Search results for "look through"

Re: [phenixbb] phaser MR

by sbiswas2＠ncsu.edu

Hi, Thanks for your response. So I did one cycle of refinement and indeed the R work goes down by 5 points when I apply twin law at P4222 space group and when I look at the map the clashes that were present before are no longer there. I will try to scale it in P4 or P422 and see how it looks. I used HKL2000 to scale the data and have no idea if it will make a difference to use SCALA. This is what I got from phenix xtriage: These values look inbetween untwinned and perfect twin Acentric reflections <I^2>/<I>^2 :1.980 (untwinned: 2.000; perfect twin 1.500) <F>^2/<F^2> :0.797 (untwinned: 0.785; perfect twin 0.885) <|E^2 - 1|> :0.727 (untwinned: 0.736; perfect twin 0.541) Centric reflections <I^2>/<I>^2 :2.863 (untwinned: 3.000; perfect twin 2.000) <F>^2/<F^2> :0.673 (untwinned: 0.637; perfect twin 0.785) <|E^2 - 1|> :0.925 (untwinned: 0.968; perfect twin 0.736) ----------------------------------------------- | Z | Nac_obs | Nac_theo | Nc_obs | Nc_theo | ----------------------------------------------- | 0.0 | 0.000 | 0.000 | 0.000 | 0.000 | | 0.1 | 0.074 | 0.095 | 0.208 | 0.248 | | 0.2 | 0.164 | 0.181 | 0.319 | 0.345 | | 0.3 | 0.246 | 0.259 | 0.391 | 0.419 | | 0.4 | 0.322 | 0.330 | 0.452 | 0.474 | | 0.5 | 0.388 | 0.394 | 0.505 | 0.520 | | 0.6 | 0.445 | 0.451 | 0.552 | 0.561 | | 0.7 | 0.497 | 0.503 | 0.592 | 0.597 | | 0.8 | 0.541 | 0.551 | 0.630 | 0.629 | | 0.9 | 0.587 | 0.593 | 0.659 | 0.657 | | 1.0 | 0.631 | 0.632 | 0.679 | 0.683 | ----------------------------------------------- | Maximum deviation acentric : 0.021 | | Maximum deviation centric : 0.040 | | | | <NZ(obs)-NZ(twinned)>_acentric : -0.009 | | <NZ(obs)-NZ(twinned)>_centric : -0.014 | Thanks again for the valuable input, Shya Shya, > > Did phaser complain that the asymmetric unit was too full? How do the > self rotation maps look? Are the crystallographic peaks exact or off > by a few degrees (your resolution data may make it difficult to see > this)? How do the N(z) cumulative intensity distributions look (make > sure to calculate this with thin resolution bins, i.e. increase BINS > in Scala I think)? Does your data look sigmoidal on this plot? > > Perfect twinning or an NCS that's close to a crystallographic axis is > difficult to diagnose from merged intensity statistics and even more > difficult with resolution worse than 2.5. I recommend Dauter Acta > Cryst (2003) D59 2004-2016 for a good discussion of this. > > Your space group might be too high. See the subgroups of P422 at > http://cci.lbl.gov/~phzwart/p422_2.png > . Reintegrate and merge the data in each space group, MR a single copy > of your model (let phaser complete the ASU) and compare the Rpim's > (from scaling/merging) and the Rwork/Rfree from a rigid body refine > without NCS, with NCS, with appropriate twin laws, and with twin laws > + NCS. No need to do a full refinement just yet. Allow phenix.refine > to create the Rfree flags. Choose the space group which gives the best > statistics. > > I recently had a case (Hardin, Reyes, Batey J. Biol. Chem., Vol. 284, > Issue 22, 15317-15324, May 29, 2009) of a protein that merged into > P422 but was difficult to refine in that space group. I brought it > back to P4 and refined with NCS+twin to give more reasonable Rwork/ > Rfree (5-7% difference from the P422 to P4). > > HTH, > > FR > > > > On Jul 23, 2009, at 3:54 PM, sbiswas2(a)ncsu.edu wrote: > >> Hi Francis, >> Thanks for your response. The matthews coefficient suggests two >> molecules >> in the AU. Phaser also finds two molecules. I ran the dataset through >> phenix xtriage it did not indicate twinning though. The molecule also >> exists in nature as a monomer. >> Shya >> >> >>> Twinning? What's your matthews coefficient say? Do you know if your >>> structure is a multimer (biochemistry, etc)? Does it agree with the >>> matthews coefficient? >>> >>> If the unit cell is not big enough to hold all of the contents,then >>> this is an indicator for twinning . >>> >>> FR >>> >>> On Jul 23, 2009, at 3:09 PM, sbiswas2(a)ncsu.edu wrote: >>> >>>> Hi all, >>>> >>>> I was trying to solve a structure by molecular replacement. I scaled >>>> the >>>> data in P4222 space group (resolution 2.7A) with two molecules in >>>> the >>>> assymmetric unit (molecule A and B) I ran phaser with my model and >>>> got a >>>> Zscore of 5.1. When I look at the map that I got from phaser I could >>>> easily see good electron density for both molecules, However upon >>>> inspection of the electron density map there were considerable >>>> interaction >>>> or clashes with molecule B and a symmetry atom. Molecule A had no >>>> clashes >>>> however with the symmetry atoms. I was wondering if anyone knows how >>>> to >>>> resolve this. Could it be a problem of space group. The statistics >>>> are >>>> good for space group P4222 and the I/sigI was good till 2.7A. >>>> Any advice is appreciated, >>>> Shya >>>> >>>> _______________________________________________ >>>> phenixbb mailing list >>>> phenixbb(a)phenix-online.org >>>> http://www.phenix-online.org/mailman/listinfo/phenixbb >>> >>> --------------------------------------------- >>> Francis Reyes M.Sc. >>> 215 UCB >>> University of Colorado at Boulder >>> >>> gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D >>> >>> 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D >>> >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://www.phenix-online.org/mailman/listinfo/phenixbb >>> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb > > --------------------------------------------- > Francis Reyes M.Sc. > 215 UCB > University of Colorado at Boulder > > gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D > > 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

16 years, 6 months

Re: [phenixbb] Adding multiple conformers beyond 4

by Pavel Afonine

Hi George, hi Ben, thanks a lot for explaining! Yes, I'm well aware of multi-model refinement/building works and even myself was involved into one: Acta Cryst. (2007). D63, 597-610. "Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models". The "proper" way would be to enable using multiple models in phenix.refine (those defined with MODEL-ENDMDL cards). Currently this is not possible, but allowing it is in our to-do list. There is a number of technical issues that we need to address first (and some of them are not entirely up to me to re-solve: ed. Ralf's PDB interpretation procedure). Yes, using altLoc identifiers solves the problem indeed, although the under-the-hood calculations become extremely inefficient, but again, you are right, it works (see remark below for potential issues!). I can go ahead and remove "max=4" limitation. One remark. Recently I went through the whole PDB and tried to re-compute the reported statistics (R-factors, for example) for all entries containing multiple models. You can do it using phenix.model_vs_data tool: phenix.model_vs_data model.pdb data.hkl So, the observation is: more models your PDB file contains, less reproducible the R-factors. The obvious reason for this is the precision filed for occupancy in PDB file, which is 1.00. This means if you have 16 models, then you report occupancy as 0.06 and NOT 1./16 = 0.0625. So the rounding errors are the issue here. What if you have 200 models? Pavel. On 9/15/09 10:58 AM, George Phillips wrote: > Pavel, > > Ben and I are here now, so here is your response from both of us. > > We are trying to do complete ensemble refinements like we used to do > with CNS. 8 or even 16 (or more)copies of the whole protein tends to > give the best R-free. See the article below. > > We can recompile if you tell us what needs to be changed (or give us > some clues where to look), but we need a lot more than four. Clearly > this is not the normal use of this feature, but it works. We are > getting drops in Rfree from your test examples in phenix even with four. > > Levin et al. Structure, 15: 1040 (2007). > > George N. Phillips, Jr., Ph.D. > Professor of Biochemistry and of > Computer Sciences > University of Wisconsin-Madison > 433 Babcock Dr. Madison, Wi 53706 > Phone/FAX (608) 263-6142 > > > > On Sep 15, 2009, at 12:22 PM, Pavel Afonine wrote: > >> Hi Ben, >> >> to allow so I will have to slightly change the code... I went through >> the whole PDB and did not find any item that has more than 3 or 4 >> conformers (at the moment of coding this). So that made my choice for >> that temporary limitation of max=4 conformers (putting aside a number >> of cases of abusing altlocs to mimic multiple models MODEL-ENDMDL). >> Unfortunately, nothing is so permanent as temporary, so we have 4 >> since that -:) >> >> May I ask you: why you need to have more than 4 conformers? If it is >> really a bottleneck and stops you from doing something important >> right now, I can go ahead and fix it. >> >> Pavel. >> >> >> On 9/15/09 9:20 AM, Ben Mueller wrote: >>> I am a relatively new Phenix user and I am trying to see if it is >>> possible to push the number of conformers beyond 4. I tried to do >>> so, and I recieved the error message: >>> >>> RuntimeError: Exceed maximum allowable number of conformers (=4). >>> >>> Is there an easy (or difficult) way around this? >>> >>> Thanks for your time, >>> >>> Ben Mueller >>> >>> Phillips Lab >>> Department of Biochemistry >>> University of Wisconsin - Madison >>> ------------------------------------------------------------------------ >>> >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://www.phenix-online.org/mailman/listinfo/phenixbb >>> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org <mailto:[email protected]> >> http://www.phenix-online.org/mailman/listinfo/phenixbb > > ------------------------------------------------------------------------ > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

16 years, 4 months

Re: [cctbxbb] Making branches by accident

by markus.gerstel＠diamond.ac.uk

I use a custom prompt so I can see what is going on when I am in a git repository folder. This is the code one could add to their ~/.bashrc: https://gist.github.com/Anthchirp/dfc9a4382f8dfc9a97fe1039c9e6789a This is what it looks like: https://postimg.org/image/8c9h72qwd/ This is what happens in the image: * yellow brackets indicate you are in git territory, and contain the current branch name * red branch name = uncommitted changes in repository * positive number: number of commits the local repository is ahead of the remote repository * the 'git pull' command causes an implicit merge commit, which I undo with the next command * negative number: number of commits the local repository is behind the remote repository * both negative and positive number: branches have diverged Maybe someone finds it useful. -Markus ________________________________ From: cctbxbb-bounces(a)phenix-online.org [cctbxbb-bounces(a)phenix-online.org] on behalf of Pavel Afonine [pafonine(a)lbl.gov] Sent: Wednesday, December 07, 2016 18:24 To: cctbxbb(a)phenix-online.org Subject: Re: [cctbxbb] Making branches by accident This happened to me a few times now, and just double-checked that my .gitconfig contains "rebase = true". Let's see if it happens again.. Pavel On 12/7/16 00:02, Graeme.Winter(a)diamond.ac.uk<mailto:[email protected]> wrote: Morning all I am seeing a certain amount of “Merge branch 'master' of github.com:cctbx/cctbx_project” coming through on the commits – this usually means you did not do a git pull –rebase before the git push. This can be set to the default by using the spell Markus sent out git config --global pull.rebase true This will need to be done on each machine you push from, else getting the habit of doing a git pull –rebase before push is a good one. We have had this on and off with DIALS but it tends to pass easily enough. What bad happens? Nothing really but the history becomes confusing… So: may be worth checking that you have the pull.rebase thing set? Cheerio Graeme -- 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

9 years, 2 months

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

18 years

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 > >

14 years, 1 month

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 >

8 years, 4 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, 7 months

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

14 years, 5 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, 9 months

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 > >

8 years, 4 months

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