[ccp4bb] Looking for the following values...
Hi All, I'm about ready to deposit my structure and have used pdb_extract to aid in the process. Unfortunately the following values were not found and are required by ADIT: 1) Under Data Collection, Reflections section: Observed criterion sigma(F) and Observed criterion sigma(I) 2) Under Refinement, Refinement Statistics section: Number unique reflections (all) I looked in my log files for HKL2000, PHASER, and PHENIX but am confused on where to find the required values above. I tried searching the logs for the mmCIF items but that didn't help. Could someone point me the right direction so I can deposit my structure with the correct values? Thanks in advance, -Jon
Re: [ccp4bb] Looking for the following values...
Hi, Generally if we use CCP4i we can find these details easily in scala log files. Gauri On Thu, Jan 13, 2011 at 2:48 PM, J. Fleming jonathan...@hotmail.com wrote: Hi All, I'm about ready to deposit my structure and have used pdb_extract to aid in the process. Unfortunately the following values were not found and are required by ADIT: 1) Under Data Collection, Reflections section: Observed criterion sigma(F) and Observed criterion sigma(I) 2) Under Refinement, Refinement Statistics section: Number unique reflections (all) I looked in my log files for HKL2000, PHASER, and PHENIX but am confused on where to find the required values above. I tried searching the logs for the mmCIF items but that didn't help. Could someone point me the right direction so I can deposit my structure with the correct values? Thanks in advance, -Jon
Re: [ccp4bb] Looking for the following values...
On 1/13/11 2:48 PM, J. Fleming wrote: Hi All, I'm about ready to deposit my structure and have used pdb_extract to aid in the process. Unfortunately the following values were not found and are required by ADIT: 1) Under Data Collection, Reflections section: Observed criterion sigma(F) and Observed criterion sigma(I) There is no criterion for sigma F applied in Denzo/HKL2000. Not least of all because data processing programs like Denzo and Scalepack work with intensities and not structure factor moduli. The default Sigma(I) cutoff is -3 See: http://www.hkl-xray.com/hkl_web1/hkl/Scalepack_Keywords.html (keyword SIGMA CUTOFF) 2) Under Refinement, Refinement Statistics section: Number unique reflections (all) If your refinement program does not write it into the header of the PDB file, and the description of the value does not make immediate sense to you, omit it. Some of the requested values are defined rather vaguely. A field matching this name doesn't show up in the REMARK 3 refinement template for PHENIX-derived PDB files. (http://www.wwpdb.org/docs.html) I haven't deposited lately but if I were to hazard a *guess* it might approximate to the number of reflections you would have used in refinement if you hadn't applied magnitude or sigma(F) cutoffs and prior to PHENIX rejecting reflections as gross statistical outliers. One straightforward way to get this number would be to use CAD to write a new MTZ file containing only reflections within the resolution limits used in refinement, and look in the log file to see what the output reflection count was. Assuming, of course, that the cell dimensions defined in your MTZ file are the same ones that you used in refinement. Refinement programs vary in their policy about handling reflections with |F|=0. The loss of reflections would manifest in a difference between the completeness in data collection and the completeness in refinement. Phil Jeffrey Princeton
Re: [ccp4bb] Looking for the following values...
Hi Jon, a partial answer: 2) Under Refinement, Refinement Statistics section: Number unique reflections (all) I looked in my log files for HKL2000, PHASER, and PHENIX but am confused on where to find the required values above. I tried searching the logs for the mmCIF items but that didn't help. Could someone point me the right direction so I can deposit my structure with the correct values? a PDB file header with phenix.refine refined structure contains this number under REMARK 3 records. Can't ADIT extract this information automatically? Look in your PDB file for something like that: REMARK 3 NUMBER OF REFLECTIONS : 15114 Although, it's derivable information, meaning that if you deposit the data used for refinement then you should be safe. Pavel.
Re: [ccp4bb] Looking for the following values...
Hi Jon - - Observed criterion sigma(F) and sigma(I) means what cutoff did your data processing package use to consider a reflection not observed, i.e. throw it out? If you processed your data with Scalepack/HKL2000, the default cutoff is on I, and it's negative 3 sigma. There is no cutoff on F. So you would enter -3 for the sigma(I) entry and leave the sigma(F) entry blank. I don't think that both of these entries are required. - The difference between all reflections and observed reflections is, as far as I can tell, that all reflections indicates the number of mathematically possible unique reflections given your space group, unit cell, and diffraction limits. I generally just leave these entries blank where I can, and where it's required, I divide my number of observed reflections by my percent completeness - for example, a dataset with 31984 unique observed reflections (you can get these numbers from the scaling log files of Scalepack or scala) with 99.8% completeness would give you (31984/0.998)=32048 as the number of all reflections. Hope that helps, Matt -- Matthew Franklin, Ph. D. Senior Research Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (646) 275-7165 _ From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of J. Fleming Sent: Thursday, January 13, 2011 2:49 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Looking for the following values... Hi All, I'm about ready to deposit my structure and have used pdb_extract to aid in the process. Unfortunately the following values were not found and are required by ADIT: 1) Under Data Collection, Reflections section: Observed criterion sigma(F) and Observed criterion sigma(I) 2) Under Refinement, Refinement Statistics section: Number unique reflections (all) I looked in my log files for HKL2000, PHASER, and PHENIX but am confused on where to find the required values above. I tried searching the logs for the mmCIF items but that didn't help. Could someone point me the right direction so I can deposit my structure with the correct values? Thanks in advance, -Jon
Re: [ccp4bb] Looking for the following values...
I find this confusing also! Phil Jeffrey wrote: On 1/13/11 2:48 PM, J. Fleming wrote: Hi All, I'm about ready to deposit my structure and have used pdb_extract to aid in the process. Unfortunately the following values were not found and are required by ADIT: 1) Under Data Collection, Reflections section: Observed criterion sigma(F) and Observed criterion sigma(I) There is no criterion for sigma F applied in Denzo/HKL2000. Not least of all because data processing programs like Denzo and Scalepack work with intensities and not structure factor moduli. Both are marked as required, but if you leave one blank the deposition will go through anyway and the annotator will not have a problem with this. Just as synthetic source and engineered source are required, but you leave them blank or NULL if your protein is from a natural source. The default Sigma(I) cutoff is -3 See: http://www.hkl-xray.com/hkl_web1/hkl/Scalepack_Keywords.html (keyword SIGMA CUTOFF) This is more complicated if there are partials - The -3 Sigma cut-off applies to measurements measurements can be full or partial (I think). I believe the reflection is rejected if any of its partials are rejected- (although theoretically it should be possible to approximate an intensity from intensity of one of its partials) The number rejected will be greater if only one of the partials needs to fail the sigma cutoff than if they are all added up before the cutoff is applied 2) Under Refinement, Refinement Statistics section: Number unique reflections (all) I think in refinement this just means test + working reflections? In data reduction it is more complicated. I think you have the following: measurements - number of spots for which denzo recorded a complete reflection or a full set of partials (different from measurements above?) reflections, possible - Theoretical number unique reflections in range reflections, measured - Unique reflections with at least one measurement reflections, observed - whats left, after aplying rejection criterion during data reduction. I would say once a reflection has been measured, it has already passed the -3sigma cutoff, we never reject a measured reflection. reflections used in refinement - after applying resolution and sigma cutoffs in refinement (Don't take my word for this- I'm confused, as you can see. Hoping for clarification) Another question- it is often suggested to use I/sigI = 2 in a shell as the criterion for resolution cutoff. And I/sigI is one of the parameters needed for deposition. But is this the average I/sigI for individual measurements, which (I think) is what you can estimate from the last table of scalepack output, or the average of I/SigI for the reduced unique reflections, which you could get from a table in truncate log file? Sigma I for the reduced reflection should be smaller than sigmaI for the individual measurements, as standard error of the mean is smaller than standard deviation of the measurement.
