Search results for "look through"

Re: [phenixbb] Gap between R and Rfree

by Young-Jin Cho

Thanks for your suggestions, Phill. When I did Ramachandran analysis, it shows 96.60% in preferred region and 2.62% in allowed regions, and 0.79% is in outlier. Geometry looks Ok. I also did optimize_wxc and optimize_wxu, and tls option. it didn't help much. Now I am trying to scale down. Thanks again. Young-Jin 0. Use Molprobity or the Validation tools in Coot to look at your structure and see what errors you can fix. 1. What is your geometry like ? Try reducing wxc_scale (try wxc_scale=0.5) and see what happens. 2. What is the variation of B-factors across bonds ? Try reducing wxu_scale - perhaps wxu_scale=0.5 or less. 2a. phenix.refine is autocratic about wxu_scale if you're using TLS so setting it yourself does not help. 3. Since R-free of 0.298 is a little high for a 2.5 Angstrom structure, you should carefully check your model. Perhaps you have a high proportion of disordered structure, which can cause this. If you feel that your model is correct, you could explore using TLS on your model. Potential TLS groups can be found using the TLSMD server at: http://skuld.bmsc.washington.edu/~tlsmd/ although the results should always be filtered through a common-sense definition of domain/group boundaries (e.g. don't break in the middle of helices unless there's a good reason to). Phil Jeffrey Princeton Young-Jin Cho wrote: > Hi everyone, > I recently got a diffraction data and am trying to refine it. The question is whatever I did the gap between R and Rfree stay far away: .2140/.2982 around 2.5 A resolution. (water added and isotropic(individual_adp) and so on). > Although I am redoing with many different approaches, if anyone can give me any comments or suggestions, it would be helpful. > > Thanks in advance, > > Young-Jin _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb -- Postdoctoral Fellow, Kern Lab Biochemistry Department/HHMI Brandeis University

15 years, 4 months

Re: [phenixbb] Refining Anomalous Groups

by Terwilliger, Thomas C

Hi Brennan, I'm sorry, part of the problem is that autosol exptl_fobs_phases_freeR_flags_1.mtz file does not retain the anomalous information. This is now on my list be fixed (not quickly though because I will be able to do it only when I convert a whole lot of other things). So in your case the best thing is to run phenix.refine with your original mtz file. You can create a freeR set in the GUI. If you do this, then use your new freeR set for everything from now on. As Nat mentions, if you choose "F(+),SIGF(+),F(-),SIGF(-)" or something like it then it should work. All the best, Tom T ________________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of Brennan Bonnet [Brennan.Bonnet(a)lightsource.ca] Sent: Monday, November 19, 2012 8:03 PM To: PHENIX user mailing list Subject: Re: [phenixbb] Refining Anomalous Groups Ok. So I used the original mtz file created from my data to determine the heavy atom substructure using HySS which I then used as input for AutoSol. Next I carried the files through to AutoBuild these files are: exptl_fobs_phases_freeR_flags_1.mtz (experimental data) resolve_1.mtz (initial map) overall_best_placed.pdb (ligands, starting model) ha_1.pdb_formatted.pdb (heavy-atom sites) Finally I carried these through to phenix.refine and now is when it complains that my data is no longer anomalous and I can't find a file that phenix is happy with. Everything worked smoothly until this step. Any idea what file(s) I might be looking for? I have tried some data from earlier steps which are unmerged and it still complains. ~Brennan~ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] On Behalf Of Nathaniel Echols [nechols(a)lbl.gov] Sent: Monday, November 19, 2012 8:29 PM To: PHENIX user mailing list Subject: Re: [phenixbb] Refining Anomalous Groups On Mon, Nov 19, 2012 at 6:11 PM, Brennan Bonnet <Brennan.Bonnet(a)lightsource.ca<mailto:[email protected]>> wrote: I am trying to use phenix.refine to refine partially occupied xenon sites using the Anomalous Groups selection under "Refinement settings". My list of anomalous scatters initially consisted of 22 peaks as located by HySS. Some of these were removed as they originated from S atoms from Met and Cys residues and a few others were removed after previous refinement steps due to having zero occupancy. My remaining sites consist of my xenons (hopefully) and other metals such as Mg or Zn which are mixed in and look like partially occupied xenon sites. My problem is that when I try to define the 11 remaining sites for the "refine anomalous groups" selection the software complains: Invalid combination: F-obs not anomalous, but refinement of 11 f_double_prime values requested (11 scatterers): Please provide anomalous reflection data or fix all f_double_prime values (see refinement.refine.anomalous_scatterer.group input blocks) I can't figure out exactly what I need to change to make it work and can't find a guide anywhere. Do I need to provide additional data or is the syntax for the sites incorrect maybe? No, the error message means exactly what it says: you need to supply anomalous data as input. This almost always means that the selected data labels should have "+" and "-" in them, and there will usually be 4 labels (e.g. "F(+),SIGF(+),F(-),SIGF(-)"). Data named "F,SIGF", on the other hand, is almost always merged/non-anomalous (although I think CNS files may break this assumption). -Nat _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb

12 years, 7 months

Re: [phenixbb] Clashes problem

by Luca Jovine

Hi, We have experienced the same problem, and what seems to work very well is the following procedure: 1) Add hydrogens to your rebuilt model with phenix.reduce: phenix.reduce input.pdb > input_h.pdb 2) Minimise the geometry of the protonated model from 1) withOUT X- ray term with: phenix.geometry_minimization --max-iterations=N input_h.pdb using a relatively low number of iterations N. You must determine this empirically by trying out a few possibilities, and chosing the highest number of iterations that improves your Molprobity clash score without over-minimising the model, as evidenced by loss of secondary structure. N=100 is a good guess. 3) Feed the geometry-minimised model to phenix.refine, as usual: phenix.refine input_h_geometry_minimized.pdb ... As Peter pointed out, this is generally an issue that one encounters at early stages of refinement, when models are still poor; therefore, in most cases you will need to mimimise geometry just once, or during the first cycles of rebuilding only. HTH, Luca ------------------------------------------------ Luca Jovine, Ph.D. Karolinska Institutet Department of Biosciences and Nutrition Hälsovägen 7, S-141 57 Huddinge, Sweden Voice: +46.(0)8.6083-301 FAX: +46.(0)8.6089-290 E-mail: luca.jovine(a)ki.se W3: http://www.biosci.ki.se/groups/ljo/ ------------------------------------------------ On 11 Feb 2008, at 16:01, Simon Kolstoe wrote: > Are there not restraints to prevent steric clashes? In cns I seem to > recall that the energy terms went through the roof if atoms got too > close together. > > Secondly, if I remove the clashes through model building and then run > phenix.refine both my R and Rfree go up, and phenix actually puts some > of the clashes back again - does the community accept deposited pdb's > with such obviously poor chemistry? > > Simon > > On 11 Feb 2008, at 14:51, Peter Zwart wrote: > >>> I am slightly concerned that a refinement program seems happy to >>> allow >>> such clashes. Is this a problem with the version of phenix.refine I >>> am >>> running, or is there a more obvious explanation that I have missed? >> >> Clash scores are not really used directly in refinement, so the >> refinement program doesn't really care about this. Adding hydrogens >> could improve the situation a bit, as would some model building do. >> >> How does your starting model look? >> >> HTH >> >> Peter

17 years, 4 months

[phenixbb] Deadline today -- IUCr SARS-CoV-2 special symposia.

by Pearce, N.M. (Nick)

Dear BB, As you might be aware, there are a few microsymposia that have been added to this year’s IUCr conference on developments around SARS-CoV-2. Given the wide interests of this board, I wanted to advertise all four of the sessions, for which the (official) deadline is TODAY: - Structural biology of coronaviruses This session covers new structural and functional insights about the life cycle and virus-host interaction of SARS-CoV-2 and other coronaviruses with a particular view to integrative uses of crystallography in connection with other methods. - New methods to fight the pandemic This session covers new methods in crystallography and structural biology to better understand SARS-CoV-2 and the COVID-19 pandemic, including advances in computational methods, beamline instrumentation and integrative structural biology. - Crystallography against Corona This session covers the efforts of the crystallographic community to find drug candidates for COVID-19 both in-silico and in the lab by using structural models of viral proteins. - Using crystallography for education during the pandemic Using crystallography for education during the pandemic *** Please submit your abstracts today! If this isn’t possible, email us to let us know you intend to submit an abstract in the coming days! *** For each session, 4 relevant abstracts will be selected for 20-minute presentations. You can submit your abstracts through the conference website: https://iucr25.org/scientific/ Looking forward to reading the abstracts, Session co-chairs

4 years, 1 month

[cctbxbb] Simple cctbx / boost c++ extension example

by Graeme.Winter＠diamond.ac.uk

Hi Folks, Just say I wanted to write a new from the ground up module for cctbx which wanted to include some C++ code, and a SConscript etc. so I can run libtbx.configure toytbx (say) And then find from toytbx import cplusplus_functions would work.... Is there an example I could follow? (I have not looked through the newsletters, I suppose I should have... but I could not seen anything obvious in the documents) Thanks, Graeme Dr. Graeme Winter Senior Software Scientist Diamond Light Source +44 1235 778091 (work) +44 7786 662784 (work mobile) -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

12 years, 5 months

Re: [phenixbb] Missing sanity check of duplicate resids within one chain?

by Schubert, Carsten [JRDUS]

Dale, Nat: thanks for the helpful comments. I was not aware that this is a “feature” of the PDB standard. Since Phenix recognizes the issue and issues a warning I assume this situation is handled correctly from the refinement side and does not cause any problems. However, at least from my end, I would like to avoid this sort of issue from the get-go. The default setting in Phenix seems to be that the program continues despite the warnings. If one operates like me and does not go through the quite lengthy log files to look for these potential issues, then the likelihood of them being missed is quite high. As a suggestion: one could either think of implementing a “strict” mode in Phenix where the program aborts on encountering a warning or print out a warning at the end of the refinement that issues/warnings were encountered warranting a follow-up. Cheers, Carsten From: Nathaniel Echols [mailto:[email protected]] Sent: Tuesday, August 26, 2014 8:44 PM To: Schubert, Carsten [JRDUS] Cc: phenixbb(a)phenix-online.org Subject: Re: [phenixbb] Missing sanity check of duplicate resids within one chain? On Tue, Aug 26, 2014 at 2:51 PM, Schubert, Carsten [JRDUS] <CSCHUBER(a)its.jnj.com<mailto:[email protected]>> wrote: Phenix (1.9-1692) seemingly happily accepted the input and proceeded with refinement and validation. After upgrading my coot installation to the latest build the error was flagged. I think this sort of mistake should have at least been flagged in the validation stage or is this out of scope for phenix? As Dale notes, this is technically allowed by the PDB format - however, we do already look out for it: nat@laptop> phenix.pdb.hierarchy carsten.pdb . . . ### WARNING: consecutive residue_groups with same resid ### number of consecutive residue groups with same resid: 1 residue group: "HETATM 9327 CL CL S 3 .*. Cl1-" next residue group: "HETATM 9328 K K S 3 .*. K1+" We could certainly present this warning elsewhere - the question is where would it be most likely to be noticed? -Nat

10 years, 10 months

Re: [phenixbb] High B-factors after Phenix restrained refinement

by Dialing Pretty

Hi Nat, I have a protein-peptide complex crystal, and I got the 3-D structure of the protein part in the complex by rigid body refinement with isomophous crystal crystal structure as the search model, and I got the peptide structure by Coot peptide building, then I refine the whole protein-peptide complex. Will you please tell me which Phenix program can be used to build the peptide as I mentioned in the situation above? I want to get a Coot alternative for the peptide building. I am looking forward to getting your reply. Cheers, Dialing ________________________________ From: Nathaniel Echols <nechols(a)lbl.gov> To: PHENIX user mailing list <phenixbb(a)phenix-online.org> Sent: Friday, 16 December 2011 3:31 PM Subject: Re: [phenixbb] High B-factors after Phenix restrained refinement On Thu, Dec 15, 2011 at 2:20 PM, Da Duan <2dd13(a)queensu.ca> wrote: > I used Phenix AutoMR to solved a structure to 3.3A and after 1 round of > rigidbody refinement with Phenix Refine I proceeded to restrained > refinement. The R/Rfree from the refinement decreased nicely as expected but > the B average is at ~100 (using Group B factor refinement option). I took > the same model and mtz through Refmac and the B average is about ~40. Has > anyone experienced this before? I am almost positive it maybe a setting > issue in Phenix Refine that i should be looking at to get the B factors to > refine correctly. How are you calculating the average B? Refmac prints "residual" B-factors in the B column of ATOM records - these do not include the contribution from TLS and Ucryst (an overall B-factor for the entire crystal). In Phenix, the ATOM records always have the total isotropic B-factor, and this will always be higher than the equivalent in Refmac. So it's quite likely that both programs are correct, they're just reporting very different things. (And for what it's worth, a mean B-factor of 100 is totally normal at 3.3A resolution.) -Nat _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb

13 years, 6 months

Re: [cctbxbb] First svn commit

by Richard Gildea

Hi James, Congratulations on your first commit! Without wanting to nitpick too much there were a couple of things that I would like to comment on: Personally I would have preferred the function name as_miller_arrays_dict(), as this would make it a lot clearer (at least to me) what to expect from the function before looking at the documentation. At first I was confused because the 'map' part of the name made me think that it was doing something to do with electron density maps (especially given the context of miller arrays). Replacing 'map' with 'dict' in the name would avoid any potential for confusion. Also, I would prefer the function arguments to be spelled out explicitly without using *args and **kwds, so that I can figure out what arguments it takes without having to read through the function source code to figure out that internally you are calling self.as_miller_arrays(), and then have to go and look up the function arguments for that. My IDE (WingIDE) shows me the function signature in its source assistant and also provides code completion for function arguments and keywords. However these won't be of much use when functions only list *args and **kwds. Cheers, Richard On 17 April 2013 21:57, James Stroud <xtald00d(a)gmail.com> wrote: > Hello All, > > Since this is my first commit, I just want to make sure that I have done > these things in the appropriate way. > > Here's what I did: > > 1. Added a wiki page: > https://sourceforge.net/p/cctbx/wiki/Subversion%20set%20up/ > 2. Added the method as_miller_arrays_map() to iotbx_mtz_ext.object, which > is declared in iotbx/mtz/__init__.py. > 3. Added a test for this functionality in the file > iotbx/mtz/tst_miller_map.py > > Please let me know if the manner in which I did anything could use > improvement. > > James > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/cctbxbb >

12 years, 2 months

Re: [phenixbb] Clashscore and average B

by Sam Tang

Hello Pavel and Robert Thanks for your replies. After re-investigating the model we didn't find any major issues and the electron densities are fitted pretty well. Even the ligand shows strong density on a SA-omit map. So I think we will stop at this stage and take this model for further analysis. Thanks again! Sam On Sat, 6 Apr 2019 at 03:30, Pavel Afonine <pafonine(a)lbl.gov> wrote: > Hi Sam, > > > I am refining a structure with Phenix.refine and encounter an issue > > which I appreciate your comments. The structure is in P1 and refined > > to 36A-3A. Rw/Rf = 23.9%/29.1%, RMS bonds 0.002, RMS angles 0.544, > > Ramachandran favoured 97.5%. The statistics is acceptable to me > > This look fine to me too! > > > but two numbers raised my concern. First is the clashscore of 7.7, > > which is below minimum of other structures shown by Polygon. > > The lower, the better. So this is good! If it's lower than the others > (as shown by Polygon) then you are doing better on this one! > > > Second is an average B of 37, with a minimum of 9.2. When I checked > > again in Coot (Average Temp fact. analysis), none of the residues or > > water look abnormal. I refined both individual and group B-factors and > > applied 'Optimize X-ray/adp weight'. > > This looks fine too. > > > So my questions are: > > (1) if a clashscore too high means a lot of bad contacts, how do you > > comprehend a clashscore too low? How can I modify my strategy to get > > around? > > It can't be "too low". Zero means you don't have any single steric > clash, which is good. > > > (2) is there an acceptable low value of B? (I sort of went through a > > similar thread in phenixbb appeared 9 years ago but seems the > > discussion did not come to a conclusion). Any advice I should reliax > > or tighten the adp restraints? > > Check out recent thread on ccp4bb: "acceptable difference between > Average B-factor and Wilson B". > Bottom line, I think what you have is just fine, unless you meaningfully > and clearly define "low". > > Pavel > >

6 years, 2 months

Re: [phenixbb] Max_reasonble_bond_distance error in phene.resl.space.refine

by Rune Thomas Kidmose

Hi Again Pavel, I should add that this (see download link for PDB file) is how the the same PDB file (last_frame.pdb from last email) looks when I have put it through phenix.RSR PDB: https://www.dropbox.com/s/ectbydhsh1fx7dh/last_frame_rsr.pdb?dl=0 The protein part of the model behaves really well, as I normally see when using phenix.RSR, however the DNA seems to move much more random, almost uncoiling. This is why I stated that the quality of the refinement seemed to suffer from the increase max bond distance. But again, I am using phenix dev-2614 so maybe that has something to do with it. Cheers Ruki ________________________________ Fra: Pavel Afonine <pafonine(a)lbl.gov> Sendt: 14. november 2017 16:20 Til: Rune Thomas Kidmose; phenixbb(a)phenix-online.org Emne: Re: [phenixbb] Max_reasonble_bond_distance error in phene.resl.space.refine Hi Ruki, I have been playing around with phenix.real.space.refine as part of a small pipeline I am making for EM structures. Testing various deposited EM structures and their corresponding maps, within my pipeline, I sometimes run in to the below error: RuntimeError: Bond distance > max_reasonable_bond_distance: 79.8663 > 50: I'm trying to chase this down and eliminate. So if you come across a case that can be reproduced please send it to me and I will start from there. For now simply set "max_reasonable_bond_distance=999" for all your refinements that will mask but not fix the problem. However, this should not affect the refinement results. Make sure you are using the latest Phenix version. Followed by a list of distances between, what I am assuming is, atom numbers and the actual distance. I can get past it simply by changing the max_reasonable_bond_distance for the run to, in this case, 80. This happens because the procedure optimizes weights by trying a large sample of possible weight values. For some values restraints may be too weak and atoms run one onto another, thus creating a huge clash and strong repulsion that stretches the bond. This leads to the crash. But I tend to see, that the final results gets significantly worse when I use this bypass. This is based on very similar models going through the pipeline, where the ones which yields the error, scores much worse when using the above mentioned bypass, compared to the models that showed no max_reasonable_distance_error. Again, I'm very keep to investigate concrete reproducible cases. So if you have anything to share that would be most helpful! B: Any ide what I can do, to avoid running into this bond distance problem? I'd say help us to identify the issue so that we fix it and then you don't run into it any more. All the best, Pavel

7 years, 7 months

Search results for query "look through"