Search results for "look through"

Re: [phenixbb] autosol w/ "no merge original index"?

by Tom Terwilliger

Hi Brian, Thanks for sending me the top of your hkl file....I added some random data after that and it runs on my version just fine. Can you possibly try again with the most recent version of phenix on the web site (rc6)? Thanks! -Tom T At 01:24 PM 12/19/2007, you wrote: >phenix 1.3b of 21-10-2007 > >confusion w/ "no merge original index" data file in phenix.autosol. this >should work, right? > >caveat - the 'nmoi' hkl is actually from scala, but that usually is fine >w/ e.g. solve-2.13. 'nmoi' requires declaration of cell='(numbers)' on >command line. > >phenix.autosol seems to go through all the usual checks fine, then >reports (in AutoSol_run_2_/LAST.LOG): >".... > The error seems to be at line 0 > Here is what the first few lines of this file look like: > 1 > -987 > 86.052 86.052 132.608 90.000 90.000 90.000 p41212 > You have set the keywords readdenzo and unmerged > Please check whether you should have set readformatted or readtrek or >premerged >...." > >... 'readdenzo' and 'unmerged' are just right for 'nmoi' files. etc. > >-bryan >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://www.phenix-online.org/mailman/listinfo/phenixbb Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

17 years, 6 months

Re: [phenixbb] Real Space Refinement with marginal data

by Rongjin

Hi Pavel can you show me how to select some residues that are excluded from refinement? You suggested this earlier but I did not know how to do it. I looked through the manual and I can see how to select a chain, but do not know how to select some residues. Thanks Rongjin ------------------ Original ------------------ From: "Pavel Afonine"<PAfonine(a)lbl.gov>; Date: Thu, Apr 15, 2010 08:08 AM To: "PHENIX user mailing list"<phenixbb(a)phenix-online.org>; Subject: Re: [phenixbb] Real Space Refinement with marginal data Hi Carsten, I was wondering if anyone had experience/advice for real space refinement with phenix using marginal data to 3A. I just did a run (SA, real-space refinement against diff_map, 2 fold NCS, grouped APD, fix_rotamers enabled) were the resulting structure showed lots of disconnected sidechains and some broken main chains. I am just repeating the run w/o real space refinement, may be the combination of SA and real space refinement was a bit harsh, but am wondering what kind of parameters make most sense to tweak in order to avoid having the molecules fall apart. this could be a weight issue (weight between real-space target and restraints). In general I didn't find it too beneficial doing real-space refinement globally, although I've seen cases where it made a good difference (but at higher than 3A resolution). You may try to switch to "simple" target (to make it run much faster) and turn on the weight optimization: real_space_refinement { mode = *simple diff_map target_weights = value *grid_search gradients_ratio rmsd_max_bonds = 0.05 rmsd_max_angles = 5 grid_search_scales = 0.25 0.5 0.75 1 1.25 1.5 1.75 2 2.5 3 } "fix_rotamers=true" (local real-space refinement for the residues that really need it, as determined automatically) is much better option. I thoroughly tested it up to 3A resolution and in all test cases it worked just great. Try it and see what happens for your data. Pavel.

15 years, 2 months

Re: [cctbxbb] Git

by markus.gerstel＠diamond.ac.uk

Dear Luc, We actually had a look at the quality of the Github svn interface when we prepared for the DIALS move. My verdict was that it is surprisingly useful. All the possible git operations are mapped rather well onto a linear SVN history. All the branches and tags are accessible either by checking out the root of the repository, ie. svn co https://github.com/dials/dials.git (not recommended, as, say, any new branch/tag will probably result in a huge update operation for you) or by checking them out directly, ie. svn co https://github.com/dials/dials.git/branches/fix_export or svn co https://github.com/dials/dials.git/tags/1.0 Forks by other people are, as is the case when using git, simply not visible. I agree that looking at the project history through SVN may not be as clear as the git history. I wonder how relevant this is though, as you can explore the history, without running any commands, on the Github website, eg. https://github.com/dials/dials/network, https://github.com/dials/dials/commits/master, etc. Creating new branches and tags and merging stuff via SVN would be a major operation. However, that has always been the case with SVN, and for that reason one generally just does not do these things in SVN. But for an SVN user group those operations would not be important – you every only need to merge stuff if you create branches – so I don’t really see the problem. If you want to tag releases you can do that on the Github website as well as with a git command. In summary, I do recognize that SVN users will have difficulties participating in branched development, and in particular will not be able to quickly switch between branches. But I don’t think that this will be a problem, or that there is a need for a policy to keep the history linear. Best wishes -Markus From: cctbxbb-bounces(a)phenix-online.org [mailto:[email protected]] On Behalf Of Luc Bourhis Sent: 11 January 2016 16:45 To: cctbx mailing list Subject: Re: [cctbxbb] Gi, Hi Graeme, Can we revisit the idea of moving to git for cctbx? This brings to mind a question I have been asking myself since the subject has been brought forth. The idea Paul wrote about on this list was a move to Github. I guess some, perhaps many, developers will keep interacting with the repository using subversion. I am worried this would clash with the workflow of those of us who would go the native git way. By that I mean creating many branches and merge points, which one would merge into the official repository when ready. I am worried the history would look very opaque for the subversion users. I would even probably create a fork on Github, making it even more opaque for a tool like subversion. Has anybody thought about such issues? My preferred solution would be for everybody to move to git but I don’t think that’s realistic. At the other end of the spectrum, there is putting in place a policy to keep the history linear. Best wishes, Luc -- 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

9 years, 5 months

Re: [phenixbb] Gap between R and Rfree

by Young-Jin Cho

Thanks everyone. First, I checked my data and showed almost no anisotropy. Second, I tried both refmac and phenix, had the similar results. Third, ncs may be the key... I re-processed hkl and cut the resolution and did ncs=true. It first generated error message and suggested to put distance limit upto 3. Then now the gap between R and Rfree is reasonable (.2834 and .3361 without substrate and water). However I tried my previous pdb that has everything with old mtz file, Final R-work = 0.2389, R-free = 0.3158. In this case, I had to expand my limit upto 6. I still need to look more or do further refine from newly generated mtz file though, (sorry that's why I was late for responding.... I wanted to confirm it). Anyway, seemingly setting up 'ncs' as Pavel mentioned is most possible answer to my case. Thanks again. YoungJin ----- Original Message ----- From: "Kendall Nettles" <knettles(a)scripps.edu> To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> Sent: Thursday, February 25, 2010 1:35:10 PM GMT -05:00 US/Canada Eastern Subject: Re: [phenixbb] Gap between R and Rfree Did you check your data Kendall On Feb 25, 2010, at 12:43 PM, "Young-Jin Cho" <yjcho(a)brandeis.edu> wrote: > > 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 > _______________________________________________

15 years, 4 months

Re: [phenixbb] Problem with molecular replacement

by Shramana Chatterjee

Thanks Roger. I am trying through looking at packing of crystal lattice.It seems that there are some gaps in the lattice. May be this is identical with the solved one because of identical cell dimension and space group. Although I think I should cross check with lattice as Matthew's analysis suggest a different number of copies. On Thu, Apr 9, 2020 at 8:51 AM Roger Rowlett <rrowlett(a)colgate.edu> wrote: > For MR solutions with more than 4 molecules in the ASU, you can improve > your chances of finding a solution by employing the following > considerations: > > The number of protein units in the ASU predicted by Matthew's analysis my > not be accurate for n>4. Always look at the molecular packing of potential > solutions in the ASU using Coot or Pymol. You may discover you have too > many molecules, and therefore overlaps, or too few molecules, leaving > protein size gaps in the crystal lattice. Lattice packing of partial > solutions may guide your thinking about the correct number of molecules in > the ASU. A good solution should normally have symmetrical and clear solvent > channels, and good contacts between all molecules. > > You may nave a better chance of obtaining a initial solution by searching > with dimers (if structurally appropriate) than monomers. > > Unless your crystal form is identical to the solved version, there is no > guarantee your N will be the same as the solved N molecules in the ASU. Use > the Matthew's analysis and lattice packing as your guide. > > Using this approach I've been able to obtain MR solutions for ASUs with > N=6-8, even with identities as low as 30%. > > Good luck. > > Roger Rowlett > Gordon & Dorothy Kline Professor, Emeritus > Colgate University > > > On Wed, Apr 8, 2020, 11:43 PM Shramana Chatterjee <schatter90(a)gmail.com> > wrote: > >> Hi, >> >> I am trying to solve a structure using a data solved by SAD as an >> reference (ensemble in phaser). The structure I am trying to solve has 100% >> sequence identity with the solved one. The problem that I am facing during >> Phaser MR is that, in the solved structure there are 6 molecules in the ASU >> although I am getting maximum 4 molecules in the ASU and also Rfree is >> around 0.49 just after the phaser. Phaser is showing a good values of LLG >> (>500) and TFZ (>8). >> >> It would be very helpful if I get any suggestion about the >> above-mentioned problem. >> >> Thank you in advance. >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> Unsubscribe: phenixbb-leave(a)phenix-online.org > >

5 years, 2 months

Re: [phenixbb] Phaser-MR output after each component placement

by Randy Read

Hi Boaz, At the moment, that is indeed the only thing you can do with the partial solution information from the log file. In the CCP4 environment, you can cut and paste lines from the log file to make a .sol file, and use that to run something like a refinement job to produce a PDB and MTZ for a partial solution, but the Phenix environment uses Python pickle files to store the transformations, so that option doesn’t apply. (Unless you run Phaser from a script, in which case the Phenix and CCP4 versions work the same.) At one point, Phaser was writing out a PDB file for the top solution at every point in the process, but we felt that led to clutter and that it was confusing. There’s a major rewrite going on at the moment, and the new phasertng will primarily be run through the phaser.voyager pipeline. One of the design criteria here was to be able to examine branches that weren’t taken or intermediate points in the ongoing search, and to be able to work with them while the overall job is still running. So there will be a better option in the hopefully not too distant future! Best wishes, Randy ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 The Keith Peters Building Fax: +44 1223 336827 Hills Road E-mail: rjr27(a)cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk > On 27 Jul 2020, at 23:02, Boaz Shaanan <bshaanan(a)bgu.ac.il> wrote: > > Hi, > The closest option that comes to mind to do what you're looking for is to take the Euler angles+translations for each of the monomers in the .sol file (or at the top of the final pdb file) and apply each of them to the initial model using any transformation program of your choice. > I am more familiar with running Phaser using the ccp4 gui but it shouldn't be very different under Phenix. > Phaser people may well suggest a more elegant option. > Stay safe, > Boaz > > Boaz Shaanan, Ph.D. > Department of Life Sciences > Ben Gurion University of the Negev > Beer Sheva > Israel > > On Jul 27, 2020 16:02, Johannes Cramer <johannes.cramer(a)gmail.com> wrote: > Dear phenix board, > > does anyone of you know if there is an option in phaser-MR to output a pdb after each placed component? > For example: I suspect there to be 5 molecules in the AU. I start a replacement with 5 molecules and phaser places 1 (I would like to inspect that), 2 (again, I would like to look at the e.g. top 10 results), 3 and so on... > Is that possible? I couldn't find the option in the gui or in the phenix documentation, but maybe in the CLI? > I know I can run one after the other, but that would potentially waste CPU time until I find time to inspect them. > > Cheers, > Johannes > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org

4 years, 11 months

Re: [cctbxbb] Automated Travis CI for phenix

by Elliot Nelson

Hi Thanks. I had suspected this after looking at the fmodel script, but hadn't yet found the maps options. I will change to call those scripts internally. Thanks elliot ________________________________ From: cctbxbb-bounces(a)phenix-online.org <cctbxbb-bounces(a)phenix-online.org> on behalf of Billy Poon <BKPoon(a)lbl.gov> Sent: 24 May 2018 19:00:18 To: cctbx mailing list Subject: Re: [cctbxbb] Automated Travis CI for phenix Hi Elliot, Also, to run those files from the command-line, you would have something like, libtbx.python <CCTBX directory>/mmtbx/command_line/fmodel.py <your command-line arguments> The libtbx.python will call python with the proper environment to be cctbx-aware. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org On Thu, May 24, 2018 at 10:39 AM Oleg Sobolev <osobolev(a)lbl.gov<mailto:[email protected]>> wrote: Hi Elliot, phenix.fmodel and phenix.maps scripts are fully available in cctbx: cctbx_project/mmtbx/command_line/fmodel.py cctbx_project/mmtbx/command_line/maps.py and have zero dependencies from Phenix closed-source repository. You can just call them with cctbx-aware python in your software. Best regards, Oleg Sobolev. On Thu, May 24, 2018 at 3:37 AM, Elliot Nelson <elliot.nelson(a)dtc.ox.ac.uk<mailto:[email protected]>> wrote: Hi I'm looking to run automated integration tests for software, which currently runs from CCTBX, but also calls phenix scripts. These are phenix.fmodel and phenix.maps. Currently I have a docker image which sources CCP4 to get access to CCTBX, but this will not allow me to test stuff reliant on the phenix scripts. As Phenix is not downloadable on command line (CCP4 build can be got through wget command), it is not obvious as the best way to setup up such a docker build on travis CI. I wouldn't want to source a local download of the software as i am unsure of the licesining implications of hosting a copy of the software. Any suggestions would be greatly appreciated? Software (with dockerfile): https://github.com/nelse003/exhaustive_search <https://github.com/nelse003/exhaustive_search>Current docker image: https://hub.docker.com/r/nelse003/ccp4_phenix_docker/ Thanks Elliot DPhil Student, Systems Approaches to Biomedical Science<http://www.sabsidc.ox.ac.uk/> Protein Crystallography<http://www.thesgc.org/groupprofile/9489>, Structural Genomics Consortium, NDM, University of Oxford Oxford Protein Informatics Group<http://opig.stats.ox.ac.uk/>, Department of Statistics, University of Oxford _______________________________________________ cctbxbb mailing list cctbxbb(a)phenix-online.org<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/cctbxbb _______________________________________________ cctbxbb mailing list cctbxbb(a)phenix-online.org<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/cctbxbb

7 years, 1 month

Re: [phenixbb] Gap between R and Rfree

by Maia Cherney

My suggestion is try a different refinement program. Maia Phil Jeffrey wrote: > More information would be very helpful for giving detailed > suggestions, however: > > 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 > >

15 years, 4 months

Re: [cctbxbb] First svn commit

by James Stroud

Thanks everyone for the feedback. I have never really collaborated on code, so I am in definite need of community opinion on matters of style. I have changed the method to reflect the present vote of 3:1 for explicit argument lists, and will keep the sentiment in mind in the future. I have also renamed the method as_miller_arrays_dict. I figure the rename is safe because it has only been a couple of hours since I pushed the original code. James On Apr 18, 2013, at 1:10 AM, <Graeme.Winter(a)diamond.ac.uk> <Graeme.Winter(a)diamond.ac.uk> wrote: > +1 > > If I want to make sense of a function the first thing I do is look at the keyword arguments: if I see "not telling" it does not make the code more usable to me. Of course if the doc strings define exactly what keywords to pass in and what they should do then fair enough: I have not looked closely enough at these examples to comment on the details. > > Unlijke Pavel I would not necessarily write my own though :o) > > Best wishes, > > Graeme > > On 18 Apr 2013, at 07:10, Pavel Afonine wrote: > >> When I look at a function and do not understand what it does given it's name and list of arguments I look no more and write my own. Always. This is because my believe that if the author of that function did not bother to make the interface clear it says something about quality of the job as a whole (to me at least), and I don't have time to take chances or waste it reading more. >> >> Pavel >> >> On 4/17/13 11:02 PM, Nathaniel Echols wrote: >>> On Wed, Apr 17, 2013 at 10:19 PM, Richard Gildea <rgildea(a)gmail.com> wrote: >>>> 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 preference is actually the opposite (I do the same thing quite a >>> bit in my code), because otherwise there is no guarantee that keyword >>> arguments added to add_miller_arrays will also be usable with >>> add_miller_arrays_map. Using *args, **kwds makes the APIs explicitly >>> the same. (That said, I'm increasing favoring using **kwds alone in >>> these circumstances.) >>> >>>> 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. >>> <insert generic snarky vi advocacy here> >>> >>> -Nat >>> _______________________________________________ >>> cctbxbb mailing list >>> cctbxbb(a)phenix-online.org >>> http://phenix-online.org/mailman/listinfo/cctbxbb >> >> _______________________________________________ >> cctbxbb mailing list >> cctbxbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/cctbxbb > > > -- > 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

12 years, 2 months

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

by Pavel Afonine

Hi All, just in case somebody else had similar problems: it seems that using a recent Phenix version 1.13rc1 (2954) fixes the max_reasonable_bond_distance issue (at least in the reported by Ruki cases). Pavel On 11/14/17 13:16, Rune Thomas Kidmose wrote: > > 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"