Search results for "look through"

Re: [phenixbb] measuring the angle between two DNA duplexes

by Pavel Afonine

Hi Ed, interesting idea! Although I was thinking to have a tool that is a little more general and a little less context dependent. Say you have two clouds of points that are (thinking in terms of macromolecules) two alpha helices (for instance), and you want to know the angle between the axes of the two helices. How would I approach this?.. First, for each helix I would compute a symmetric 3x3 matrix like this: sum(xn-xc)**2 sum(xn-xc)*(yn-xc) sum(xn-xc)*(zn-zc) sum(xn-xc)*(yn-xc) sum(yn-yc)**2 sum(yn-yc)*(yz-zc) sum(xn-xc)*(zn-zc) sum(yn-yc)*(yz-zc) sum(zn-zc)**2 where (xn,yn,zn) is the coordinate of nth atom, the sum is taken over all atoms, and (xc,yc,zc) is the coordinate of the center of mass. Second, for each of the two matrices I would find its eigen-values and eigen-vectors, and select eigen-vectors corresponding to largest eigenvalues. Finally, the desired angle is the angle between the two eigen-vectors found above, which is computed trivially. I think this a little simpler than finding the best fit for a 3D line. What you think? Pavel On 1/20/14, 2:14 PM, Edward A. Berry wrote: > > > Pavel Afonine wrote: > . . > >> The underlying procedure would do the following: >> - extract two sets of coordinates of atoms corresponding to two >> provided atom selections; >> - draw two optimal lines (LS fit) passing through the above sets >> of coordinates; >> - compute and report angle between those two lines? >> > > This could be innacurate for very short helices (admittedly not the > case one usually would be looking for angles), or determining the axis > of a short portion of a curved helix. A more accurate way to > determine the axis- have a long canonical duplex constructed with its > axis along Z (0,0,1). Superimpose as many residues of that as required > on the duplex being tested, using only backbone atoms or even only > phosphates. Operate on (0,0,1) with the resulting operator (i.e. take > the third column of the rotation matrix) and use that as a vector > parallel to the axis of the duplex being tested. > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb

11 years, 5 months

Re: [phenixbb] Fwd: [ccp4bb] Phenix; converting a map to structure factors

by Mayer, Mark (NIH/NICHD) [E]

Hi Pavel, Would reciprocal space refinement improve maps - or would all the improvement come from model bias? i.e. would maps look nicer, but with no new information content? I guess the difference from X-ray is that while each HKL has contributions from all atoms in the ASU, for an EM map converted to structure factors this is not true. Also, EM maps have substantial local resolution differences, and I don't understand how this would impact SF calculation. I know that some in the EM community, who are not used to hands on (i.e. coot/O etc) real space refinement, are disappointed by the small radius of convergence for automatic real space refinement that is not guided by a human being sitting at a graphics terminal. I doubt that reciprocal space refinement would change that, but would Fo-Fc maps make it easier to choose between good and bad fits to EM maps? I'm hoping that people with more experience will chime in; I believe this is an active issue for CCP4 (refmac) users as well. Mark ________________________________________ From: Pavel Afonine [pafonine(a)lbl.gov] Sent: Friday, July 10, 2015 9:56 PM To: Terwilliger, Thomas Charles; Mayer, Mark (NIH/NICHD) [E]; PHENIX user mailing list Subject: Re: Fwd: [phenixbb] [ccp4bb] Phenix; converting a map to structure factors Hi Mark, Tom copied me your email. As I'm sure you are aware there is tremendous interest in building into and refining against low resolution (by X-ray standards) EM maps. Could you comment to the phenix BB about whether its appropriate to convert maps to reciprocal space and use ML refinement? While it is a possible way of doing this (and this is how it's been done in the past) I don't think it is a good route to follow. In case of cryo-EM your data is map, so why not just refine against the map? Why take a detour through reciprocal-space by converting map into structure factors (=manipulating your original data) and doing reciprocal space using refinement programs that were designed for crystallography? With this in mind we have developed a new refinement tool in Phenix (it is still in active development!) called phenix.real_space_refine that is designed to refine atomic models directly into maps (any map: X-ray, neutron, cryo-EM, low or high resolution), for quick summary see http://phenix-online.org/presentations/real_space_refine.pdf as well as documentation page (at the bottom): http://phenix-online.org/documentation/ and newsletter article (page 43): http://phenix-online.org/newsletter/CCN_2013_07.pdf Let me know if you have any questions or comments! Pavel

9 years, 11 months

[phenixbb] Postdoc position, Plant Hormone Transporting Membrane Proteins (Denmark)

by Bjørn Panyella Pedersen

Dear colleagues, I have an open postdoc position funded by the ERC (details below). Please pass this along to anyone who might be interested. Thanks! /Bjørn Postdoctoral position in Structure of Plant Hormone Transporting Membrane Proteins at Aarhus University, Denmark. (https://tinyurl.com/MBGpostdoc) We are looking for a highly skilled and motivated postdoc with an interest in working on plant hormone transporting membrane transporters and preferably with a proven track record in the area of structural and/or functional analysis of membrane proteins and an interest for plant biology. Starting date is negotiable. Funding is available through an ERC grant for at least 2 years of employment. An extension is possible for up to a total maximum of 4 years of employment as a postdoc. The position: The position seeks to strengthen ongoing activities in the laboratory of Bjørn P. Pedersen on structure, related to the function and mechanism of plant hormone-transporting membrane proteins as defined by the ERC project MUM-GROW (pedersenlab.dk). Exact project will be shaped out in dialogue with top runners. The laboratory's interest is the interplay between structure and function of transmembrane transport processes with a focus on metabolite uptake systems, and the methods uses are primarily crystallography and cryo-EM. The group is part of the Section of Structural Biology at Aarhus University. The candidate: A successful candidate has a relevant Ph.D. degree and a solid and documented background in structural biology, biochemistry and/or biophysics. Experience with membrane protein expression and purification is favored, and the candidate must demonstrate an ability and interest to work with membrane proteins with a structural aim. Applicants should be ambitious, show strong collaborative skills, and be able to take initiatives and responsibility within the work environment. The successful candidate is offered: - access to a well-developed research infrastructure. - a research climate inviting lively, open and critical discussion within and across different fields of research. - a working environment with teamwork, close working relations, network activities among young scientists and social activities. - a workplace characterized by professionalism, equality and a healthy work-life balance. The city: In Aarhus you have easy access to beautiful nature, an exciting culture and city life as well as a safe environment for children - a great place for the whole family. The city of Aarhus has everything you need: exciting national and international jobs, delightful residential areas, a rich cultural life, and beautiful surrounding landscape of woods and coastline that make Aarhus a wonderful place to live and work. See https://international.au.dk/life/ for details. Aarhus University offers relocation service to international researchers. You can read more about it at https://international.au.dk/life/researcherscomingtoau/. Deadline: All applications must be made online (https://tinyurl.com/MBGpostdoc) and received by March 1st 2021.

4 years, 5 months

[phenixbb] Postdoc position, Plant Hormone Transporting Membrane Proteins (Denmark)

by Bjørn Panyella Pedersen

Dear colleagues, I have an open postdoc position funded by the ERC (details below). Please pass this along to anyone who might be interested. Thanks! /Bjørn Postdoctoral position in Structure of Plant Hormone Transporting Membrane Proteins at Aarhus University, Denmark. online posting: https://tinyurl.com/MBGpostdoc We are looking for a highly skilled and motivated postdoc with an interest in working on plant hormone transporting membrane transporters and preferably with a proven track record in the area of structural and/or functional analysis of membrane proteins and an interest for plant biology. Starting date is negotiable. Funding is available through an ERC grant for at least 2 years of employment. An extension is possible for up to a total maximum of 4 years of employment as a postdoc. The position: The position seeks to strengthen ongoing activities in the laboratory of Bjørn P. Pedersen on structure, related to the function and mechanism of plant hormone-transporting membrane proteins as defined by the ERC project MUM-GROW (pedersenlab.dk). Exact project will be shaped out in dialogue with top runners. The laboratory's interest is the interplay between structure and function of transmembrane transport processes with a focus on metabolite uptake systems, and the methods uses are primarily crystallography and cryo-EM. The group is part of the Section of Structural Biology at Aarhus University. The candidate: A successful candidate has a relevant Ph.D. degree and a solid and documented background in structural biology, biochemistry and/or biophysics. Experience with membrane protein expression and purification is favored, and the candidate must demonstrate an ability and interest to work with membrane proteins with a structural aim. Applicants should be ambitious, show strong collaborative skills, and be able to take initiatives and responsibility within the work environment. The successful candidate is offered: - access to a well-developed research infrastructure. - a research climate inviting lively, open and critical discussion within and across different fields of research. - a working environment with teamwork, close working relations, network activities among young scientists and social activities. - a workplace characterized by professionalism, equality and a healthy work-life balance. The city: In Aarhus you have easy access to beautiful nature, an exciting culture and city life as well as a safe environment for children - a great place for the whole family. The city of Aarhus has everything you need: exciting national and international jobs, delightful residential areas, a rich cultural life, and beautiful surrounding landscape of woods and coastline that make Aarhus a wonderful place to live and work. See https://international.au.dk/life/ for details. Aarhus University offers relocation service to international researchers. You can read more about it at https://international.au.dk/life/researcherscomingtoau/. Deadline: All applications must be made online (https://tinyurl.com/MBGpostdoc) and received by March 1st 2021.

4 years, 4 months

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

by Tom Terwilliger

Hi Bryan, Yes, "No merge original index" files should work fine. This file should be converted by the autosol wizard to premerged scalepack during the run. In your case this seems to be so as the file header that is being read during the middle of the run 1 -987 86.052 86.052 132.608 90.000 90.000 90.000 p41212 is premerged scalepack. Now what does not make sense is the error message "You have set the keywords readdenzo and unmerged". I am not sure where that has come from. I just ran a SAD dataset to test this with an unmerged original index file, and it ran fine for me. If this doesn't help, could you send me (terwilliger(a)lanl.gov) your input script and datafile ( or even the first 1000 lines of the datafile) and I can try to debug it. 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] Adding multiple conformers beyond 4

by George Phillips

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 > http://www.phenix-online.org/mailman/listinfo/phenixbb

15 years, 9 months

Re: [phenixbb] AutoSol/PhaserSAD with more than one anomalously-scattering atom produces error...

by Thomas C. Terwilliger

Hi Francis, I am sorry about the problem! I didn't know that 1.6-289 had this bug...but it seems to be corrected in my current version (1.6-609) so I think that moving to a more recent version is the best solution. I just ran this: phenix.autosol w1.sca seq_file=seq.dat quick=True ncs_copies=1 build=false se mad_ha_add_list="Br Pt" mad_ha_add_f_prime_list=" -7 -10" mad_ha_add_f_double_prime_list=" 4.2 12" sites_file=ha.pdb and it added the two extra ha types fine and read the sites from ha.pdb. Hopefully this will do what you are looking for. All the best, Tom T >> Hi all >> >> I'm getting an error... >> >> "'InputEP_SAD' object has no attribute 'addSCAT_TYPE'" >> >> >> from autosol. >> >> Facts: >> >> - phenix-1.6-289 >> >> - SAD experiment with two types of anomalous scatterers in the xtal, >> data is the peak wavelength of one of the anomalous scatterers. >> >> - sites are input from a previous phaser run (ha_x.pdb_formatted.pdb) >> >> - the atom positions are likely correct, but the atom types are all >> the same atom (I'd like phenix/phaser to go through the list and >> reannotate/refine based on the proper heavy atom identities) >> >> - additional atom types/f'/f'' defined in autosol.eff, Using the >> documentation example "SAD with more than one anomalously-scattering >> atom" (http://www.phenix-online.org/documentation/autosol.htm). >> >> >> Thanks! >> >> F >> >> --------------------------------------------- >> Francis E. 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://phenix-online.org/mailman/listinfo/phenixbb >>

14 years, 6 months

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

by richard.gildea＠diamond.ac.uk

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:[email protected]>> 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:[email protected]> [cctbxbb-bounces(a)phenix-online.org<mailto:[email protected]>] on behalf of richard.gildea(a)diamond.ac.uk<mailto:[email protected]> [richard.gildea(a)diamond.ac.uk<mailto:[email protected]>] 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:[email protected]> [cctbxbb-bounces(a)phenix-online.org<mailto:[email protected]>] 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

7 years, 9 months

Re: [phenixbb] Autobuild

by Heather L Condurso

Tom, First, I had refine input model before rebuilding turned off. I thought this meant whether it would refine before doing anything else which I didn't really think was necessary but maybe I was wrong. I found an autobuild.eff file and it looks like all that was different in my refinement was that I hadn't selected simulated annealing in autobuild and had in refine. I can run it again with these adjusted parameters to see if I get a better result. As for the maps, the refine maps are definitely better than the autobuild maps but not by all that much. These missing regions are pretty long so fit_loops hasn't been too helpful. I also had the problem that once I ran fit_loops, I would get an error if I tried to put the new pdb file through refinement. Something about missing fields but it had only added a residue here and there across many monomers so I gave up. I guess what would be helpful to me is how best to use my computing time to try to get autobuild to get me the best possible model it can. I can input my refined structure but what parameters will make autobuild focus on extending the model to build in the missing regions instead of continually trying to rebuild a model that is already at a CC=0.90 around the built atoms? Thanks, Heather On Fri, Sep 6, 2013 at 6:32 PM, Terwilliger, Thomas C <terwilliger(a)lanl.gov>wrote: > Hi Heather, > > Hmm... a little hard to tell what the problem is. > > So first: autobuild should have refined this model as one of the first > things it did. Did it get about the same R that you got when refining it > directly with phenix.refine? If no, then have a look at the refinement > .eff files (the autobuild one is in AutoBuild_run_1_/TEMP0 unless that was > cleaned up) and see what is different. > > Next....what happens if you just run phenix.refine to get a map, also > take the map from this autobuild run, and look at them along with your > model. Is one a lot better than the other? > > If you take your best working map and run phenix.fit_loops with this > model...how does that do? > > All the best, > Tom T > > ------------------------------ > *From:* phenixbb-bounces(a)phenix-online.org [ > phenixbb-bounces(a)phenix-online.org] on behalf of Heather L Condurso [ > condurso(a)bc.edu] > *Sent:* Friday, September 06, 2013 3:54 PM > *To:* PHENIX user mailing list > *Subject:* [phenixbb] Autobuild > > I'm a bit confused about what is going on with my autobuild run. I > solved a structure from anomalous data to 2.7A but many loops are missing. > I ran phaser with the current model and native data that extends to 2.4A > and got a solution and started autobuild from there. I used mostly the > default settings and rebuild_in_place=False. After a pretty short time I > realized the run was over and at the bottom of the log I see this: > > Cycle 3 R/Rfree=0.28/0.35 Built=488 Placed=467 > > > AutoBuild_build_cycle AutoBuild Run 162 Fri Sep 6 14:33:39 2013 > > > > Deciding if we should continue... > > Recent R change per cycle: 0.0 > > > Ending these build cycles as the recent change in R per cycle has been > > 0.0 and the required value of change is -0.005 > > and the R is somewhat acceptable at 0.276670644792 > > All done with build cycles in this region > > > AutoBuild_set_up_build AutoBuild Run 162 Fri Sep 6 14:33:40 2013 > > > All omit/non-omit regions completed > > > finished AutoBuild Run 162 Fri Sep 6 14:33:40 2013 > > > Finishing AutoBuild Run 162 > > Facts written to AutoBuild_run_162_/AutoBuild_Facts.dat > > AutoBuild Run 162 > > > Summary of model-building for run 162 Fri Sep 6 14:33:40 2013 > > Files are in the directory: /Users/heather/Desktop/M/AutoBuild_run_162_/ > > > > Starting mtz file: > /Users/heather/Desktop/M/ImportRawData_run_4_/A-3_xx_PHX.mtz > > Sequence file: /Users/heather/Desktop/M/m.pir > > > Best solution on cycle: 2 R/Rfree=0.26/0.33 > > > Summary of output files for Solution 1 from rebuild cycle 2 > > > --- Model (PDB file) --- > > pdb_file: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.pdb > > > --- Model (CIF file) --- > > cif_pdb_file: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.cif > > > --- Refinement log file --- > > log_refine: > /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.log_refine > > > --- Model-building log file --- > > log: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.log > > > --- Model-map correlation log file --- > > log_eval: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.log_eval > > > --- 2FoFc and FoFc map coefficients from refinement 2FOFCWT PH2FOFCWT > FOFCWT PHFOFCWT --- > > refine_map_coeffs: > /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best_refine_map_coeffs.mtz > > > --- Data for refinement FP SIGFP PHIM FOMM HLAM HLBM HLCM HLDM > FreeR_flag --- > > refine_data: > /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best_refine_data.mtz > > > --- Density-modified map coefficients FWT PHWT --- > > denmod_map_coeffs: > /Users/heather/Desktop//AutoBuild_run_162_/overall_best_denmod_map_coeffs.mtz > > > > You might consider making one very good model now with: > > > phenix.autobuild \ > > data=/Users/heather/Desktop/M/AutoBuild_run_162_/overall_best_refine_data.mtz > \ > > model=/Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.pdb \ > > rebuild_in_place=True \ > > seq_file=/Users/heather/Desktop/M/m.pir > > > My full sequence is 325 amino acids so only about 75% is build in. I am > hoping autobuild can help find at least some of these missing residues. > Why would the change in R be zero? What is meant by "You might consider > making one very good model now with:"? I tried running autobuild with > these new files and rebuild_in_place=true and get the same type of message. > Is this the best that autobuild can do? I also ran the phaser solution > through refinement and can significantly lower the Rs from 0.26/0.33 to > 0.22/0.30. I appreciate any advice on how best to proceed. > > I am using 1.8.2-1472 if that matters. > > > Thanks, > Heather > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > >

11 years, 9 months

Re: [cctbxbb] some thoughts on cctbx and pip

by Graeme.Winter＠Diamond.ac.uk

Hi Aaron Re: talk about if interest I think it would be very useful to have a roadmap of where this is going, the intentions and how we expect it to play with other cctbx-dependent projects - have I missed this? Having it somewhere e.g. on the wiki would be a big help Thanks Graeme On 17 Aug 2019, at 00:36, Aaron Brewster <asbrewster(a)lbl.gov<mailto:[email protected]>> wrote: Hi Luc, thanks. I did recall someone working on this a while back. For conda, there are a couple more things to finish and then we hope to have cctbx available through conda. 1) There is work being done in a branch to make cctbx use boost in standard locations (e.g. the system boost, or a conda boost). That will allow us to use install boost by conda and not build it ourselves. (https://github.com/cctbx/cctbx_project/tree/conda_boost). Also, newer versions of boost are being tested (up through 1.70). (This will also enable python 3.7 support.) 2) We need to work on getting a make install step in place so that we can build the conda package and upload it. 3) We want to split the dependencies up by builder (cctbx, cctbx-lite, dials, phenix, etc.) into meta packages and their associated manifests. I can talk more about this if there is interest. Thanks, -Aaron On Fri, Aug 16, 2019 at 1:48 PM Luc Bourhis <luc_j_bourhis(a)mac.com<mailto:[email protected]>> wrote: Hi, I did look into that many years ago, and even toyed with building a pip installer. What stopped me is the exact conclusion you reached too: the user would not have the pip experience he expects. You are right that it is a lot of effort but is it worth it? Considering that remark, I don’t think so. Now, Conda was created specifically to go beyond pip pure-python-only support. Since cctbx has garnered support for Conda, the best avenue imho is to go the extra length to have a package on Anaconda.org<http://anaconda.org/>, and then to advertise it hard to every potential user out there. Best wishes, Luc On 16 Aug 2019, at 21:45, Aaron Brewster <asbrewster(a)lbl.gov<mailto:[email protected]>> wrote: Hi, to avoid clouding Dorothee's documentation email thread, which I think is a highly useful enterprise, here's some thoughts about putting cctbx into pip. Pip doesn't install non-python dependencies well. I don't think boost is available as a package on pip (at least the package version we use). wxPython4 isn't portable through pip (https://wiki.wxpython.org/How%20to%20install%20wxPython#Installing_wxPython…). MPI libraries are system dependent. If cctbx were a pure python package, pip would be fine, but cctbx is not. All that said, we could build a manylinux1 version of cctbx and upload it to PyPi (I'm just learning about this). For a pip package to be portable (which is a requirement for cctbx), it needs to conform to PEP513, the manylinux1 standard (https://www.python.org/dev/peps/pep-0513/). For example, numpy is built according to this standard (see https://pypi.org/project/numpy/#files, where you'll see the manylinux1 wheel). Note, the manylinux1 standard is built with Centos 5.11 which we no longer support. There is also a manylinux2010 standard, which is based on Centos 6 (https://www.python.org/dev/peps/pep-0571/). This is likely a more attainable target (note though by default C++11 is not supported on Centos 6). If we built a manylinuxX version of cctbx and uploaded it to PyPi, the user would need all the non-python dependencies. There's no way to specify these in pip. For example, cctbx requires boost 1.63 or better. The user will need to have it in a place their python can find it, or we could package it ourselves and supply it, similar to how the pip h5py package now comes with an hd5f library, or how the pip numpy package includes an openblas library. We'd have to do the same for any packages we depend on that aren't on pip using the manylinux standards, such as wxPython4. Further, we need to think about how dials and other cctbx-based packages interact. If pip install cctbx is set up, how does pip install dials work, such that any dials shared libraries can find the cctbx libraries? Can shared libraries from one pip package link against libraries in another pip package? Would each package need to supply its own boost? Possibly this is well understood in the pip field, but not by me :) Finally, there's the option of providing a source pip package. This would require the full compiler toolchain for any given platform (macOS, linux, windows). These are likely available for developers, but not for general users. Anyway, these are some of the obstacles. Not saying it isn't possible, it's just a lot of effort. Thanks, -Aaron _______________________________________________ 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<mailto:[email protected]> 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. 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