Dear All, Thanks everyone for the suggestions and clarifications. As Eleanor and Garib wrote, I cannot find real differences in map quality or statistics after refinement depending if I set or not the resolution edges. This is more a matter of how the remarks in the pdb are recorded for validation/deposition for which a big red exclamation mark is pointing to the mismatch values. This is happening only when the ccp4i2 interface is used for refmab but not with ccp4i. Maybe a script problem for the pdb remark data extrapolation? Also if I manually set the resolution I found that the pdb remark is still not correct exactly (in ccp4i2). But when I ran with the same files a refmac refinement using the ccp4i interface, everything is running smoothly and perfectly with no "error" at all.
Just as an open question: As seems more a pdb file writing issue than a refinement problem, correcting the pdb file manually writing with a text editor in in the remark the exact low resolution, could be also a fix or can be considered as faking the file? ( I didn't test it yet, just mornings idea...) All the best, Roberto ------------------------------- Dr. Roberto Orru, Ph.D. Insitute of molecular biology (IMB) and JGU - Institut für Molekulare Physiologie (AG Prof. Wolf) Mainz, Germany From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Garib Murshudov Sent: Sunday, March 18, 2018 5:14 PM To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] Resolution mismatch aimless/refmac On 18 Mar 2018, at 16:02, Eleanor Dodson <eleanor.dod...@york.ac.uk<mailto:eleanor.dod...@york.ac.uk>> wrote: Does it matter? The refinement will only use observed reflections. It should not matter for refinement and map calculations (needs to be checked carefully). However it does matter for deposition when multiple entries are analysed and the PDB deposition software (rightly so) says that you have information mismatch. And it confuses users and most of all it confuses deposition. It would confuse me. Best wishes, Garib As Andrew says your output from dataprocessing includes a complete list of all possible indices to the upper resolution limit with a Free R flag assigned to the indices. This makes it easier to keep the same FreeR assignments for all your sets of measurements, which is a good thing.. There is a library call which REFMAC could use which would return the actual limits of the observed data - that small modification to the program would give a more sensible log file for the refinement. At present the REFMAC outputs a reflection list will include all indices, with the Fcalc PHIcalc information listed for missing data . I find that quite useful in some cases, but if you do not wish to use the terms there are ways of excluding them from subsequent calculations.. Eleanor On 18 March 2018 at 12:04, Garib Murshudov <ga...@mrc-lmb.cam.ac.uk<mailto:ga...@mrc-lmb.cam.ac.uk>> wrote: Dear All, As far as I know it could happen when you are using i2. We are working to fix this problem. At the moment the best solution is to use advanced options in the refmac interface and define resolution limits explicitly. For example you can add in the advanced options: resolution 37 2.5 where these resolution limits are from the aimless output. Low resolution limit should not affect refinement behaviour, however it may cause problem during deposition. We will have better solution soon. I2 has many good features. Please report if you see some misbehaviours. Best wishes, Garib P.S. you can also use advanced options to do things that are not available on the interface yet. 1) refinement against electron diffraction. Add source EC MB # electron form factor will be used using Mott-Bethe formula 2) you can add occupancy refinement etc On 18 Mar 2018, at 10:46, "Orru, Dr. Roberto" <ro...@uni-mainz.de<mailto:ro...@uni-mainz.de>> wrote: Dear All, I am noticing that the low resolution in the reflections files after scaling with aimless and after refinement with refmac does not coincide. In a case I have 37A with aimless but for some reason refmac is 67A. Any idea? All the best, R. Dr Garib N Murshudov MRC-LMB Francis Crick Avenue Cambridge CB2 0QH UK Web http://www.mrc-lmb.cam.ac.uk<http://www.mrc-lmb.cam.ac.uk/>, http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/ Dr Garib N Murshudov MRC-LMB Francis Crick Avenue Cambridge CB2 0QH UK Web http://www.mrc-lmb.cam.ac.uk, http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/
