Search results for "look through"

Re: [phenixbb] An easier explanation of the regions in omit map

by Nathaniel Echols

On Mon, May 17, 2010 at 10:53 AM, xaravich ivan <xaravich.ivan(a)gmail.com>wrote: > So I have quite a few regions build by the SA_omit map of phenix. But How > do I go about looking at these maps. What am I looking for here. Should I > look at the regions where the occupancy was set zero in all these outputs > and find if I could build some thing from one of the maps? I guess I am > asking, How do I use this information to move forward in refinement? There > are 24 regions map and .pdb output in the /OMIT directory. > Ignore these - only the final map is useful. If you are generating a composite omit map, you want to make sure that what you've built still matches the density reasonably well. Obvious things to look at: - flexible or missing loops - ligands - anywhere the mFo-DFc map shows large blobs at +/- 3sigma - any outliers flagged by validation (both geometry and real-space correlation) I don't usually find it productive to go through the structure residue-by-residue, but this may depend on the data and model quality. What is your resolution and current R-free? (If you are just omitting part of the structure, then you only need to look at the map around those atoms - the rest won't be much different.) -Nat

15 years, 8 months

Re: [phenixbb] phenix.cif_as_mtz

by Pavel Afonine

Hi Bryan, I systematically run phenix.cif_as_mtz through the whole PDB and if I correctly remember it is able to convert ~95% of files, so it is pretty well exercised. Most of those not converted contain multiple datasets. I can't really tell what is wrong in your case without looking at your file.cif. Can you please send it to me so I can tell what's wrong? Thanks, Pavel. On 11/12/09 8:55 AM, Bryan W. Lepore wrote: > [ v. 1.5 release tag 2 intex-linux-2.6 redhat-e4.8 ] > > `phenix.cif_as_mtz file.cif --symmetry=FILE.pdb --show-log > --show-details-if-error` > > .. reports "No data extracted from input cif file.", nothing else. > command works w/ other .cif/.pdb's, CRYST1 lines, etc. look comparable > between them,... not sure where to look next. thanks for any > suggestsions. > > -bryan > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

16 years, 2 months

[phenixbb] TRIED resolve ...NEED A BIGGER VERSION... message

by Ben Eisenbraun

Howdy Phenixians, One of my users is running phenix.autobuild, and while it seems to run okay, the output contains this warning: TRIED resolve ...NEED A BIGGER VERSION... Looking through phenix/phenix/autosol/run_resolve.py, it seems like this is an informational message, but I'm not sure, so I figured I'd ask. Is this actually an error? This is phenix-1.3-final on OS X 10.5. Thanks. -ben -- Ben Eisenbraun Structural Biology Grid Harvard Medical School http://sbgrid.org http://hms.harvard.edu

17 years, 1 month

Re: [phenixbb] R-free rules

by Ralf W. Grosse-Kunstleve

> [ phenix.refine v1.5 rel. tag 2 intel linux 2.6 ] > > if i provide the test set .mtz (flag = "1") in refinement separately from > the data .mtz, it looks like reflection_file_converter.py does not flag > the work set as "0", if the work set lacks such a flag -- is that right? I think that's true. Nat wrote a more comprehensive tool for generating R-free flags, which are included in recent nightly builds. I'm pretty sure Nat generates the flags for all possible reflections. > i.e. when providing the test set, it looks like all observed data must be > in the test set, however the work set has flag "0". Hm... not sure I understand, but try Nat's new tools first. It is easiest through the GUI, but there's also a command-line version, phenix.reflection_file_editor. Ralf

16 years, 2 months

Re: [phenixbb] [ccp4bb] phenix installtion problem

by Alexandre OURJOUMTSEV

Dear Weifei, I am neither in the Phenix nor in the CCP4 teams so I let me remark that it does not look reasonable, just a few minutes after Tom Terwilliger's mail : "I'll answer you on the Phenix BB as you've asked specific questions about Phenix tools." sending your mail (see below) asking explicitly phenix questions again through the CCP4bb. I do not think that you "disturb", you should not sorry for this, the BB are for this, but we need to follow the rules. I ask everybody to respect both ccp4 and phenix teams, who assures a lot of service and help for our community, and send your requests properly (for your own benefit), through the BB concerned. My another request (luckily not applicable to the Weifei mail) is that people always sign properly their mails and give their name when asking their questions : ccp4, phenix teams and other experts answer you openly and this looks quite weird seeing anonymous requests. Again, this is for your own benefit, for your better integration into the research community. With best regards, Sacha Urzhumtsev ________________________________ De : CCP4 bulletin board <CCP4BB(a)JISCMAIL.AC.UK> de la part de ChenWeiFei <weifei_c(a)OUTLOOK.COM> Envoyé : vendredi 26 juin 2015 15:05 À : CCP4BB(a)JISCMAIL.AC.UK Objet : [ccp4bb] phenix installtion problem Dear all, Sorry to disturb you. I have install Phenix to my computer Centos 7.0. When I want to use it I need to cd /usr/local/phenix-1.9-1692/ and . /usr/local/phenix-1.9-1692/phenix_env.sh then type phenix in the command line every time. I wish to use phenix in every terminate window and just type phenix. Some told me use export PATH to do it but I don't know how to do it. I am new to linux(centos) Thank you so much! Best, Weifei

10 years, 7 months

[phenixbb] COOT not "connected" to PHENIX

by Yuri

Hello everyone, I am running 1.7.2-869 and coot 0.6.2 By telling phenix where hte path is, I can get it to launch from any phenix job tab. However in one of my machines, even though COOT launches through phenix it is not connected to it which does not allow me to look at clashes when building in coot- a very useful feature may I add!!! In one of my RHEL5 machines it is working nicely, and I dont see any obvious differences between the working and the non-working one. Any ideas? Thank you much -- Yuri Pompeu

14 years, 3 months

Re: [cctbxbb] mmtbx/examples/simulate_experimental_data.py

by Elliot Nelson

Hi Pavel/ CCTBXBB, I have used phenix.fmodel to generate structure factors (Fcalc) from given atomic model in merged.pdb file. As previously suggested I am using the type=real flag to populate the Fobs with these Fcalc values: phenix.fmodel data_column_label="F,SIGF" merged.pdb free.mtz type=real In the merged.pdb file I set the isotropic B-factor (through u_iso) to a known value (i.e. b=40), and occupancy of the involved ligand/ground state. i.e Occupancy of ligand/ bound state atoms (0.05) and ground state atoms (0.95), all with B Factor =40. Does phenix.fmodel generate its mtz regarding the B factor of individual atoms? To give context to this question: I then use these Fcalc values to test a brute force search of occupancy and b_factor values. I am searching through Fcalc(1)-Fcalc(2) maps, where Fcalc(1) is the Fcalc generated by phenix.fmodel. Fcalc(2) is generated from the same pdb file, but with occupancy and u_iso of atoms in the ligand/ground state varied (occ 0.05 to 0.95, u_iso 0.2 to 1.2). After this search, I look at the mean over points near bound/ground state of |Fcalc(1)-Fcalc(2)|. My test should be able to uniquely identify the occupancy and B factor values supplied in the merged.pdb file. I can recapitulate the expected occupancy, however I cannot recapitulate this supplied B factor. Thanks Elliot ________________________________ From: Pavel Afonine <pafonine(a)lbl.gov> Sent: 06 April 2018 01:07 To: cctbx mailing list; Elliot Nelson Cc: Pearce, N.M. (Nick); Frank Von Delft Subject: Re: [cctbxbb] mmtbx/examples/simulate_experimental_data.py Hi Elliot, I'm trying to generate some simulated mtz files. My main aim is to test a script which looks to determine ligand occupancy (https://github.com/nelse003/exhaustive_search/blob/master/exhaustive_search…) by looking at |Fo-Fc| over the ligand/ ground-state the ligand replaces. it isn't clear what you are trying to do.. What you call "simulated mtz files". MTZ is just a file format.. What you expect in these MTZ files? To test this I would like to generate mtz files from pdb models with a ligand occupancy that has varied between 0-1, which the above script would hopefully recover the occupancy. OK. phenix.fmodel model.pdb high_res=2.3 will calculate Fcalc from given atomic model in model.pdb file. You can pretend it to be Fobs: phenix.fmodel model.pdb high_res=2.3 type=real There is a more sophisticated tool that will actually go to some length trying to mimic actual Fobs data phenix.fake_f_obs It's not documented anywhere.. So have a look at the code to see what it actually does. If you describe what exactly you want to do and how you want to do it, then we may be able to come up with a more tailored to your goal solution. All the best, Pavel

7 years, 9 months

[phenixbb] Symposium on Understanding Biology through Structure, May 13-17, 2017, Santa Fe

by Wladek Minor

Dear Colleagues, As a member of the organizing committee of "Understanding Biology through Structure", I'd like to encourage you to come to Santa Fe May 13-17 to attend this exciting Symposium. In addition to an exceptional set of talks including X-ray crystallography, cryo-EM, biochemical and biophysical methods, the Symposium will emphasize interactions between junior and senior researchers. We hope that this will present a special opportunity for junior researchers to present posters and meet senior scientists, for senior researchers to meet the next generation of structural biologists, and for all to discuss science in an informal setting. The meeting website is at https://conferences.newmexicoconsortium.org/conferences/ubts_17 and the program can be seen at https://conferences.newmexicoconsortium.org/conferences/ubts_17/program Looking forward to seeing you there, Wladek Minor -- Dr. Wladek Minor Harrison Distinguished Professor Department of Molecular Physiology and Biological Physics Phone: 434-243-6865 Fax: 434-243-2981 http://krzys.med.virginia.edu/CrystUVa/wladek.htm US-mail address: Department of Molecular Physiology and Biological Physics University of Virginia PO Box 800736, Charlottesville, VA 22908-0736 Fed-Ex address: Department of Molecular Physiology and Biological Physics 1340 Jefferson Park Avenue University of Virginia Charlottesville, VA 22908 ----

8 years, 9 months

Re: [phenixbb] HKL_base

by Ralf W. Grosse-Kunstleve

Hi Ed, > Curious. Both phenix.mtz.dump and ccp4 mtzdmp indicate that HKL_base is > present, yet when you actually look at the headers it's missing. The > mtzlib description says that HKL_base will be inserted automatically if > missing, perhaps this is what happens when mtz file is dumped? Honestly, I never really understood how the HKL_base mechnism is supposed to work. Practically: to my knowledge, you are the first ever to report trouble reading phenix.refine mtz files. How exactly are you reading them? Maybe a small adjustment could make your reader work? We are reading everything through the ccp4 cmtz library, just through C++ wrappers that hide the technicalities of the C interfaces. Therefore I think any other program using the cmtz library should also be able to read our files. The mtz code used by phenix.refine is in this directory: http://cci.lbl.gov/cctbx_sources/iotbx/mtz/ The main files are object.h, object.cpp, and __init__.py which contains a .set_hkl_base() method. I guess I could try to assign the H,K,L columns to crystal 1 as Nat suggested, but nobody knows what problems such a change would trigger, and it will probably take a decade anyway before the current implementation is flushed out of the system. I think modifying your reader to work with our files is the best solution and should be very easy. Ralf

15 years, 5 months

[cctbxbb] Inserting F000 into reflection (mtg) file

by Nicholas Pearce

Hi Everyone, I’ve been looking through the cctbx/phenix scripts and although there’s a script for estimating F000 (phenix.f000), I can’t find any way of inserting it into an mtz file to make it accessible for easy map generation. Is this implemented anywhere/what do people use as the best way of doing this? If the insertion of F000 into an mtz file has been purposefully avoided, I presume it's done because we don't want the possibility of someone refining a model where F000 is used in refinement. Unless there’s another reason? Thanks, Nick

9 years, 5 months

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