Search results for "look through"

Re: [cctbxbb] some thoughts on cctbx and pip

by Aaron Brewster

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> 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, 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> 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 > http://phenix-online.org/mailman/listinfo/cctbxbb > > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/cctbxbb >

5 years, 10 months

Re: [cctbxbb] using scatterer flags?

by Pavel Afonine

I added "use" flag (at the time when I was adding all other scatterer flags) rather as a placeholder for a future use, so yes, indeed, currently it is not respected in fcalc and gradients calculation (though it should be respected!). Perhaps it's time to start using it... Pavel On 4/15/13 11:58 AM, Richard Gildea wrote: > Are the same scatterers contributing to f_calc for every calculation, > or will the scatterers that are contributing vary from calculation to > calculation? In the case of the former it might be simplest to create > a new copy of the xray_structure with only those scatterers. > > It looks the "use" flag isn't actually respected in the structure > factor or gradient calculations as far as I can tell. If you feel you > need something like this rather than creating new copies of the > xray_structure with only the scatterers you need or alternatively > setting the occupancy to zero, then this is probably something we can > add into the code. There is some code in cctbx/xray/scatterer_flags.h > for flags_set_grad_*() that will set a selection of gradients all at > once in C++, but I don't see an equivalent for set_use_*(). I suspect > that the overhead of looping through the scatterers to set flags in > Python would be small compared to the cost of calculating the > structure factors in the first place. > > Cheers, > > Richard > > > On 15 April 2013 10:40, Jan Marten Simons <marten(a)xtal.rwth-aachen.de > <mailto:[email protected]>> wrote: > > Am Montag 15 April 2013 18:33:00 schrieb Jan Marten Simons: > > Hi, > > > > while working on a really fast way to calculate the structure > factors of a > > few millions of different modifications of a structure with only the > > selected scatterers contributing to f_calc .... > > [...] > > > (I think building a larger structure and working with > > selections might be faster than creating lots of different > structures > > containing only the desired scatterers, but I might be wrong on > this.) > > I've found "flags" might be what I'm looking for. So if I could > set the "use" > flag for all scatterers at once and if it was taken into > consideration during > structure factor calculation then I think it would most likely be > the fastest > way to enable or disable the contribution of individual scatterers > to the > structure factors. Am I right on this and how would I best > interface with the > flags mechanism (from python)? > > Cheers, > > Jan > _______________________________________________ > 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

12 years, 2 months

Re: [phenixbb] Problematic dataset

by Peter Zwart

Hi Lucas, It would be very informative to see the whole log file, especially the section on intensity statistics. Furthermore, please run the data in P21 through xtriage and find that it is pseudo C222 with a single twin law. I guess you have close to perfect twinning on the operator -h,-h+k,-l (which will look different in P21). Please try phenix.refine twinning=True twin_law=<whatever xtriage gives you> model.pdb data.mtz I hope you have choosen your free set with phenix.refine or iotbx.reflection_file_converter to get twin law compatible free set (done by default in phenix.refine, even if no twin law is specified). Let me know if you have any other problems, Peter Lucas Bleicher wrote: > I have a 1.9A dataset that could, in principle, be > used to a molecular replacement solution. Phaser finds > a solution which yields reasonable map to model > agreement, but R factors do not fall down from values > greater than 40%. > > It looked like a P21 (systematic absences are clear), > so there was not much options on symmetry. I > reprocessed the dataset in P1 and ran phenix.xtriage, > and these lines called my attention: > > --------------------------------------------- > Analysing possible twin law : -h,-k,l > --------------------------------------------- > > > Results of the H-test on a-centric data: > > (Only 50.0% of the strongest twin pairs were used) > > mean |H| : 0.053 (0.50: untwinned; 0.0: 50% twinned) > mean H^2 : 0.005 (0.33: untwinned; 0.0: 50% twinned) > Estimation of twin fraction via mean |H|: 0.447 > Estimation of twin fraction via cum. dist. of H: 0.449 > > > --------------------------------------------- > Analysing possible twin law : -h,-h+k,-l > --------------------------------------------- > > > Results of the H-test on a-centric data: > > (Only 50.0% of the strongest twin pairs were used) > > mean |H| : 0.093 (0.50: untwinned; 0.0: 50% twinned) > mean H^2 : 0.015 (0.33: untwinned; 0.0: 50% twinned) > Estimation of twin fraction via mean |H|: 0.407 > Estimation of twin fraction via cum. dist. of H: 0.407 > > --------------------------------------------- > Analysing possible twin law : h,h-k,-l > --------------------------------------------- > > > Results of the H-test on a-centric data: > > (Only 50.0% of the strongest twin pairs were used) > > mean |H| : 0.085 (0.50: untwinned; 0.0: 50% twinned) > mean H^2 : 0.013 (0.33: untwinned; 0.0: 50% twinned) > Estimation of twin fraction via mean |H|: 0.415 > Estimation of twin fraction via cum. dist. of H: 0.417 > > > ========= > > I have never dealt with twinned datasets before. Is > there something I could try to do to obtain useful > data from this? > > Lucas > > P.S.: Unfortunately, growing more crystals is not an option. > > > Alertas do Yahoo! Mail em seu celular. Saiba mais em http://br.mobile.yahoo.com/mailalertas/ > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

17 years, 10 months

Re: [phenixbb] Reduce NQH

by jp d

hi, we have no chains defined that column is empty for all atoms thanks jpd ________________________________ From: Pavel Afonine <pafonine(a)lbl.gov> To: phenixbb(a)phenix-online.org Sent: Thursday, December 19, 2013 4:39 PM Subject: Re: [phenixbb] Reduce NQH Hello, do you have two-letter chain IDs in PDB file? Pavel On 12/19/13, 4:33 PM, jp d wrote: hi, >we were going through the logs recently and see something odd during Reduce N/Q/H analysis >the log file looks like this: >================================== NQH flips ================================== >r_work=0.3047 r_free=0.3518 >Analyzing N/Q/H residues for possible flip corrections... >segID AL01 renamed chain A for Reduce N/Q/H analysis >segID AL02 renamed chain B for Reduce N/Q/H analysis >... >segID AL29 renamed chain Y for Reduce N/Q/H analysis >segID AL30 renamed chain Z for Reduce N/Q/H analysis >segID AL32 renamed chain a for Reduce N/Q/H analysis >segID AL33 renamed chain a for Reduce N/Q/H analysis >segID AL34 renamed chain b for Reduce N/Q/H analysis >segID AL35 renamed chain b for Reduce N/Q/H analysis >... >segID BL28 renamed chain z for Reduce N/Q/H analysis >segID BL31 renamed chain z for Reduce N/Q/H analysis >segID BL13 renamed chain AA for Reduce N/Q/H analysis >segID BL29 renamed chain AB for Reduce N/Q/H analysis >... > > > >we noticed that the lower case chain letters start to duplicate themselves and are not unique to each segid. >when it starts the two letter chain, everything seems unique again. >forgive me if that is expected, it just seems kind of strange > > > >this was seen in mutlple log files and we are using version >Version: 1.8.4 >Release tag: 1496 >if you need our files or more details, let me know > > >thanks >jpd > > > >_______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb

11 years, 6 months

Re: [phenixbb] smaller the cell parameter of EM map

by Pavel Afonine

Hi, have a look at the documentation: https://www.phenix-online.org/documentation/reference/map_box.html Reading through it I find this phenix.map_box map.mrc density_select=true should do it. Let us know if it doesn't. Pavel On 12/29/18 07:46, dancingdream(a)163.com wrote: > Thanks for the quick replay! > But my case is that no homology model for the target protein and it > should be built directly from the em map. What should I do in this case ? > > > > > -- > Wei Ding > P.O.Box 603 > The Institute of Physics,Chinese Academy of Sciences > Beijing,China > 100190 > Tel: +86-10-82649083 > E-mail: dingwei(a)iphy.ac.cn <mailto:[email protected]> > > At 2018-12-29 15:30:51, "Pavel Afonine" <pafonine(a)lbl.gov> wrote: > > Hi Wei, > > cutting out a box with model and map around it may be a solution > for your case. A tool for this is phenix.map_box or its GUI > equivalent. > > Pavel > > P.S.: phenix.real_space_refine does this internally so > 'irrelevant' box size never affects runtime of refinement. > > > On 12/28/18 23:14, dancingdream(a)163.com wrote: >> Dear all, >> The cell parameter of the EM map is always too large, which will >> make the model building program running very slow. >> But in factor, the structure is a smal part of cell. So can I >> smaller the cell parameter when I use >> phenix.map_to_structure_factors to convert the EM map to mtz file. >> Thank a lot! >> >> Wei >> >> >> >> >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> Unsubscribe:[email protected] > > >

6 years, 6 months

[phenixbb] Excellent Opportunity for Postdoc in Ion-Channel Structural Biology

by Pramod Kumar

Dear Structural Biology Scholars, I would like to bring your attention to an excellent opportunity to unravel the structure-function details of ion-channels as a postdoc. The Grosman lab at the University of Illinois at Urbana-Champaign is actively looking to fill a recent opening of NIH-funded postdoctoral position. The laboratory has an excellent record in combining high-resolution electrophysiology, molecular simulations, and structural biology to address fundamental questions about ion-channel mechanisms. Previous experience with the purification of eukaryotic membrane proteins is a plus and structure determination using single-particle cryo-EM is highly preferred. Salary commensurate with the experience level. The University of Illinois Urbana Champaign is an excellent place for research and life with an easy commute, lower-cost housing, easy access to all needs, and a vibrant community with easily accessible cities like Chicago, Indianapolis, St. Louis. Interested individuals should contact Prof. Claudio Grosman ( grosman(a)illinois.edu) with a CV, a 1–2 page description of previous research, and names and contact information of 2–3 references. Students in their final year of Ph.D. training are also welcome to apply. Recent select publications from the Grosman lab are listed below. A complete list of publications from the Grosman lab can be found on Prof. Claudio Grosman’s NCBI bibliography page ( https://www.ncbi.nlm.nih.gov/myncbi/claudio.grosman.1/bibliography/public <https://urldefense.com/v3/__https:/www.ncbi.nlm.nih.gov/myncbi/claudio.gros…> ). *Recent Select Publications * *· Kumar P, Cymes GD, Grosman C. Structure and function at the lipid-protein interface of a pentameric ligand-gated ion channel. Proc. Natl. Acad. Sci. USA. 2021;118(23). * *doi: 10.1073/pnas.2100164118 * *· Cymes GD, Grosman C. Signal transduction through Cys-loop receptors is mediated by the nonspecific bumping of closely apposed domains. Proc. Natl. Acad. Sci. USA. 2021;118(14). doi: 10.1073/pnas.2021016118 * *doi: 10.1038/s41467-021-21680-9 * *· Kumar P, Wang Y, Zhang Z, Zhao Z, Cymes GD, Tajkhorshid E, Grosman C. Cryo-EM structures of a lipid-sensitive pentameric ligand-gated ion channel embedded in a phosphatidylcholine-only bilayer. Proc. Natl. Acad. Sci. USA. 2020;117(3):1788-1798. * *doi: 10.1073/pnas.1906823117 * -- Pramod Kumar, Ph.D.

3 years, 5 months

Re: [phenixbb] Recovering Autobuild from tty disconnect

by Thomas C. Terwilliger

Hi Francis, If you run from the GUI and choose to run "detached" I would think that should do the job....(You may have to specify "edit parameters and run/ run detached to get this option). For AutoBuild, no there is no way to restart the job. However you might just look through the log file, pick out the best model so far, and restart with that one. All the best, Tom T >> Our job submission node disconnects 'idle' after 4 hours of inactivity. As >> most grid / autobuild jobs take about that long I end being disconnected >> while the grid jobs complete. >> >> [1] Screen is not an option since access to the job submission node is via >> a load balancer and none of the job submission nodes allow access unless >> you're coming from the load balancer . i.e. there's no way to get to >> original machine where your screen has been started >> >> [2] all processes are sent SIGKILL during this automatic logout preventing >> the use of nohup.. will background=True work? >> >> [3] In the meantime, is it possible to resurrect the current autobuild? >> I've got FINISHED in all the autobuild's submitted to the grid, but >> everytime I try to combine_only=True run=my_run_number, I start from the >> beginning (with submitting the autobuild jobs to the cluster) even when >> I've moved the best of each build into MULTIPLE_MODELS. >> >> >> Thanks! >> >> F >> >> >> --------------------------------------------- >> Francis E. Reyes M.Sc. >> 215 UCB >> University of Colorado at Boulder >> >> >> >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

13 years, 10 months

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

by Aaron Brewster

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(a)phenix-online.org] > on behalf of richard.gildea(a)diamond.ac.uk [richard.gildea(a)diamond.ac.uk] > Sent: Friday, September 22, 2017 12:08 > To: cctbxbb(a)phenix-online.org > Subject: Re: [cctbxbb] rstbx test is failing without indication in > test_all_parallel > > As far as I recall rstbx/simage was a research project by Ralf that hasn't > been touched for over 5 years, and isn't used by any code outside of > rstbx/simage. Could this code be potentially "retired" somewhere outside of > cctbx? > > Dr Richard Gildea > Data Analysis Scientist > Tel: +441235 77 8078 > > Diamond Light Source Ltd. > Diamond House > Harwell Science & Innovation Campus > Didcot > Oxfordshire > OX11 0DE > ________________________________ > From: cctbxbb-bounces(a)phenix-online.org [cctbxbb-bounces(a)phenix-online.org] > on behalf of Oleg Sobolev [osobolev(a)lbl.gov] > Sent: 20 September 2017 19:33 > To: cctbx mailing list > Subject: [cctbxbb] rstbx test is failing without indication in > test_all_parallel > > Dear colleagues, > > Accidentally I found out that this command: > > rstbx.simage.solver d_min=5 lattice_symmetry=P422 intensity_symmetry=P4 > index_and_integrate=True multiprocessing=True > finishes with traceback. > > It is run as part of > phenix_regression/misc/tst_rstbx.csh > > The second problem is that test_all_parallel script fails to detect an > actual failure. > > It would be great if somebody who is in charge of rstbx and testing could > look at this. > > Best regards, > Oleg Sobolev. > > -- > This e-mail and any attachments may contain confidential, copyright and or > privileged material, and are for the use of the intended addressee only. If > you are not the intended addressee or an authorised recipient of the > addressee please notify us of receipt by returning the e-mail and do not > use, copy, retain, distribute or disclose the information in or attached to > the e-mail. > Any opinions expressed within this e-mail are those of the individual and > not necessarily of Diamond Light Source Ltd. > Diamond Light Source Ltd. cannot guarantee that this e-mail or any > attachments are free from viruses and we cannot accept liability for any > damage which you may sustain as a result of software viruses which may be > transmitted in or with the message. > Diamond Light Source Limited (company no. 4375679). Registered in England > and Wales with its registered office at Diamond House, Harwell Science and > Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom > > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/cctbxbb > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/cctbxbb >

7 years, 9 months

[phenixbb] Reminder, CCP4 crystallographic summer school at the APS, June 21 - 29, 2016

by Sanishvili, Ruslan

Dear Colleagues, This is a reminder that the application deadline for the 9th annual CCP4/APS crystallographic school is on April 21, 2016. Applications received after this date will not be considered. The school will take place from June 21 through June 29, 2016 at the Advanced Photon Source, Argonne National Laboratory, near Chicago. All aspects of macromolecular crystallography from data collection to structure refinement and validation, as well as functional assessment, will be covered. Instructions and hands-on assistance will be provided by the authors and developers of the represented software, and/or by other premier experts. >From our past experience, the majority of participants bring with them the crystallographic problems they cannot resolve independently and almost all these problems are resolved at the school. Some of the publications, acknowledging the contribution of the school, are listed here: http://www.ccp4.ac.uk/schools/APS-school/publications.php Each registered participant will be provided with a Linux computer with all covered software already installed and configured. Lodging is on-campus and all meals and refreshments will be provided at the venue. These and other details, such as the fees, the on-line application, the program, the contact information etc. can be found here: http://www.ccp4.ac.uk/schools/APS-2016/index.php We are looking forward to meeting you in Argonne this summer. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Lemont, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov ________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of Sanishvili, Ruslan [rsanishvili(a)anl.gov] Sent: Tuesday, February 23, 2016 7:48 AM To: phenixbb(a)phenix-online.org Subject: [phenixbb] CCP4 crystallographic summer school at the APS, June 21 - 29, 2016 Dear Colleagues, We are pleased to announce the 9th annual CCP4 crystallographic summer school at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All details can be found at http://www.ccp4.ac.uk/schools/APS-2016/index.php Title: CCP4 crystallographic school: From data collection to structure refinement and beyond Dates: June 21 through 29, 2016 Site: Advanced Photon Source, Argonne National Laboratory, Argonne (Near Chicago), Illinois, USA The school comprises Data collection workshop the first three days: beamline training and data collection on GM/CA@APS beamlines 23ID-B and 23ID-D. For data collection, only the participants' crystals will be used. Crystallographic computation workshop: The rest of the time after data collection will feature many modern crystallographic software packages taught by authors and other experts. The daily schedule will be organized in three sections – lectures, tutorials, and hands-on, interactive trouble-shooting. There will be model data sets available for tutorials but data, provided by participants, will have higher priority for the hands-on sessions. Applicants: Graduate students, postdoctoral researchers and young scientists at the assistant professor level, along with commercial/industrial researchers are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection and/or computation workshops. Application: Application deadline is April 21. The application form, the program, contact info and other details can be found at http://www.ccp4.ac.uk/schools/APS-2016/index.php Registration fees: The registration fee for the selected participants is $400 for the academic and $950 for the industrial researchers. The link for the on-line payments and instructions will be provided once the selection process is completed. The students will be responsible for their transportation and lodging. The workshop organizers can assist in making the reservations at economical lodging at the Argonne Guest House. The workshop will cover all other expenses. We hope to see you at the school, Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Lemont, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov

9 years, 3 months

Re: [phenixbb] XDS data

by Tim Gruene

Dear Nat, I won't need to send the header, the first line looks as you expect. FRIEDEL'S_LAW=TRUE in the XDS_ASCII.HKL does not mean that the Friedel pairs are merged (it would, though in XSCALE output in combination with MERGE=TRUE). The former keyword affects the scaling, and both Wolfgang Kabsch and George Sheldrick are of the opinion the scaling gives better results by using twice the number of data without hampering with the data quality by ignoring the anomalous differences. XDS does not have the keyword 'merge', only xscale does, but there is not reason to scale the data twice, as XDS output data are already scaled. I will see how far I get with xscale output, but scientifically it would be beneficial for phenix to allow said XDS format (I agree that shelx hkl-format is not a joy for GUIs). We are using the latest release, version 1.8.4. Cheers, Tim On 01/14/2014 04:53 PM, Nathaniel Echols wrote: > On Tue, Jan 14, 2014 at 4:42 AM, Tim Gruene <tg(a)shelx.uni-ac.gwdg.de> wrote: > >> I would like to run Phaser-EP through the phenix GUI. When I first >> uploaded the XDS_ASCII.HKL file, there was an error message about "No >> valid observed reflections found in this file". > > > Can you send me the first three lines of the file? My guess is that it > looks like this: > > !FORMAT=XDS_ASCII MERGE=FALSE FRIEDEL'S_LAW=TRUE > > which would be interpreted by our XDS reader as being non-anomalous, even > though since it's unmerged there is probably nothing stopping us from using > the anomalous data anyway. (I need to double-check this, because I don't > understand why it would claim "FRIEDEL'S_LAW=TRUE" if I+ and I- are > actually kept separate.) If you instead produce a file that starts like > this: > > !FORMAT=XDS_ASCII MERGE=TRUE FRIEDEL'S_LAW=FALSE > > then it will be accepted by the Phaser-EP GUI. > > Subsequently I >> uploaded an unmerged hklf4 file. The GUI tells me I need to let phenix >> know about it being hklf4 by appending '=hklf4'. However, when I do >> so, there is an error message the file did not exist and the Data file >> line goes red. Where should I correctly append '=hklf4'? >> > > This may simply be a bug. Which version are you using? I had attempted to > make the GUI handle SHELX files more sensibly (to the extent that's even > possible), but I can't remember how successful I was, and it may have been > after version 1.8.4 was released. In general, SHELX format is the least > compatible of the supported inputs; it's just missing too much information. > > -Nat > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A

11 years, 5 months

Search results for query "look through"