Search results for "look through"

Re: [phenixbb] Phaser annoyance

by Nathaniel Echols

Never mind, I should have looked through my daily pile of bug reports before responding. I forgot to check something in until yesterday afternoon - it should be fixed in the next build. (Which should have been done by now, but there appears to be a problem updating the code for the CCP4 libraries.) -Nat On Tue, Feb 5, 2013 at 7:34 AM, Nathaniel Echols <nechols(a)lbl.gov> wrote: > On Tue, Feb 5, 2013 at 3:51 AM, Morten Groftehauge > <mortengroftehauge.work(a)gmail.com> wrote: >> The pop-up warning from Phaser about lack of eLLG for the resolution of the >> data would be more informative if you added the value of eLLG so one >> wouldn't have to scroll back in the log to find it. It would also allow the >> user to see with a glance whether the warning is because eLLG is under 120 >> or under 60. > > Which version? I thought I'd fixed this so it wouldn't pop up any > more (because it was happening with every single job I ran), but this > would have been well after 1.8.1 was released. > >> And it seems like the 'non-simple' Phaser GUI is broken in 1.8.2-1288. At >> least I haven't been able to open it, neither from the main window or by >> opening a previous job (Ubuntu 10.04). > > Do you get any kind of error message? I am downloading the installer > now to try it myself, but the current code appears okay. > > -Nat

13 years

Re: [phenixbb] Using the Same Test Set in AutoBuild and Phenix.Refine

by Pavel Afonine

Hi Dale, >> 1) Why you specify reflection MTZ file twice in phenix.refine script? >> >> > I put the mtz in twice because if I put it in once phenix.refine > complains that I have no free R flags. It seems to want one file with > the amplitudes and another with the flags. Since I have both in the > same file I put that file on the line twice and phenix.refine finds > everything it needs. > phenix.refine looks for free-R flags in your main data file (1M50-2.mtz). Optionally you can provide a separate file containing free-R flags (I have to write about this in the manual). However, if your 1M50-2.mtz contains free-R flags then you don't need to give it twice. So clearly something is wrong at this step and we need to find out what is wrong before doing anything else. Could you send the result of the command "phenix.mtz.dump 1M50-2.mtz" to see what's inside of your data file? Or I can debug it myself if you send me the data and model. > If the MD5 hash of the test set depends on the resolution then certainly > I could be in trouble. No. It must always use the original files before any processing. > Does the resolution limit affect the MD5 hash of the test set? > No. If it does then it is a very bad bug. I will play with this myself later tonight. > >> 3) Does this work: >> >> (...) > > I'll try these but it will take a bit of time. > Don't run it until completion. Just make sure it passed through the processing step. Pavel.

18 years, 1 month

Re: [phenixbb] Completeness issue by phenix

by Rupert Russell

Dear Ralf, I too have experienced this issue many times before. My .mtz files were generated through the ccp4i "import merged data" tab (default parameters), after the data were processed with scalepack. Letting phenix use the .sca file instead overcomes this but this is not an ideal situation for cross-compatibility between different programs. Cheers Rupert Russell Ralf W. Grosse-Kunstleve wrote: > Hi YoungJin, > > I suspect phenix.refine decided your mtz file contains anomalous data > when you actually have non-anomalous data. Could you look in the > phenix.refine output for something like this: > > ================================== X-ray data ================================= > > F-obs: > 1yjp.mtz:FOBS_X,SIGFOBS_X > > R-free flags: > 1yjp.mtz:R-free-flags > > Miller array info: 1yjp.mtz:FOBS_X,SIGFOBS_X > Observation type: xray.amplitude > Type of data: double, size=495 > Type of sigmas: double, size=495 > Number of Miller indices: 495 > Anomalous flag: False > ^^^^^ > in particular here > > If you see "Anomalous flag: True" try adding this to the phenix.refine > command line: > > xray_data.force_anomalous_flag_to_be_equal_to=False > > Let me know if this doesn't help. > If it does help, I'd be interested to know how the .mtz file was > generated. > > Ralf > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb > > >

17 years, 1 month

Re: [phenixbb] Missing plotting libraries

by Leigh Allen

ERROR: Reading package lists... Done Building dependency tree Reading state information... Done E: Couldn't find package lapack3 Thanks for your help. I've tried installing lapack and/or lapack3 through apt-get and synaptic... and I can't find it. I'll continue looking and potentially ask the Ubuntu people since this is not a Phenix problem. Thanks again, Leigh On Mon, May 4, 2009 at 1:00 PM, Nathaniel Echols <NEchols(a)lbl.gov> wrote: > On May 4, 2009, at 8:56 AM, Leigh Allen wrote: > > How do I fix this? > > You appear to be missing one or more libraries required by the > > plotting module; plots will be disabled for now. The original > > error is shown below. > > As Ralf said, the quick solution is to install lapack - it's usually > there already, but some systems don't include it by default. On > Ubuntu, "apt-get install lapack3" will take care of it. I will see if > I can add it to the installer - this will probably not happen until > next week, though. For now, I've fixed the code so it will fail more > gracefully if plotting is disabled - that will be in 1.4-56 (tomorrow > morning). > > thanks, > Nat > > ------------------- > Nathaniel Echols > Lawrence Berkeley Lab > 510-486-5136 > NEchols(a)lbl.gov > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

16 years, 9 months

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

by Steiner, Roberto

Hi Da Even if you deposit a structure refined with Refmac the PDB now expects the total B values being present. Have a look at http://deposit.rcsb.org/adit/REFMAC.html What you call "more" correct does not really make much sense to me if I understand you properly. If you follow the link given above (or use TLSANL directly from the CCP4) and get 'total Bs' from Refmac I am sure they will be more or less the same and the Bs from phenix.refine. R On 16 Dec 2011, at 15:54, Da Duan wrote: Hi Nat I was just looking at the average B in the refinement log files from Refmac and Phenix Refine. Thanks for the clarification on how Refmac and Phenix calculate the average B. My next question is when depositing the structure, is it more common to deposit structures with the "residual" B-factors or B-factors generated by Phenix that includes the TLS and Ucryst contribution? I also performed sfcheck and the average B generated by the Wilson plot is ~100 which seems to suggest that the Phenix average B is probably "more" correct? Thanks again Da On Fri, Dec 16, 2011 at 12:31 AM, Nathaniel Echols <nechols(a)lbl.gov<mailto:[email protected]>> wrote: On Thu, Dec 15, 2011 at 2:20 PM, Da Duan <2dd13(a)queensu.ca<mailto:[email protected]>> 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<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/phenixbb <ATT00001..c> Roberto Steiner, PhD Randall Division of Cell and Molecular Biophysics Group Leader King's College London Room 3.10A New Hunt's House Guy's Campus SE1 1UL, London, UK Tel 0044-20-78488216 Fax 0044-20-78486435 roberto.steiner(a)kcl.ac.uk<mailto:[email protected]>

14 years, 1 month

[phenixbb] Re: Structure with high clashscore

by Bruno KLAHOLZ

Dear Jerome, some ideas to check: - MD: you probably mean MR (molecular replacement) - before starting refinement, if you found a solution by MR, did you look at the structure, crystal packing etc., no big clashes between molecules? - related with that, did you validate the space group? Run several MR's with different space groups (which make sense from indexing) and compare the results - refinement: run simulated annealing (initially with rather high temperatures, later in refinements at lower temperature), this helps to get out of local energy minima; energy minimization is done as part of that also - include hydrogens in the refinement, this reduces clashes throughout the structure (they are added as riding hydrogens, i.e. predicted from geometry, they don't need to be resolved in the map for that) - check your atomic model and do model building, e.g. in Coot, use Ramachandran restraints etc., go through the structure and refine manually, reinject that model into Phenix for further refinement; iterate; check whether your map improves - run composite omit or polder maps if you have doubts about some regions, e.g. to figure out a loop conformation etc. - is the diffraction isotropic? i.e. does the crystal diffract equally well in all directions? anisotropic diffraction can make refinement more difficult, but it can be corrected for - use the phenix.predict_and_build tool to improve your AlphaFold prediction and refine your atomic model, see https://phenix-online.org/documentation/reference/alphafold.html Best, Bruno -----Original Message----- From: JEROME JOHNSON via phenixbb <phenixbb(a)phenix-online.org> Sent: lundi 21 juillet 2025 20:16 To: phenixbb(a)phenix-online.org Subject: [phenixbb] Structure with high clashscore Hello all, I'm happy to join the forum! I have a problem with clashscores and would be grateful for support. I have diffraction data for a 3HP-CoA Synthetase from N. maritimus resolved to 2.7 Angstroms. For MD, I used an alphafold structure (as I understand commonly results in high clashscore values) and after numerous rounds of refinement, the clashscore remains high at 11. I recently tried using gromacs to energy minimize and got values of 5 and 3 (according to molprobity), but after refinement these values immediately jumped back up to ~30. I wondered if you could describe the best way to reduce these? Attached is my latest round of refinement should you wish to take a look! Best, Jerome _______________________________________________ phenixbb mailing list -- phenixbb(a)phenix-online.org To unsubscribe send an email to phenixbb-leave(a)phenix-online.org Unsubscribe: phenixbb-leave@%(host_name)s

6 months, 2 weeks

Re: [cctbxbb] rstbx test is failing without indication in test_all_parallel

by markus.gerstel＠diamond.ac.uk

This appears to be true: looking through cctbx_project, dials, labelit, phenix, phenix_regression I found no references apart from the tests that sparked this thread. I would just remove it for retirement - it will be preserved in the history. -Markus ________________________________________ From: cctbxbb-bounces(a)phenix-online.org [cctbxbb-bounces(a)phenix-online.org] on behalf of richard.gildea(a)diamond.ac.uk [richard.gildea(a)diamond.ac.uk] Sent: Friday, September 22, 2017 12:08 To: cctbxbb(a)phenix-online.org Subject: Re: [cctbxbb] rstbx test is failing without indication in test_all_parallel As far as I recall rstbx/simage was a research project by Ralf that hasn't been touched for over 5 years, and isn't used by any code outside of rstbx/simage. Could this code be potentially "retired" somewhere outside of cctbx? Dr Richard Gildea Data Analysis Scientist Tel: +441235 77 8078 Diamond Light Source Ltd. Diamond House Harwell Science & Innovation Campus Didcot Oxfordshire OX11 0DE ________________________________ From: cctbxbb-bounces(a)phenix-online.org [cctbxbb-bounces(a)phenix-online.org] on behalf of Oleg Sobolev [osobolev(a)lbl.gov] Sent: 20 September 2017 19:33 To: cctbx mailing list Subject: [cctbxbb] rstbx test is failing without indication in test_all_parallel Dear colleagues, Accidentally I found out that this command: rstbx.simage.solver d_min=5 lattice_symmetry=P422 intensity_symmetry=P4 index_and_integrate=True multiprocessing=True finishes with traceback. It is run as part of phenix_regression/misc/tst_rstbx.csh The second problem is that test_all_parallel script fails to detect an actual failure. It would be great if somebody who is in charge of rstbx and testing could look at this. Best regards, Oleg Sobolev. -- 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 _______________________________________________ cctbxbb mailing list cctbxbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/cctbxbb

8 years, 4 months

[phenixbb] Job vacancy: Institute Research Investigator within the Therapeutics Discovery Division at MD Anderson Cancer Center

by Leonard,Paul G

Hi, The Structural Chemistry group, within the Therapeutics Discovery Division of MD Anderson Cancer Center is looking for a highly motivated individual with a strong background in structural biology, using X-ray crystallography and/or single particle cryo-EM to determine high resolution structures of proteins and protein complexes. Our mission is to integrate novel biological insights with drug discovery expertise to accelerate the development of innovative, targeted, small-molecule therapeutics for the treatment of cancer or neurodegenerative diseases. Our work is conducted in a team science environment that brings together excellence in both academic and pharmaceutical discovery. The structural chemistry group provides structural biology support for several drug discovery programs in our pipeline, spanning from early stage drug discovery through lead optimization. For a full job description and to submit an application please use the following link... https://jobs.mdanderson.org/search/jobdetails/institute-research-investigat… kind regards, Paul Leonard Senior Institute Research Scientist MD Anderson Cancer Center 1881 East Road Houston TX 77054 USA The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.

4 years, 2 months

Re: [phenixbb] on reciprocal space refine of the electronic microscopy map by Phenix

by Pavel Afonine

Hi Smith, if you've got cryo-EM map, built an initial model into it and want to refine it then the most natural way to do so is to refine the model against the map directly and NOT take a detour through reciprocal space by converting the map into structure factors and then using the crystallography-specific refinement programs. There is a Phenix refinement tool specifically designed for this - refinement of atomic models into cryo-EM maps or low-resolution X-ray maps, described here: https://www.dropbox.com/s/imv2yzwodik13in/afonine_etal_wcpcw2015.pdf?dl=0 If for whatever reason you still want to do it the old way, then here are two steps: - convert the map into structure factors: phenix.map_to_structure_factors map.ccp4 - then run phenix.refine the usual way. More info at the bottom of this page: http://phenix-online.org/documentation/ Pavel On 4/4/15 6:38 AM, Smith Liu wrote: > Dear All, > Recently there are cryo-electronic microscopy papers which refine the > reciprocal space of the electronic mcroscopy map by phenix refine. For > the electronic mcroscopy map, what does it mean for the reciprocal > space? How to get the reciprocal space map from the electronic > mcroscopy map? In order to realize this kind of refine in phenx, we > only process the xyz coordinates strategy refine in the graphical > interface, right? > I am looking forward to getting your reply. > Smith > > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org

10 years, 10 months

Re: [phenixbb] GUI parameter files

by Nathaniel Echols

On Thu, Mar 15, 2012 at 12:29 PM, Leonid Sazanov <sazanov(a)mrc-mbu.cam.ac.uk> wrote: > If I restore a previous job in refine GUI, to run it with modified settings, > and include a new parameter file .eff with definitinon of secondary > structure restrains, these new restrains are combined with previously used > restrains. > How do i get rid of previous restrains? Older file is not visible in inputs, > but its settings are still used. It's messy - click "Graphics" on the toolbar, then "Sec. Str." on the toolbar of the graphics window, which will open the editor for these restraints. I will make this more accessible ASAP, and I'll add a menu option to simply wipe out the current definitions. > And in general, how can one be sure which parameters are used at the start > of each refine run? > If older settings loaded from .eff or .param file are not visible, the only > way is to look through new .eff file, which takes a lot of time. The "Edit parameters and run" option is the best solution, although that does involve reading the .eff file. Alternately, "View all parameters" in the Settings menu will show you a tree version of this, which may be easier to navigate. > Has this been solved in latest builds perhaps? Not exactly- the other custom geometry restraints are handled much better now, but the problem you describe could still be an issue. However, what it will now do is include the parameter files as actual parameters, instead of merging them in. This won't fix your current problem but it will prevent it from happening again in the future, I hope. -Nat

13 years, 10 months

Search results for query "look through"