Re: [ccp4bb] Stuck with Refinement
Dear Silvia, I look at those stats in the log file and worry about your data processing. There are some wild outliers in the measurements Unit cell: (129.59, 129.59, 118.84, 90, 90, 120) Space group: P 61 2 2 >From the log file: outliers Miller Index : Intensity : Sigma : Bin Mean Intensity (1, 0, 47)-28060.000 20530.0002751.006 (2, -1, 47)-5700.000 29950.0002751.006 (13, 0, 45)-35490.000 73370.0002751.006 (18, -9, 44)-35640.000 25140.0002751.006 (18, 0, 43)-7384.000 30540.0002751.006 (20, 0, 42)-13600.000 31490.0002751.006 (41, 0, 18)-27470.000 29190.0002751.006 (42, -21, 27)594.400 66990.0002751.006 (3, -1, 47)3046.000 44930.0002751.006 (10, -2, 46)9610.000 15160.0002751.006 (11, -5, 46)-42010.000 83820.0002751.006 (15, -7, 45)15970.000 34970.0002751.006 (15, -6, 45)64660.000 80650.0002751.006 (16, -1, 44)-3856.000 17690.0002751.006 (17, -3, 44)2622.000 25320.0002751.006 (18, -8, 44)22440.000 20130.0002751.006 (18, -7, 44)6847.000 28640.0002751.006 (19, -2, 43)-11360.000 88170.0002751.006 (20, -5, 43)81040.000 28430.0002751.006 (21, -2, 42)54000.000 77760.0002751.006 (22, -5, 42)22820.000 22740.0002751.006 (23, -11, 42)8416.000 20160.0002751.006 etc - I note they all have L indices in the range 40-47 and very high Sigmas. That makes me think there is an oddity.. Maybe you have processed your data to too high a resolution? Or is it very anisotropic? If you did the data reduction in CCP4I2 do you have the report? That would analyse data quality.. Then I wouldn't worry too much about the Rfactors yet. They fell satisfactorily in the refinement run. COOT indicates there are quite a few corrections to be made, so the stats will improve. I don't worry too much about ramachandran plots at your stage.. I look for bad residues flagged by the COOT density fit.. and difference map peaks which usually flag errors. Are you using NCS restraints? At this resolution I think that is sensible. Good luck Eleanor On Thu, 6 Aug 2020 at 17:48, Paul Emsley wrote: > On 06/08/2020 16:39, Silvia Napolitano wrote: > > Dear CCP4BB community, > > > Dear Silvia, > > > > > > I am working on a crystal structure and I am a bit stuck with the > refinement. > > > > To build the model I use Coot and to refine I use Phenix. > > I may be able to offer some insight about the first part. > > > > > > First, I noticed that the geometry analysis of exactly the same files is > quite different between Coot 0.8 and Coot 0.9 (see PowerPoint attached, > slides 1 and 2); isn't that a bit strange? > > > The restraints generation and weighting was completely rewritten between > 0.8 and 0.9. I suspect that what you are seeing is a result of using a > more sensitive scaling. With some experience, I had noticed that the > bars in the geometry analysis as a result of modern refinement were very > often too small - in a non-useful way. So I scaled them up a bit. I > haven't looked at this sort of side by side analysis for many years so > your figures 1 & 2 were a bit of a surprise (that the scaling was so > different), but on the whole I think that the current scaling is better. > > > > Anyway, I tried to fix the Ramachandran outliers, geometry, and > rotamers, obtaining, I think, a decent model (see PowerPoint attached, > slides 3-5). > > > Yes, they look good. > > > > > > However, when I input this model for refinement, the statistics and the > geometry obtained at the end of the refinement cycles are very bad (see > PowerPoint attached, slide 6). > > A useful data point here is how the same analysis looks at the start of > (i.e. before) the refinement. Then one can distinguish between the cases > of the refinement being given a good model and chewing it up and the the > refinement being given what it thinks is a bad model and throwing up its > (metaphorical) hands. > > Also, the underlying data which is used by Coot is different to that > used by Phenix. The Ramachandran plot data is different, the CB > distortion model is different, the non-bonded contact model is different > - and the means to assess "bad contacts" is different. > > FWIW, the rotamer database is much the same (or, at least it used to be > - I haven't updated it in about 10 years). > > > Regards, > > Paul. > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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
Re: [ccp4bb] Stuck with Refinement
On 06/08/2020 16:39, Silvia Napolitano wrote: Dear CCP4BB community, Dear Silvia, I am working on a crystal structure and I am a bit stuck with the refinement. To build the model I use Coot and to refine I use Phenix. I may be able to offer some insight about the first part. First, I noticed that the geometry analysis of exactly the same files is quite different between Coot 0.8 and Coot 0.9 (see PowerPoint attached, slides 1 and 2); isn't that a bit strange? The restraints generation and weighting was completely rewritten between 0.8 and 0.9. I suspect that what you are seeing is a result of using a more sensitive scaling. With some experience, I had noticed that the bars in the geometry analysis as a result of modern refinement were very often too small - in a non-useful way. So I scaled them up a bit. I haven't looked at this sort of side by side analysis for many years so your figures 1 & 2 were a bit of a surprise (that the scaling was so different), but on the whole I think that the current scaling is better. Anyway, I tried to fix the Ramachandran outliers, geometry, and rotamers, obtaining, I think, a decent model (see PowerPoint attached, slides 3-5). Yes, they look good. However, when I input this model for refinement, the statistics and the geometry obtained at the end of the refinement cycles are very bad (see PowerPoint attached, slide 6). A useful data point here is how the same analysis looks at the start of (i.e. before) the refinement. Then one can distinguish between the cases of the refinement being given a good model and chewing it up and the the refinement being given what it thinks is a bad model and throwing up its (metaphorical) hands. Also, the underlying data which is used by Coot is different to that used by Phenix. The Ramachandran plot data is different, the CB distortion model is different, the non-bonded contact model is different - and the means to assess "bad contacts" is different. FWIW, the rotamer database is much the same (or, at least it used to be - I haven't updated it in about 10 years). Regards, Paul. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
Re: [ccp4bb] Stuck with Refinement
Hello, I think you are at a mid-refinement stage (R-free mid-thirties and map clearly still needing a lot more fitting work to be done on it) so I would not worry too much about the geometry stats at this point! I should pick someone's brains locally on model-building and get the fit to the map as good as possible. Best wishes, Jon Cooper. jon.b.coo...@protonmail.com Original Message On 6 Aug 2020, 16:39, Silvia Napolitano wrote: > Dear CCP4BB community, > > I am working on a crystal structure and I am a bit stuck with the refinement. > > To build the model I use Coot and to refine I use Phenix. > > First, I noticed that the geometry analysis of exactly the same files is > quite different between Coot 0.8 and Coot 0.9 (see PowerPoint attached, > slides 1 and 2); isn't that a bit strange? > Anyway, I tried to fix the Ramachandran outliers, geometry, and rotamers, > obtaining, I think, a decent model (see PowerPoint attached, slides 3-5). > > However, when I input this model for refinement, the statistics and the > geometry obtained at the end of the refinement cycles are very bad (see > PowerPoint attached, slide 6). I am a very basic user, so I was wondering if > some of you have some suggestions on what I can do and which parameters I can > set for the refinement that might improve the model. I also attached the .log > file and the .eff file of the last refinement I performed. > > Many thanks in advance for your precious help! > > I wish you a nice evening/day. > > Best > > Silvia > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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=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/
[ccp4bb] virtual ACA meeting - Ronglie Award presentation
Hello all! For those who may have missed it, the ACA meeting this year has gone virtual: https://www.acameeting.com/ Much cheaper to register than ever before, and there are a few days left! Yesterday morning, I had the honor of receiving the ACA's Ronglie Award, and I am sharing my presentation here: https://www.dropbox.com/s/x8zirb4p4f3zfnp/ACA_Rognlie_2020.mp4 alternate location and slides: https://bl831.als.lbl.gov/~jamesh/powerpoint/ACA_Rognlie_2020.mp4 https://bl831.als.lbl.gov/~jamesh/powerpoint/ACA_Rognlie_2020.pptx My title is "If I had a trillion dollars ...", and I encourage everyone to contemplate the same fortune every now and then. I think our community is stronger when we think outside normal financial constraints, and it can be fun! In the last 10 minutes I outline a design for an inexpensive and scalable SARS-CoV-2 test I have been thinking about, and I'd like to ask the members of this community to contribute to it. Goal is to keep the per-test price below $1 and scale to 7 billion tests/day. Do you see any show-stoppers? Has anyone ever tried doing fluorescence detection without optics? How about in your own kitchen? I think if we work together this might actually work. Please do let me know if I missed anything! -James Holton MAD Scientist To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
