processing. The GUI is simple, tries to be self-explanatory and should be straightforward to operate. Noteworthy may be the TOOLS tab which offers a means to run commandline scripts upon a click with the mouse. This tab accepts user modifications which should make it attractive also for expert users - they can run their own scripts. This is the first version made publicly available. There are probaby bugs and I would like to learn about these. In particular, Mac experts please tell me how to solve the problems explained at the bottom of the Wiki article ... thanks, Kay -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: kay.diederi...@uni-konstanz.de mailto:kay.diederi...@uni-konstanz.de Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box 647, D-78457 Konstanz -- *Sebastiano Pasqualato, PhD* Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990
Re: [ccp4bb] announcement: (another) GUI for XDS
Hmm, My XDS-Viewer.app installation is not in a standard place, more likely you need: cd /usr/local/bin ln -s /Applications/XDS-Viewer.app/Contents/MacOS/xds-viewer-bin . Cheers, Miguel Ortiz Lombardía Architecture et Fonction des Macromolécules Biologiques (UMR7257) CNRS, Aix-Marseille Université Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 86 44 Fax: +33(0) 491 26 67 20 mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia Le 26/06/13 17:08, Miguel Ortiz Lombardía a écrit : Hi Sebastiano, Yes, you have to put the xds-viewer executable in your PATH. In the Mac and assuming /usr/local/bin is in your PATH: cd /usr/local/bin ln -s /Applications/Sci/Struct/XDS-Viewer.app/Contents/MacOS/xds-viewer-bin . Cheers, Miguel Ortiz Lombardía Architecture et Fonction des Macromolécules Biologiques (UMR7257) CNRS, Aix-Marseille Université Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 86 44 Fax: +33(0) 491 26 67 20 mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia Le 26/06/13 16:50, Sebastiano Pasqualato a écrit : Hi Kay, hi all, sorry to bother again, but I was wondering if people is experiencing the same problem I am. With the nice new XDS graphical interface, I cannot manage to have the show frame with predicted spots script to work. It looks like all the steps are performed correctly, but then XDS-viewer does not display the frame (here you can see what happens: https://dl.dropboxusercontent.com/u/4914553/Screen%20Shot%202013-06-26%20at%204.44.40%20PM.png). Is anybody else experiencing this? Any hint on how to make XDS-viewer to work in this case? Thanks in advance, Sebastiano On Jun 15, 2013, at 9:49 AM, Kay Diederichs kay.diederi...@uni-konstanz.de mailto:kay.diederi...@uni-konstanz.de wrote: Hi everybody, I developed a GUI for academic users of XDS which is documented at http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/XDSgui . This XDSwiki article also has the links to binaries of xdsGUI (or XDSgui or xds-gui; this has not been decided yet ...), for Linux 32 and 64 bit (compiled on a RHEL 6 clone), and Mac OS X (compiled on 10.7). The 'added value' of the GUI is that it produces informative plots which should greatly help to make decisions in data processing. The GUI is simple, tries to be self-explanatory and should be straightforward to operate. Noteworthy may be the TOOLS tab which offers a means to run commandline scripts upon a click with the mouse. This tab accepts user modifications which should make it attractive also for expert users - they can run their own scripts. This is the first version made publicly available. There are probaby bugs and I would like to learn about these. In particular, Mac experts please tell me how to solve the problems explained at the bottom of the Wiki article ... thanks, Kay -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: kay.diederi...@uni-konstanz.de mailto:kay.diederi...@uni-konstanz.de Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box 647, D-78457 Konstanz -- *Sebastiano Pasqualato, PhD* Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990
Re: [ccp4bb] Rfree is 20%,why still green and red density?
Hi Bernhard, The formula from Tickly applies to the weighted/generalized/Hamilton free R-factor. From k-fold cross validation tests we observed that the 'regular' R-free has a standard deviation of R-free*(Nref )^-1/2 Cheers, Robbie -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bernhard Rupp Sent: Wednesday, June 26, 2013 13:31 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Rfree is 20%,why still green and red density? you may have only a few hundred and thus not get a reliable Rfree value. The estimate for the error in R free as a function of the number of reflections is as follows: Brunger initially estimated^35 that the uncertainty in R-free is proportional to (Nref )^-1/2, which is reasonable to assume because this is how uncertainties vary with sample size. Tickle et al. finally showed^38 that the relative uncertainty in Rfree is exactly equal to (2Nref )^-1/2 confirming Brunger's initial estimate, with constant of proportionality as 2^-1/2. Following this proportionality, ~1000 reflections are sufficient to obtain a better than 1% precision for an overall R-free in the 20-30% range, i.e. 'a few hundred' is still not too bad. Best, BR
[ccp4bb] R too low?
Hello Everyone I have two data sets, from the same crystal form (space group P32) of the same protein, collected at 100 K at SSRL, about 2.2 A resolution, that refining to R = 0.14, Rf = 0.26 (refmac/TLS). This is a molecular replacement solution, from a model with about 40% homology (after MR density was apparent for some missing or misbuilt residues, so I don't think the structure is stuck in the wrong place. The Fo-Fc map is essentially featureless. The 2Fo-Fc map doesn't look as good as it should - for instance, there are very few water molecules to be found. The data reduction statistics look OK, the resolution cutoff is pretty conservative. There is one molecule in the asymmetric unit, so no NCS. There is no twinning either. It seemed to me that the R is too low, not Rf too high. More normally, R ends up about .18 - .20 for a data set at this resolution. I reprocessed the images with a different data processing program and redid the MR. The data reduction statistics look similar, the resolution is the same, but now the structure refines to R = 0.20, Rf = 0.24 (same free R set of reflections chosen, still refmac/TLS.) The maps look more normal. Further rebuilding took us to R = 0.18, Rf = 0.22 So, the question I have (and that I've been asked by the student and PI) is: What was the problem with the original data set? What should I be looking for in the data reduction log files, for instance, or in the refinement log? The large R - free R spread is characteristic of overfitting, but the geometry is not too loose (rmsd bonds = 0.14), there are plenty of reflections (both working and free). Can anyone point me toward a reason R would be low? Thanks Sue Dr. Sue A. Roberts Dept. of Chemistry and Biochemistry University of Arizona 1041 E. Lowell St., Tucson, AZ 85721 Phone: 520 621 8171 or 520 621 4168 s...@email.arizona.edu http://www.cbc.arizona.edu/xray or http://www.cbc.arizona.edu/facilities/x-ray_diffraction
Re: [ccp4bb] R too low?
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Sue, if you made your rmsd (bonds) 20-30 times smaller I would agree they were not too loose. 0.14A is pretty high. So two suggestions: a) check the molprobity report of your PDB if its geometry is sane b) check the CC plot of one data set against the other one to check if the problem is due to two different data or due to the PDB file (xprep can do this plot conveniently). Did you check if you converted the data twice to amplitudes, or maybe not at all? Best, Tim On 06/26/2013 05:44 PM, Roberts, Sue A - (suer) wrote: Hello Everyone I have two data sets, from the same crystal form (space group P32) of the same protein, collected at 100 K at SSRL, about 2.2 A resolution, that refining to R = 0.14, Rf = 0.26 (refmac/TLS). This is a molecular replacement solution, from a model with about 40% homology (after MR density was apparent for some missing or misbuilt residues, so I don't think the structure is stuck in the wrong place. The Fo-Fc map is essentially featureless. The 2Fo-Fc map doesn't look as good as it should - for instance, there are very few water molecules to be found. The data reduction statistics look OK, the resolution cutoff is pretty conservative. There is one molecule in the asymmetric unit, so no NCS. There is no twinning either. It seemed to me that the R is too low, not Rf too high. More normally, R ends up about .18 - .20 for a data set at this resolution. I reprocessed the images with a different data processing program and redid the MR. The data reduction statistics look similar, the resolution is the same, but now the structure refines to R = 0.20, Rf = 0.24 (same free R set of reflections chosen, still refmac/TLS.) The maps look more normal. Further rebuilding took us to R = 0.18, Rf = 0.22 So, the question I have (and that I've been asked by the student and PI) is: What was the problem with the original data set? What should I be looking for in the data reduction log files, for instance, or in the refinement log? The large R - free R spread is characteristic of overfitting, but the geometry is not too loose (rmsd bonds = 0.14), there are plenty of reflections (both working and free). Can anyone point me toward a reason R would be low? Thanks Sue Dr. Sue A. Roberts Dept. of Chemistry and Biochemistry University of Arizona 1041 E. Lowell St., Tucson, AZ 85721 Phone: 520 621 8171 or 520 621 4168 s...@email.arizona.edu http://www.cbc.arizona.edu/xray or http://www.cbc.arizona.edu/facilities/x-ray_diffraction - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFRyw6vUxlJ7aRr7hoRAq4HAKCJJf+FfRVT7u3UOrty0vTOFMN+mgCgtHz8 MYe+23hH+MKy/7E/h2w25+Q= =WAsD -END PGP SIGNATURE-
Re: [ccp4bb] R too low?
HI Sue, Can you give rmsZ for the bond and angles (from the Refmac output)? I never could figure these rmsd values out... I'm guessing that the restraint are too loose, or at least not optimal. Perhaps, they went overboard with the TLS as well (sometimes fewer TLS goups give much better R and R-free values). I'm not sure anything in particular is wrong with the data processing. They should optimize the restraint weights in refinement first. In this case tighter B-factor restraint weights might do the trick. Gratuitous plug: throw the model and data into PDB_REDO (which uses Refmac too) and see if it gives better refinement results. Cheers, Robbie -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Roberts, Sue A - (suer) Sent: Wednesday, June 26, 2013 17:45 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] R too low? Hello Everyone I have two data sets, from the same crystal form (space group P32) of the same protein, collected at 100 K at SSRL, about 2.2 A resolution, that refining to R = 0.14, Rf = 0.26 (refmac/TLS). This is a molecular replacement solution, from a model with about 40% homology (after MR density was apparent for some missing or misbuilt residues, so I don't think the structure is stuck in the wrong place. The Fo-Fc map is essentially featureless. The 2Fo-Fc map doesn't look as good as it should - for instance, there are very few water molecules to be found. The data reduction statistics look OK, the resolution cutoff is pretty conservative. There is one molecule in the asymmetric unit, so no NCS. There is no twinning either. It seemed to me that the R is too low, not Rf too high. More normally, R ends up about .18 - .20 for a data set at this resolution. I reprocessed the images with a different data processing program and redid the MR. The data reduction statistics look similar, the resolution is the same, but now the structure refines to R = 0.20, Rf = 0.24 (same free R set of reflections chosen, still refmac/TLS.) The maps look more normal. Further rebuilding took us to R = 0.18, Rf = 0.22 So, the question I have (and that I've been asked by the student and PI) is: What was the problem with the original data set? What should I be looking for in the data reduction log files, for instance, or in the refinement log? The large R - free R spread is characteristic of overfitting, but the geometry is not too loose (rmsd bonds = 0.14), there are plenty of reflections (both working and free). Can anyone point me toward a reason R would be low? Thanks Sue Dr. Sue A. Roberts Dept. of Chemistry and Biochemistry University of Arizona 1041 E. Lowell St., Tucson, AZ 85721 Phone: 520 621 8171 or 520 621 4168 s...@email.arizona.edu http://www.cbc.arizona.edu/xray or http://www.cbc.arizona.edu/facilities/x-ray_diffraction
Re: [ccp4bb] announcement: (another) GUI for XDS
Yep, sorry that is the link I actually made, I wrote it too hastily, my bad. Miguel Ortiz Lombardía Architecture et Fonction des Macromolécules Biologiques (UMR7257) CNRS, Aix-Marseille Université Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia El 26/06/13 19:46, Kay Diederichs escribió: Hi Sebastiano, ok, I think I have the solution, and, hoping it's correct, have put it into http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/XDSgui#Installation What you need is the symlink ln -s /Applications/XDS-Viewer.app/Contents/MacOS/xds-viewer-bin /usr/local/bin/xds-viewer In the above please note the xds-viewer-bin - I guess you have it differently. HTH, Kay Am 26.06.13 19:23, schrieb Sebastiano Pasqualato: Hi Kay, xds nicely outputs the FRAME_##.cbf image in the temp directory. The problem is that the command xds-viewer FRAME_10.cbf does not open the frame, but only the viewer, without loading the frame. If I then open the frame from the FIle -- Load image menu commands, I have it. Of course that's ok, but a little more tedious. Miguel, the xds-viewer command is nicely added to the path, I guess, by exporting the directory in the .bashrc export XDSVIEWERPATH=/Applications/XDS-Viewer.app/Contents/MacOS/ I have tried setting the link as you suggested, but that does not make the command above open the image directly. Still puzzled, Sebastiano On Jun 26, 2013, at 5:04 PM, Kay Diederichs kay.diederi...@uni-konstanz.de mailto:kay.diederi...@uni-konstanz.de wrote: Hi Sebastiano, sorry, I don't see immediately what's wrong. The console seems to show the XDS output of an INTEGRATE job that only looked at a single (judging from the small number of reflections ...) frame (number 10, I'd guess; you could check this if you scroll up a bit). Could you please check the contents of the temp directory? It should have a file FRAME_10.cbf . If you use the console window, cd to that directory and run xds-viewer FRAME_10.cbf then you should be able to see what you want to see. If that works, then I do not understand why the script fails. If the file is _not_ there or xds-viewer FRAME_10.cbf does _not_ show it, then we'll have to sort this out. I suggest to move the debugging to private email, though, and to only post the solution. But maybe someone else has the solution already? By the way, a newer version of xdsGUI is available for download, and there's also versions that run on older Linux systems. best, Kay -- *Sebastiano Pasqualato, PhD* Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990
[ccp4bb] Supplier for X-ray sensitive paper
Hi All, I have done a few searches of the archive and googled a few times but not found what I am looking for. Could someone point me in the direction of a supplier of the X-ray sensitive paper I have used in the past to confirm beam position on a home source. I am specifically after this type of paper rather than X-ray film so as not to have to go through any developing stage and quickly visualize the location of the beam at different points beyond the position of the goniometer towards the detector. A USA supplier would be great but any would do. Many thanks, Joe P -- Confidentiality Notice: This message is private and may contain confidential and proprietary information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorized use or disclosure of the contents of this message is not permitted and may be unlawful.
Re: [ccp4bb] Supplier for X-ray sensitive paper
Hi Joe - This is what I've used in the past. It's film, not paper, but needs no developer and is instant-readout. I think the find a distributor link should help you obtain it. http://www.ashland.com/products/gafchromic-radiology-films - Matt On 6/26/13 3:51 PM, Patel, Joe wrote: Hi All, I have done a few searches of the archive and googled a few times but not found what I am looking for. Could someone point me in the direction of a supplier of the X-ray sensitive paper I have used in the past to confirm beam position on a home source. I am specifically after this type of paper rather than X-ray film so as not to have to go through any developing stage and quickly visualize the location of the beam at different points beyond the position of the goniometer towards the detector. A USA supplier would be great but any would do. Many thanks, Joe P -- Confidentiality Notice: This message is private and may contain confidential and proprietary information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorized use or disclosure of the contents of this message is not permitted and may be unlawful. -- Matthew Franklin, Ph. D. Senior Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (212) 939-0660 ext. 9374
[ccp4bb] cluster Ta6Br12 in phaser
We are trying to get SAD phases using a Ta6Br12 cluster using phaser. Sites were found with ShelxD and we have set the ha.pdb in the form: ATOM 1 TX HAT 1 24.569 195.940 54.912 1.00 20.00 TX and we define the scatterer in phaser.inp with: SCATTERING TYPE TX FP = -25.31 FDP = 11.7 FIX OFF but get the error: INPUT ERROR: Type T not element or cluster We've tried a few permutations of columns 14-15 and 78-79 of ha.pdb but phaser hasn't been able to successfully interpret the scattering type. I haven't been able to find detailed information about the format of the input pdb file with the HA sites to bypass this error. We're using phaser from ccp4-6.3.0 distributed by sbgrid. Any help will be much appreciated, Kevin Jude
