Dear Arpita, I'll try to answer below -
On Mon, 12 Feb 2024 13:57:28 +0530, Arpita Goswami <bt.arp...@gmail.com> wrote: >Dear all, > >Greetings to all! Apologies if the below query seems very naive! > >This is to query on the consensus to use Staraniso for pdb submission. We >have solved a structure previously at 2.3 A resolution. The same data >(after reindexing the diffraction images in autoPROC) and after >reprocessing by ellipsoidal scaling in Staraniso gave structure at ~2.16 A. > >The previously solved structure did not have significant anisotropy >according to Aimless, so anisotropic scaling was not performed that time. Maybe different resolution cutoffs were used: previously the data were cut a 2.3A (according to some rule, e.g. "cut at <I/sigma>=2"), now they are cut at ~2.16A (according to a different rule, e.g. "cut at <I/sigma>=1.5"). Alternatively, different programs were used for data processing, and for the processing by the one used previously, the rule said "you should cut at 2.3A", and for the one used now, the same rule said "cut at ~2.16A". After all, different programs give different data! Speaking of rules, there are different "schools of thought" concerning the "best" or "correct" rule for finding the resolution cutoff. I don't want to repeat the arguments here. It is important to know that there exists an experimental and practical way (called "paired refinement") to find a meaningful resolution cutoff, and this requires refinement of a model, and comparison of (basically) Rfree values. The CCP4 program for this purpose is called PAIREF. There is also a web server called PDB-REDO that does paired refinement with your data and model. > >The overall spherical completeness of Staraniso structure is low (~73%) >while Ellipsoidal completeness is ~94%. Parallel isotropic scaling gives >structure with 99.6% completeness (but 2.3 A resolution). The statistics (R >merge and others) are better for Staraniso structure (also benefited from >removing specific frames with high R merge as indicated by Staraniso). Also I understand that, based on what you wrote, autoPROC was used for processing the most recent data. Actually, Staraniso is run from autoPROC; it is part of the autoPROC expert system (but there is also a web server for it). The removal of specific frames is done by a different part of autoPROC, not by Staraniso. >the interatomic distances in regions of interest in the staraniso structure >is on par with parallel molecular dynamics simulation data. This needs a lot more explanation and context information, and discussion. > >The questions are: > >1. Can the Staraniso structure be submitted to pdb saying reprocessed >structure at higher resolution (through Staraniso)? As recently reported here on CCP4BB (IIRC), there exists a PDB policy that only the previous authors of the PDB entry can re-submit. If existing data are re-processed and a new PDB entry submitted, then this must be accompanied by a paper. > >2. What is the factor more important for a structure: completeness >(spherical vs ellipsoidal) or R statistics? You ask the correct general question: how do I obtain the best structure? The answer to your specific question is: it depends. There is not one answer that fits all situations. Paired refinement should help you to find the best dataset for refinement. > >3. Why is the extra resolution not detected during indexing by iMOSFLM or >XDS (using default setup)? The indexed outputs of either of them did not >give extra resolution (through anisotropic scaling) in Staraniso, although >it said some data was missing. I'm afraid there is some confusion here. To try and clarify: indexing has nothing to do with resolution (indexing means assigning indices, i.e. hkl triples, to reflections that are found during an initial spot finding procedure), so it is not clear that "extra resolution not detected during indexing" is an appropriate description for what you see. > >4. Is there any option for using all reflections detection (like autoPROC) >in iMOSFLM or XDS? Again, there is some confusion here: autoPROC is an expert system that uses XDS. More explicitly: autoPROC creates XDS.INP and then runs XDS. Then it analyzes the XDS results, and afterwards uses that analysis to create an improved XDS.INP, and re-runs XDS. There is nothing to prevent you from running XDS manually, to obtain results like those that autoPROC obtains (or even better!). If you want to learn about these options: some of them are discussed at https://wiki.uni-konstanz.de/xds/index.php/Optimisation , or elsewhere in XDSwiki. Similarly, iMOSFLM can be optimized for your data, and this will result in better data, and higher resolution than is obtained with default parameters. I'd google "imosflm tutorial"; there are some interesting hits. There are workshops, organized by CCP4 and others, where you can learn these things. Hope this helps, Kay > > >Thanks in advance, > >Best Regards, > >Arpita > >######################################################################## > >To unsubscribe from the CCP4BB list, click the following link: >https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > >This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing >list hosted by www.jiscmail.ac.uk, terms & conditions are available at >https://www.jiscmail.ac.uk/policyandsecurity/ > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
