Re: [ccp4bb] anomalous signal
Look at the aimless plot of CCanom . That is the best indicator I think and very sensitive when you have such high redundancy Eleanor On 25 Apr 2014, at 22:13, Jim Pflugrath wrote: d/sig should be above 0.80 There seems to be plenty of signal there with all values above 1.02. We have solved structures with less multiplicity and lower d/sig. There is a different criteria of signal for when you know the positions of the anomalous substructure atoms and when you need to find the positions of the anomalous substructure atoms. As for no signal, I think I am on record that there is always an anomalous signal. :) But can you detect it? Jim From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Faisal Tarique [faisaltari...@gmail.com] Sent: Friday, April 25, 2014 4:06 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] anomalous signal Dear all sorry about my previous mail where i forgot to mention that the data was collected on home source at Cuk alpha and at 1.54A. written below is the log file of an anomalous data processed through SHELXC..my question is ..what is the strength of anomalous signal ?? as it is said For zero signal d'/sig and d/sig should be about 0.80. Then in the present case is there really a signal or can be assumed no signal..we are expecting one Ca atom bound to the protein at its active site..the redundancy of the data is 11.6..with this signal strength can we assume Ca to be present there or whatever little anomalous if present is due to something elseor there is no signal at all ??... Resl. Inf - 8.0 - 6.0 - 5.0 - 4.0 - 3.8 - 3.6 - 3.4 - 3.2 - 3.0 - 2.8 - 2.60 N(data) 375 493 580 1319 450 538 679 866 1081 1414 1709 I/sig58.8 38.6 32.6 38.3 27.7 27.2 21.9 18.4 12.6 9.5 6.1 %Complete 94.7 99.0 99.3 99.5 100.0 99.6 99.7 99.8 99.6 99.6 90.9 d/sig 1.65 1.27 1.18 1.25 1.19 1.12 1.11 1.11 0.97 1.02 1.05 -- Regards Faisal School of Life Sciences JNU
Re: [ccp4bb] anomalous signal
Dear Faisal, the lack of the CCanom line in the shelxc output suggests that your data are already merged, and my guess is you processed your data with HKL2000 - all other integration programs I am aware of do not merge the data at such an early stage giving you access to the CCanom Eleanor mentioned. There might be a switch in HKL2000 to not merge the data. A CCanom 30% is a good indicator of the presence of an anomalous signal. Best, Tim On 04/26/2014 12:18 PM, Eleanor Dodson wrote: Look at the aimless plot of CCanom . That is the best indicator I think and very sensitive when you have such high redundancy Eleanor On 25 Apr 2014, at 22:13, Jim Pflugrath wrote: d/sig should be above 0.80 There seems to be plenty of signal there with all values above 1.02. We have solved structures with less multiplicity and lower d/sig. There is a different criteria of signal for when you know the positions of the anomalous substructure atoms and when you need to find the positions of the anomalous substructure atoms. As for no signal, I think I am on record that there is always an anomalous signal. :) But can you detect it? Jim From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Faisal Tarique [faisaltari...@gmail.com] Sent: Friday, April 25, 2014 4:06 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] anomalous signal Dear all sorry about my previous mail where i forgot to mention that the data was collected on home source at Cuk alpha and at 1.54A. written below is the log file of an anomalous data processed through SHELXC..my question is ..what is the strength of anomalous signal ?? as it is said For zero signal d'/sig and d/sig should be about 0.80. Then in the present case is there really a signal or can be assumed no signal..we are expecting one Ca atom bound to the protein at its active site..the redundancy of the data is 11.6..with this signal strength can we assume Ca to be present there or whatever little anomalous if present is due to something elseor there is no signal at all ??... Resl. Inf - 8.0 - 6.0 - 5.0 - 4.0 - 3.8 - 3.6 - 3.4 - 3.2 - 3.0 - 2.8 - 2.60 N(data) 375 493 580 1319 450 538 679 866 1081 1414 1709 I/sig58.8 38.6 32.6 38.3 27.7 27.2 21.9 18.4 12.6 9.5 6.1 %Complete 94.7 99.0 99.3 99.5 100.0 99.6 99.7 99.8 99.6 99.6 90.9 d/sig 1.65 1.27 1.18 1.25 1.19 1.12 1.11 1.11 0.97 1.02 1.05 -- Regards Faisal School of Life Sciences JNU -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: OpenPGP digital signature
Re: [ccp4bb] Summary of feedback on diffuse streaks in diffraction pattern
... and there will be (shameless self-advertising): Ponnusamy et al. 2014 Acta D accepted You may also want to make pseudo-precession photographs using LABELIT. This will give you a better indication on the characteristics and directionality of the disorder. Bernhard Thanks to all who responded to my somewhat uninformative posting. Here are some references that were provided on what is most likely a lattice translocation disorder in one direction in these crystals, Porta et al. 2009 (Acta Cryst. D67, 628-638) Wagner et al., 2009, Acta Cryst. B65, 249-268 Sauter et al. 2010 (Acta Cryst. D43, 611-616) Wang et al., 2005, Acta Cryst. D61, 67-74 Laurie Betts On Mon, Apr 7, 2014 at 7:26 AM, Ivan Campeotto i.campeo...@imperial.ac.uk mailto:i.campeo...@imperial.ac.uk wrote: Dear Laurie, I think you may be dealing with a modulated structure, superposition of multiple lattices or a lattice-translocation defect, it is hard to judge based only on the diffraction pattern profile. For the first case, I would suggest to have a look at Porta et al. 2009 (Acta Cryst. D67, 628-638), where they describe the usage of Eval15 to process the data. In this scenario, the position of the satellite reflections can be described by an extra vector q, which can have from 1 to 3 components and it is added to the canonical scattering vector S (see also Wagner et al., 2009, Acta Cryst. B65, 249-268). However, from your image, the spots are not resolved inside the streaks, indicating that perhaps this is not the case. For the second case, I would recommend Sauter et al., 2010 (Acta Cryst. D43, 611-616), where the usage of LABELIT is described to deal with superposed lattices. For the third possible case, the lattice-traslocation defects, it is important to define how a translocation can occur between the two lattices (see details in Wang et al., 2005, Acta Cryst. D61, 67-74). Their diffraction images look very similar to yours. You do not comment whether you were able to perform data reduction. I suspect that it would be rather difficult, although the integration programs may reject the streaks at a certain price in terms of integration statistics etc. In any case I would recommend to deal with the issue as early as possible, i.e. data collection stage or indexing stage, to avoid of carrying the problem over into the next steps of structure solution / structure refinement. Out of curiosity, it would be nice to know the appearance of the streaks, if you collect data with fine slicing (i.e by using a Pilatus detector) or with a kappa goniometer (you may have already done this of course). Do you see these streaks in all crystal orientations? Can you resolve spots within the streaks and what is your resolution? Good luck! Best wishes Dr. Ivan Campeotto Imperial College London London, UK
Re: [ccp4bb] anomalous signal
Was there a reason that you turned off the scaling in Aimless (onlymerge)? If the data have come from Mosflm, this is definitely wrong - the result is that (among other things) you have negative CCanom values which is unusual to say the least Just run it with the default options, that's usually the best thing to do to start with Phil On 26 Apr 2014, at 14:38, Faisal Tarique faisaltari...@gmail.com wrote: Dear Eleanor and Tim. i have reprocessed the data through imosflm and run the aimless through the unmerged output mtz..i am attaching the output log file of the aimless..please tell me how to interpret the anomalous signal from the log file and where the information is written.. Thanks again for your much needed help. regards Faisal On Sat, Apr 26, 2014 at 5:22 PM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: Dear Faisal, the lack of the CCanom line in the shelxc output suggests that your data are already merged, and my guess is you processed your data with HKL2000 - all other integration programs I am aware of do not merge the data at such an early stage giving you access to the CCanom Eleanor mentioned. There might be a switch in HKL2000 to not merge the data. A CCanom 30% is a good indicator of the presence of an anomalous signal. Best, Tim On 04/26/2014 12:18 PM, Eleanor Dodson wrote: Look at the aimless plot of CCanom . That is the best indicator I think and very sensitive when you have such high redundancy Eleanor On 25 Apr 2014, at 22:13, Jim Pflugrath wrote: d/sig should be above 0.80 There seems to be plenty of signal there with all values above 1.02. We have solved structures with less multiplicity and lower d/sig. There is a different criteria of signal for when you know the positions of the anomalous substructure atoms and when you need to find the positions of the anomalous substructure atoms. As for no signal, I think I am on record that there is always an anomalous signal. :) But can you detect it? Jim From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Faisal Tarique [faisaltari...@gmail.com] Sent: Friday, April 25, 2014 4:06 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] anomalous signal Dear all sorry about my previous mail where i forgot to mention that the data was collected on home source at Cuk alpha and at 1.54A. written below is the log file of an anomalous data processed through SHELXC..my question is ..what is the strength of anomalous signal ?? as it is said For zero signal d'/sig and d/sig should be about 0.80. Then in the present case is there really a signal or can be assumed no signal..we are expecting one Ca atom bound to the protein at its active site..the redundancy of the data is 11.6..with this signal strength can we assume Ca to be present there or whatever little anomalous if present is due to something elseor there is no signal at all ??... Resl. Inf - 8.0 - 6.0 - 5.0 - 4.0 - 3.8 - 3.6 - 3.4 - 3.2 - 3.0 - 2.8 - 2.60 N(data) 375 493 580 1319 450 538 679 866 1081 1414 1709 I/sig58.8 38.6 32.6 38.3 27.7 27.2 21.9 18.4 12.6 9.5 6.1 %Complete 94.7 99.0 99.3 99.5 100.0 99.6 99.7 99.8 99.6 99.6 90.9 d/sig 1.65 1.27 1.18 1.25 1.19 1.12 1.11 1.11 0.97 1.02 1.05 -- Regards Faisal School of Life Sciences JNU -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -- Regards Faisal School of Life Sciences JNU 223_aimless.log
Re: [ccp4bb] Validation reports for all X-ray structures in the PDB
Any chance validation reports will ever be made for obsoleted entries? Eric On Wed, Apr 16, 2014 at 1:01 PM, Gerard DVD Kleywegt ger...@xray.bmc.uu.sewrote: Hi all, You may not have noticed, but 19 March 2014 was VR Day - the day that new style wwPDB validation reports for all X-ray structures were made publicly available - see http://www.wwpdb.org/news/news_2014.html#18-March-2014 The validation-related files for individual X-ray PDB entries can be accessed through the web sites and ftp sites of the various wwPDB partners. Speaking for PDBe, if you go to the summary page of an X-ray PDB entry, for instance: http://pdbe.org/1cbs you will see the percentile sliders displayed in the PDBportfolio widget (http://pdbe.org/portfolio) on the right of the page. (Clicking the big white arrow will start a slideshow of images related to this entry.) The legend of the percentile-slider plot contains a direct link to the validation report (as a PDF file; in this case http://www.ebi.ac.uk/pdbe/ entry-files/1cbs_validation.pdf). If you are not yet familiar with these new style validation reports, have a look here: http://www.wwpdb.org/validation-reports.html - in particular the user guide may be of interest: http://www.wwpdb.org/ ValidationPDFNotes.html If you want to download the full report (which lists all outliers for many of the validation criteria, instead of just the worst 5 or the first 5), or a graphic image of the percentile-slider plot, or an XML file with all validation data in machine-readable form, go to the downloads page of any X-ray PDB entry, either through clicking the Downloads link in the menu on the left, or directly by going to a URL of the form: http://pdbe.org/1cbs/downloads The section labelled Validation of the table provides the relevant links. Note that sites that include PDBportfolio in their pages now automatically display the percentile-slider plot and download link as well! To see this in action, go to the EDS page (if any) of your favourite X-ray PDB entry, e.g.: http://eds.bmc.uu.se/cgi-bin/eds/uusfs?pdbCode=1cbs Please send any comments, questions or suggestions on the new style validation reports to validat...@mail.wwpdb.org Questions about PDBe-specific pages and services can be sent to pdbeh...@ebi.ac.uk --Gerard --- Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK ger...@ebi.ac.uk . pdbe.org Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk
