Search results for "look through"

Re: [phenixbb] Autosol Feedback and questions

by Tom Terwilliger

Hi Partha, At 03:53 AM 1/2/2008, you wrote: >Happy new year everybody, > >I had quite a bit of difficulty with a SAD dataset which also showed >Sulphur. Previously I had tried SHELEX to find sites, MLPHARE to >refine, AddSOLVE to find more , and both SOLVE and PHASER to solve >but it did not get to a point where I could do manual building. >Autosol worked beautifully, the input files were scalepack merged >data, ha.pdb (from addsolve step), and the sequence. PHASER to solve >and TEXTAL & RESOLVE with through build option. > >This actually leave me with some confusions / questions: > >1. When I compare the other "solutions", they look like the right >one, just not good enough. Where exactly is the autosol making a >difference? Is it the ability of of TEXTAL to build something more >meaningful when the solution is not good or number of iterations? Autosol uses the quality of the model built as a score, if any model is built (R-factor if < 0.40; number of residues built less 2 * number of chains otherwise).. If no model is built, it uses the standard 4 or 5 criteria that are printed out on the AutoSol wizard screen (CC and R-factor for density modification; skew of electron density histograms, FOM, CC of NCS). >2. How does PHASER know the different anomalous atoms? Does is use a >different scaling factor for SE and S? It can tell by the ratio of anomalous to real scattering corresponding to each atom. >3. I see that phenix.refine has been used in the internal runs, I >have used phenix.refine earlier. But after playing with the side >chains in Coot, when I tried to use the modified pdb file and >resolve.mtz, it complained about the good old Free_R flag. However, >it ran directly in Refmac. Is it a known problem or maybe I did >something stupid? I could do a dry run and change the read mtz and >not cns if that would solve the problem. As Pavel and Ralf have mentioned, this is because AutoSol has tossed a few (usually blank) reflections from your reflection file when it created the refinement file exptl_fobs_phases_freeR_flags_15.mtz # or something similar. Without the "_15" if from AutoBuild The solution is to either (1) use the refinement file from AutoSol (exptl_fobs_phases_freeR_flags_15.mtz), or to delete the MD5 remark record from the AutoSol/AutoBuild PDB file. >4. Lastly, is it possible to use multiple processors to run the job? As Pavel mentioned...we are thinking about this but do not have anything yet. -Tom T 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, 5 months

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

by Da Duan

Thanks to everyone who've replied to this thread. I really appreciated the help and the useful information. Merry Xmas and Happy New Year everyone!! Cheers Da On Fri, Dec 16, 2011 at 11:56 AM, Pavel Afonine <pafonine(a)lbl.gov> wrote: > I agree, it is a matter of convention. The total ADP is: > Utotal=Ucryst+Ugroup+Ulocal. You can either output the total Utotal into > ATOM/ANISOU records or keep Ucryst+Ugroup in REMARKs and output Ulocal into > ATOMs. Both ways are valid as long as they yield identical Utotal. > > For more relevant information, summary and some review, see: > > - pages 23-29 here: > http://phenix-online.org/presentations/latest/pavel_refinement_general.pdf > > - article "On atomic displacement parameters (ADP) and their > parameterization in PHENIX" here: > http://phenix-online.org/newsletter/ > > Pavel > > > On 12/16/11 8:11 AM, Steiner, Roberto wrote: > > 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>wrote: > >> 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 >> > > <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 > > > > > > _______________________________________________ > phenixbb mailing [email protected]://phenix-online.org/mailman/listinfo/phenixbb > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > >

13 years, 6 months

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

by Nicholas Sauter

Billy Poon has said that he will look into the matter next week. Nick Nicholas K. Sauter, Ph. D. Senior Scientist, Molecular Biophysics & Integrated Bioimaging Division Lawrence Berkeley National Laboratory 1 Cyclotron Rd., Bldg. 33R0345 Berkeley, CA 94720 (510) 486-5713 On Fri, Sep 22, 2017 at 8:58 AM, <richard.gildea(a)diamond.ac.uk> wrote: > I was unaware that the code was actually used by anyone. > > So does anyone know enough about the code to fix the failing test that > Oleg and Graeme both complained about? > > Cheers, > > Richard > > 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 Aaron Brewster [asbrewster(a)lbl.gov] > Sent: 22 September 2017 15:56 > To: cctbx mailing list > Subject: Re: [cctbxbb] rstbx test is failing without indication in > test_all_parallel > > FWIW I have used it on several occasions to understand how diffraction > looks for different settings. For example, when I was working on amyloids > on the cspad detector I would run it like this: > > rstbx.simage.wx_display unit_cell=24.1460,4.8614,22.2291,90.000,107.319,90.000 > wavelength=1.452514 detector.distance=111 detector.size=194.15,194.15 > detector.pixels=1765,1765 ewald_proximity=0.042500 point_spread=20 > > Twiddle the rotx, roty and rotz. It's nifty. > > I don't see any reason to kill this code. > > -Aaron > > > On Fri, Sep 22, 2017 at 4:22 AM, <markus.gerstel(a)diamond.ac.uk<mailto: > markus.gerstel(a)diamond.ac.uk>> wrote: > 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<mailto:cctbxbb-bounces@ > phenix-online.org> [cctbxbb-bounces(a)phenix-online.org<mailto:cctbxbb- > bounces(a)phenix-online.org>] on behalf of richard.gildea(a)diamond.ac.uk< > mailto:[email protected]> [richard.gildea(a)diamond.ac.uk<mailto: > richard.gildea(a)diamond.ac.uk>] > Sent: Friday, September 22, 2017 12:08 > To: cctbxbb(a)phenix-online.org<mailto:[email protected]> > 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<tel:%2B441235%2077%208078> > > Diamond Light Source Ltd. > Diamond House > Harwell Science & Innovation Campus > Didcot > Oxfordshire > OX11 0DE > ________________________________ > From: cctbxbb-bounces(a)phenix-online.org<mailto:cctbxbb-bounces@ > phenix-online.org> [cctbxbb-bounces(a)phenix-online.org<mailto:cctbxbb- > bounces(a)phenix-online.org>] on behalf of Oleg Sobolev [osobolev(a)lbl.gov > <mailto:[email protected]>] > 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<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 > > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/cctbxbb >

7 years, 9 months

[phenixbb] Two postdoc positions in Ubiquitin Signalling, WEHI, Melbourne, Australia

by Bernhard Lechtenberg

Dear colleagues, The Ubiquitin Signalling Division at The Walter and Eliza Hall Institute (WEHI) is looking to recruit two Research Officers (Postdocs) to join our teams in the Lechtenberg and Komander labs. WEHI in Melbourne is Australia’s pre-eminent medical research institute. The Ubiquitin Signalling Division at WEHI was established in 2018, and offers a vibrant, multi-disciplinary and highly collaborative environment at the forefront of ubiquitin research with access to state-of-the art facilities in proteomics, structural biology (Titan Krios G4, Australian Synchrotron), biophysics (SEC-MALS, ITC, SPR, mass photometry, MST), cell manipulation (CRISPR) and imaging facilities, and drug discovery through the National Drug Discovery Centre (NDDC). The division features a continuous stream of excellent publications, exciting preliminary data, and opportunities to establish research ideas in a multidisciplinary environment. The Lechtenberg lab seeks to recruit a postdoc with structural biology (crystallography or cryo-EM) and biochemistry expertise to study large RBR E3 ligase complexes. Preliminary data include an established mammalian expression system. Details and applications: https://wehi.wd3.myworkdayjobs.com/en-US/WEHI/job/Research-Officer---Struct… Contact: Dr. Bernhard Lechtenberg, lechtenberg.b(a)wehi.edu.au<mailto:[email protected]> The Komander lab seeks to recruit a postdoc with structural biology and protein biochemistry background to embark on an early-stage drug discovery project in the area of mitophagy and Parkinson’s disease, with excellent academic and translational / entrepreneurial outputs expected. Details and applications: https://wehi.wd3.myworkdayjobs.com/en-US/WEHI/job/Parkville-Victoria-Austra… Contact: Prof. David Komander, dk(a)wehi.edu.au<mailto:[email protected]> We offer three-year contracts with highly competitive salaries and benefits. Pre-application enquiries are encouraged via the contact details provided. Please share this information within your networks. Kind regards, Bernhard Bernhard C. Lechtenberg PhD NHMRC Emerging Leadership Fellow Laboratory Head Ubiquitin Signalling Division E lechtenberg.b(a)wehi.edu.au<mailto:[email protected]> T +61 3 9345 2217 [WEHI Logo] Walter and Eliza Hall Institute of Medical Research 1G Royal Parade Parkville Victoria 3052 Australia www.wehi.edu.au<https://wehi.edu.au> Twitter<https://twitter.com/WEHI_research> | Facebook<https://www.facebook.com/WEHIresearch/> | Instagram<https://www.instagram.com/wehi_research> | Youtube<https://www.youtube.com/user/WEHImovies> | LinkedIn<https://www.linkedin.com/company/wehi_research> WEHI acknowledges the Wurundjeri people of the Kulin Nation as the traditional owners of the land where our campuses are located and the continuing connection to country and community. Private and confidential The content of this e-mail and any attachments may be private and confidential, intended only for use of the individual or entity named. If you are not the intended recipient of this message you must not read, forward, print, copy, disclose, use or store in any way the information this e-mail or any attachment contains. If you are not the intended recipient, please notify the sender immediately and delete or destroy all copies of this e-mail and any attachment.

2 years

Re: [phenixbb] matplotlib

by Francis E Reyes

Since we're talking about phenix distributions.... <flamebait> So when are we going to see phenix on the App Store? I hear the next version of OS X will only run binaries signed by Apple. </flamebait> F On Aug 18, 2011, at 12:06 PM, Nathaniel Echols wrote: > On Thu, Aug 18, 2011 at 10:39 AM, Ed Pozharski <epozh001(a)umaryland.edu> wrote: > In a nutshell, phenix gui may in some circumstances screw up other > programs that use matplotlib. > > It's not the fault of Phenix; matplotlib is unusually inflexible in how it deals with these cache files, and it is nearly unique among Python modules in its dependence on writing to the user's home directory. This isn't the only problem; another issue is that matplotlib creates these caches, and the maintainers appear to never have considered what would happen if the cached directory were removed. So when you run the GUI in version X of Phenix, then remove version X and install version Y, it will still look for the fonts installed with version X. I complained about this last December, and it remains unsolved in any of the official releases (one of which was this year). > > The likely cause is that phinix gui calls on bundled matplotlib which is > different from one I have installed (not to mention that I am using > Lucid (because it's LTS) which has python 2.6 and not the 2.7 that is > bundled with phenix). However, it still writes into the same > ~/.matplotlib folder, thus I end up with incompatible data. Certainly, > the problem will be gone when matplotlib gets bumped up to 1.0.1 in next > Ubuntu release. > > The issue with removing installations will remain, however. You could avoid the incompatibility problem by running "phenix.wxpython" if you need to use matplotlib. (We're using Python 2.7.2 right now, and generally update to the latest release in the 2.x series shortly after it comes out.) > > This is yet another example of why the standalone installation approach > is ideologically objectionable on modern Linux. But of course, the > practical advantage gained by not having to package the software for any > possible OS flavor/version users may choose outweighs the lower risks of > package incompatibility and the reduced size of the packaged product. > > We don't have the resources to support a more ideologically pure distribution mechanism - the installers are maintained by me and Ralf in between other projects. Also, we often depend on new features in the various dependencies that would not be immediately available through the package managers (for instance, we switched to Python 2.6 almost immediately because I needed the multiprocessing module). There are many things in the current installers that I'm unhappy with, but they don't take very much time to maintain, which is essential. > > -Nat > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

13 years, 10 months

Re: [phenixbb] phenix.refine Ile peptide bond breaks

by Pavel Afonine

Hi Katherine, sorry for the problem! From what you describe I can't really see what is wrong... So let's approach it this way: - Are you using the latest version of PHENIX (or at least not older than a few months)? If not, please get the latest: http://www.phenix-online.org/download/ and try the refinement again. - It is nearly impossible to tell what is wrong without actually looking at the PDB file. Could you please send me the PDB file? Also, I will need the exact command and parameters file (if you use one) that you use to run refinement. At this point I don't need the data, since I can simulate it given the PDB file. Please indicate the bonds that get broken. I will look into this problem once I get the file and the command. Pavel. On 5/6/09 6:07 PM, SIPPEL,KATHERINE H wrote: > Hi all, > > I've got a 2.1 angstrom structure that I am refining. The space > group is P212121. The structure is a dimer which I am refining > without NCS restraints. Each monomer has 333 residues and one > ligand, there are 33 Ile residues in each monomer. The first > couple of rounds of refinement I had no problems, but during the > third round phenix started breaking the main chain at the peptide > bond and the side chain between CA and CB on some of the Ile > residues. Specifically there are two breaks in chain A and four > breaks in chain B, with two additional residues in chain B > breaking only the CA-CB bond. Only one of the breaks is between > the same residue in both chains. > > I'll be boring and run through my refinement process. This is the > first time I've used phenix for anything but AutoSol and it is > very likely that I have messed something up. Feel free to correct > anything else I've done wrong along the way. > > Round 1, I rigid body refined chain A and B independently, > performed simulated annealing, and refined individual coordinates. > In COOT I manually refined and removed some bad loops. A few of > the Ile were deleted but none of the problem ones > > Round 2, I refined individual_sites and individual_adp and turned > off simulated annealing. In COOT I rebuilt some of the loops and > fitted the ligand into the density. I generated a .cif file in > eLBOW. > > Round 3, I refined the same as round 2 except that I included the > .cif file. This is when I got the peptide bond breaks for Ile > residues. I figured it was a fluke, fixed the breaks in COOT and > rebuilt a few more residues in the loops. > > I ran another round of refinement and the same breaks showed up in > the pdb file. I double checked the .geo file to see if Real Space > Refine had made the bond distances were too long, but all the > input distances were within one or two hundredths of an angstrom > from ideal. > > I considered it was maybe the ADP refinement as I was borderline > pushing the number of parameters I was refining given the number > of reflections I had. I turned off the individual_adp refinement > and reran refine_003. No luck. > > I tried increasing the weight of the geometry restraints over the > observed data. I did this by increasing target_weights.wxc_scale > = 1.5. (I suspect that I got this wrong. As I understood the > wxc_scale is the ratio of the geometry restraints to the observed > data. Feel free to point and laugh as long as you also provide an > explanation as to what this parameter really means and how I > should have done it,please.) Still no luck. > > For future information none of the problem isoleucines were > located near the ligand or near any of the loops I was > rebuilding. > > I think that's everything. Any help would be appreciated, > > Thanks, > > Kat > > > -- > SIPPEL,KATHERINE H > Ph. D. candidate > McKenna Lab > Department of Biochemistry and Molecular Biology > College of Medicine > University of Florida > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

16 years, 1 month

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

by Nicholas Sauter

Agreed. This is stable, mature code. No reason to kill it. Nick Nicholas K. Sauter, Ph. D. Senior Scientist, Molecular Biophysics & Integrated Bioimaging Division Lawrence Berkeley National Laboratory 1 Cyclotron Rd., Bldg. 33R0345 Berkeley, CA 94720 (510) 486-5713 On Fri, Sep 22, 2017 at 7:56 AM, Aaron Brewster <asbrewster(a)lbl.gov> wrote: > FWIW I have used it on several occasions to understand how diffraction > looks for different settings. For example, when I was working on amyloids > on the cspad detector I would run it like this: > > rstbx.simage.wx_display unit_cell=24.1460,4.8614,22.2291,90.000,107.319,90.000 > wavelength=1.452514 detector.distance=111 detector.size=194.15,194.15 > detector.pixels=1765,1765 ewald_proximity=0.042500 point_spread=20 > > Twiddle the rotx, roty and rotz. It's nifty. > > I don't see any reason to kill this code. > > -Aaron > > > On Fri, Sep 22, 2017 at 4:22 AM, <markus.gerstel(a)diamond.ac.uk> wrote: > >> 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@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@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 >> >> _______________________________________________ >> 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 > >

7 years, 9 months

[phenixbb] Re: red blobs (Andrea Smith)

by Dr. Kevin M Jude

Jumping on an old thread… I have a similar situation to Andrea’s; optimize_mask converged to the default values of rsolve and rshrink, but running phenix.mosaic produced quite improved maps. I’m trying, using version 1.21.2-5419, to run phenix.refine with main.mosaic=True and can’t find the setting in the gui, nor is it recognized when I run from the command line. Is it implemented in this version, or in some other version I can download? Best wishes Kevin -- Kevin M. Jude, PhD Structural Biology Research Specialist, Garcia Lab Howard Hughes Medical Institute Stanford University School of Medicine Beckman B177, 279 Campus Drive, Stanford CA 94305 From: phenixbb-bounces(a)phenix-online.org <phenixbb-bounces(a)phenix-online.org> on behalf of Pavel Afonine <pafonine(a)lbl.gov> Date: Thursday, March 28, 2024 at 7:49 AM To: Andrea Smith <andrea.smith(a)uochb.cas.cz> Cc: phenixbb(a)phenix-online.org <phenixbb(a)phenix-online.org>, Kay Diederichs <Kay.Diederichs(a)uni-konstanz.de> Subject: Re: [phenixbb] red blobs (Andrea Smith) Hi Andrea, here is what you can do today.. phenix.mosaic model.pdb data.mtz (yes, command line only, so far). This will take a minute or less (or more if the model is very large) and create model_mosaic.mtz file that contains the following Fourier map coefficients for mFo-DFc and 2mFo-DFc kind of maps: mFo-DFc_whole mFo-DFc_main mFo-DFc_mosaic 2mFo-DFc_whole 2mFo-DFc_main 2mFo-DFc_mosaic (you can see the MTZ file content by using this command: phenix.mtz.dump model_mosaic.mtz) The suffixes 'whole', 'main' and 'mosaic' refer to the types of masks used in calculation of each map and are explained in the paper: https://onlinelibrary.wiley.com/doi/abs/10.1002/pro.4909 To reiterate: 'whole' refers to the standard default bulk-solvent mask; 'main' refers to the largest part of the standard default bulk-solvent mask (small mask droplets inside protein region are removed); 'mosaic' refers to the mosaic mask, which is essentially the 'main' mask plus only those smaller masks that contain measurable amounts of the bulk-solvent (the rest, empty ones, that are responsible for 'red blobs' are removed). Next, you load these maps and your atomic model into Coot and inspect. Artifacts such as 'red blobs' you reported earlier should be absent in 'mFo-DFc_mosaic' map. This may lead to improvement of corresponding '2mFo-DFc_mosaic' map. Now, as you can see, this is separate from refinement. Here is what you should be able to do tomorrow.. Today I will add a parameter to phenix.refine (main.mosaic=True/False), which means if you get and install tomorrow's nightly build of Phenix (dev-5285 and up) the mosaic maps, both mFo-DFc_main and 2mFo-DFc_mosaic, will be present in the MTZ file created by phenix.refine (which is available in both CL and GUI). Let me know if you have any questions! Good luck! Pavel On 3/28/24 06:24, Andrea Smith wrote: > Hi all, > > can anyone please tell me how to use the mosaic model? I went through > the phenix documentation and didn't find anything about how to use it. > > Thank you, > Andrea > > > > On Friday, March 15, 2024 22:14 CET, "Andrea Smith" > <andrea.smith(a)uochb.cas.cz> wrote: >> Hi, >> >> I went through the paper quickly during the day thinking I will have >> a thorough look at home only to realize I don't have acces to it. >> >> From the quick look it seemed that my biological background will not >> be enough to understand all of it, but I remember that it said at the >> end that the mosaic model is implemented in phenix. However, I don't >> know where. I went through the parameters in GUI and didn't find >> anything that seemed to fit the description. >> >> Could you please explain what setting I need to use in the refinement? >> >> Thank you, best, >> Andrea >> >> On Friday, March 15, 2024 16:16 CET, Pavel Afonine <pafonine(a)lbl.gov> >> wrote: >>> Hi All, >>> >>> The explanation of the reason for these blobs and the solution is both >>> detailed in depth in this paper: >>> >>> https://onlinelibrary.wiley.com/doi/abs/10.1002/pro.4909 >>> >>> Quick facts are: >>> >>> - These blobs are artifacts of bulk-solvent modeling. >>> - You can efficiently deal with them in Phenix. >>> - In some cases (which I witnessed myself), it is important to deal with >>> them for map improvements elsewhere (for example, in regions of >>> interest, such as ligands). >>> >>> Let me know if you have any questions! >>> >>> All the best, >>> Pavel >>> >>> >>> On 3/15/24 07:39, Mitchell D. Miller wrote: >>> > Hi Andrea, >>> > >>> > You can also put a few zero occupancy atoms in the negative >>> > density to force phenix.refine to exclude the region >>> > from the bulk solvent mask. >>> > >>> > (You may also need to set >>> > refinement.mask.ignore_zero_occupancy_atoms = False >>> > so that the zero occupancy atoms are included in the mask) >>> > >>> > Regards, >>> > Mitch >>> > >>> > >>> > >>> > Quoting Kay Diederichs <kay.diederichs(a)uni-konstanz.de>: >>> > >>> >> Hi Andrea, >>> >> >>> >> hmm, did phenix.refine actually use optimize_mask=true ? >>> >> >>> >> If you compare the logfiles of phenix.refine (for the default run >>> >> with opimize_mask=false, and the new run with optimize_mask=true) >>> >> side-by-side with xxdiff or vimdiff (yes this needs to be run from a >>> >> command-line) then there should be a difference. >>> >> >>> >> Making peace with the red blobs is somewhat unsatisfactory from a >>> >> technical viewpoint, but probably not relevant from a biological one. >>> >> >>> >> I'd guess that the authors of >>> >> https://journals.iucr.org/a/issues/2024/02/00/pl5035/index.html would >>> >> be interested to look at your case ... >>> >> >>> >> Best wishes, >>> >> Kay >>> >> >>> >> >>> >> Am 15.03.24 um 08:27 schrieb Andrea Smith: >>> >>> Hi Kay, >>> >>> >>> >>> I tried the mask optimization and there is no change in how the >>> >>> final map looks like. >>> >>> >>> >>> Should I just make peace with it? >>> >>> >>> >>> Best, >>> >>> Andrea >>> >>> >>> >>> On Thursday, March 14, 2024 23:11 CET, Kay Diederichs >>> >>> <kay.diederichs(a)uni-konstanz.de> wrote: >>> >>>> Hi Andrea, >>> >>>> >>> >>>> in your case, phenix.refine seems to fill bulk solvent into volumes >>> >>>> that >>> >>>> are not actually filled by solvent. >>> >>>> It might help to optimize the mask, see >>> >>>> >>> https://phenix-online.org/documentation/reference/refinement.html#bulk-solv… >>> >>>> >>> >>>> "6. Mask parameters". >>> >>>> >>> >>>> Best, >>> >>>> Kay >>> >>>> -- >>> >>>> Kay Diederichs http://strucbio.biologie.uni-konstanz.de >>> >>>> email: Kay.Diederichs(a)uni-konstanz.de Tel +49 7531 88 4049 >>> >>>> Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 >>> Konstanz >>> >>>> >>> >>>> This e-mail is digitally signed. If your e-mail client does not >>> >>>> have the >>> >>>> necessary capabilities, just ignore the attached signature >>> >>>> "smime.p7s". >>> >>>> _______________________________________________ >>> >>>> phenixbb mailing list >>> >>>> phenixbb(a)phenix-online.org >>> >>>> http://phenix-online.org/mailman/listinfo/phenixbb >>> >>>> Unsubscribe: phenixbb-leave(a)phenix-online.org >>> >> >>> >> -- >>> >> Kay Diederichs http://strucbio.biologie.uni-konstanz.de >>> >> email: Kay.Diederichs(a)uni-konstanz.de Tel +49 7531 88 >>> 4049 >>> >> Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 >>> Konstanz >>> >> >>> >> This e-mail is digitally signed. If your e-mail client does not >>> have the >>> >> necessary capabilities, just ignore the attached signature >>> "smime.p7s". >>> > >>> > >>> > >>> > >>> > _______________________________________________ >>> > phenixbb mailing list >>> > phenixbb(a)phenix-online.org >>> > http://phenix-online.org/mailman/listinfo/phenixbb >>> > Unsubscribe: phenixbb-leave(a)phenix-online.org _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: phenixbb-leave(a)phenix-online.org

8 months

Re: [phenixbb] Discrepancy between Phenix GUI and command line for MR

by Xavier Brazzolotto

For information Apple M2 running Ventura 13.4.1 with 64 Go memory Phenix 1.20.1-4487 (Intel one). I’ve run MR of the same dataset (2.15A - I422) with the same model both with the command line and through the GUI. Command line (phenix.phaser) : 48 secs. GUI (Phaser-MR simple one component interface): 18 mins ! In copy the two log files if this helps > Le 4 juil. 2023 à 12:54, Luca Jovine <luca.jovine(a)ki.se> a écrit : > > Hi Xavier and Randy, I'm also experiencing the same on a M2 Mac! > -Luca > > -----Original Message----- > From: <phenixbb-bounces(a)phenix-online.org <mailto:[email protected]>> on behalf of Xavier Brazzolotto <xbrazzolotto(a)gmail.com <mailto:[email protected]>> > Date: Tuesday, 4 July 2023 at 12:38 > To: Randy John Read <rjr27(a)cam.ac.uk <mailto:[email protected]>> > Cc: PHENIX user mailing list <phenixbb(a)phenix-online.org <mailto:[email protected]>> > Subject: Re: [phenixbb] Discrepancy between Phenix GUI and command line for MR > > > Hi Randy, > > > Indeed I’m running Phenix on a brand new M2 Mac. > I will benchmark the two processes (GUI vs command line) and post them here. > > >> Le 4 juil. 2023 à 12:32, Randy John Read <rjr27(a)cam.ac.uk <mailto:[email protected]>> a écrit : >> >> Hi Xavier, >> >> We haven’t noticed that, or at least any effect is small enough not to stand out. There shouldn’t be a lot of overhead in communicating with the GUI (i.e. updating the terse log output and the graphs) but if there is we should look into it and see if we can do something about it. >> >> Could you tell me how much longer (say, in percentage terms) a job takes when you run it through the GUI compared to running the same job outside the GUI on the same computer? Also, it’s possible the architecture matters so could you say which type of computer and operating system you’re using? If it’s a Mac, is it one with an Intel processor or an ARM (M1 or M2) processor? (By the way, we finally managed to track down and fix an issue that cause Phaser to run really slowly on an M1 or M2 Mac when using the version compiled for Intel, once I got my hands on a new Mac.) >> >> Best wishes, >> >> Randy >> >>> On 4 Jul 2023, at 10:44, Xavier Brazzolotto <xbrazzolotto(a)gmail.com <mailto:[email protected]>> wrote: >>> >>> Dear Phenix users >>> >>> I’ve noticed that molecular replacement was clearly slower while running from the GUI compared to using the command line (phenix.phaser). >>> >>> Did you also observe such behavior? >>> >>> Best >>> Xavier >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org <mailto:[email protected]> >>> http://phenix-online.org/mailman/listinfo/phenixbb <http://phenix-online.org/mailman/listinfo/phenixbb> >>> Unsubscribe: phenixbb-leave(a)phenix-online.org <mailto:[email protected]> >> >> >> ----- >> Randy J. Read >> Department of Haematology, University of Cambridge >> Cambridge Institute for Medical Research Tel: +44 1223 336500 >> The Keith Peters Building >> Hills Road E-mail: rjr27(a)cam.ac.uk <mailto:[email protected]> >> Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk >> > > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org <mailto:[email protected]> > http://phenix-online.org/mailman/listinfo/phenixbb <http://phenix-online.org/mailman/listinfo/phenixbb> > Unsubscribe: phenixbb-leave(a)phenix-online.org <mailto:[email protected]> > > > > När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. > > > Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>.

1 year, 11 months

Re: [phenixbb] alternatives to RMSD

by Pavel Afonine

Hi Patrick, supposing models are superposed appropriately (see previous comments on phenixbb), step-by-step I see it as following: - compute density map for model A (or its Fourier synthesis of resolution 1A or higher), - compute density map for model B (or its Fourier synthesis of resolution 1A or higher), - compute map CC per residue or per atom between maps corresponding to A and B. I would think that "superposed appropriately" is a key here. Pavel On 7/5/14, 7:22 AM, PC wrote: > Hi Pavel, > > Thank you very much, this sounds very interesting. > > I have used ccp4, coot and phenix but I am no expert but I am > definitely interested in trying this method if you could give more > information. > > Thank you, > Patrick. > > > -----Original Message----- > *From:* pafonine(a)lbl.gov > *Sent:* Fri, 04 Jul 2014 20:34:33 -0700 > *To:* patrick.cossins(a)inbox.com, phenixbb(a)phenix-online.org > *Subject:* Re: [phenixbb] alternatives to RMSD > > Hi Patrick, > > RMSD is a poor measure in this case as it does not account for > B-factors, occupancies, alternative conformations and so on > information a crystal structure model may make available. > Macromolecules are not a bunch of points in space. > > While I'm sure more thorough methods exist, I would vote for the > simplest, most direct and obvious one. You can calculate electron > density map using a Gaussian approximation from model A and B > (yes, electron density map - not a Fourier image of it!). That > will naturally account for all: B-factors, occupancies, other > disorder. Then you can calculate a map similarity measure, such as > map correlation, for instance. After all, why use a cannon to kill > a fly?! > > If you are interested to follow this route I can explain the details. > > All the best, > Pavel > >> Hi Phenix users, >> >> I am not a crystallographer but I though you guys might be a good >> place to ask this question. >> >> I have 2 super secondary structures, A and B and they consist of >> Helix-turn-Strand >> >> Due to the turn the two structures have a poor RMSD because the >> two flanking fragments of Helix and Strand are far from each >> other but when I superimpose the two fragments >> individually(helixA with helix B and standA with strandB in Pymol >> they align very well). >> >> Now, is there a way to express this instead of using the RMSD? >> When the two structures align well the RMSD is very good but a >> slight movement and the RMSD is awful. >> But looking at the two structures I can see they follow the same >> path through space. >> >> Thank you, >> Patrick > > ------------------------------------------------------------------------ > Protect your computer files with professional cloud backup. Get PCRx > Backup and upload unlimited files automatically. > <http://backup.pcrx.com/mail>

10 years, 11 months

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