Search results for "look through"

[phenixbb] changing the project directory

by Charisse Crenshaw

Hello, I have recently started a project whose folder was located on my desktop. I would like to move that folder off of my desktop as I've heard that having a messy desktop slows down one's computer. I moved the project directory somewhere else, and this resulted in Phenix not being able to find the project (understandably). So I moved it back to its original location and Phenix could then open the project. So, in an X11 shell, I copied the project folder to the new desired location, then changed the output directory in the Phenix main window to that new path. But when I clicked on the project again, the output directory that is indicated changes back to the original path. Now I am looking through the preferences etc for a way to change the path of the project directory within Phenix and I cannot. Can anyone tell me if this is possible and if so, how do I do it? Thanks, Charisse The Salk Institute for Biological Studies

14 years, 10 months

Re: [phenixbb] Question about structure quality

by Nathaniel Echols

On Tue, Apr 5, 2011 at 1:57 PM, Pavel Afonine <pafonine(a)lbl.gov> wrote: > - Often using Ramachandran restraints fixes the problem right away, so I > would probably do it first, and then walk through the list of outliers that > you had before refinement run with Ramachandran restraints, and see *how* > these outliers were fixed. Nat's suggestion should work too but might > require more up-front work. It will "fix" the problem only to the extent that the Ramachandran statistics/plot look better - this does not automatically mean that the structure is more accurate. When you are refining against one of the primary validation criteria, more up-front work is essential. (The restraints will also not automatically fix every problem, so if you blindly turn them on without any rebuilding, the result will likely be worse than if you correct as many residues as possible yourself.) -Nat

14 years, 10 months

Re: [phenixbb] COOT not "connected" to PHENIX

by Nathaniel Echols

On Tue, Oct 25, 2011 at 7:14 AM, Yuri <yuri.pompeu(a)ufl.edu> wrote: > 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. What is the output of "coot --version"? Also, when you click one of the buttons in PHENIX to launch Coot for the first time, it should print out several pages of log on the terminal (as usual). Could you please send me this text? -Nat

14 years, 3 months

Re: [cctbxbb] Not wishing to raise this again but...

by Nicholas Sauter

Then how would you return to the current state of affairs? git checkout master? Nicholas K. Sauter, Ph. D. Computer Staff Scientist, Molecular Biophysics and Integrated Bioimaging Division Lawrence Berkeley National Laboratory 1 Cyclotron Rd., Bldg. 33R0345 Berkeley, CA 94720 (510) 486-5713 On Mon, Jun 13, 2016 at 3:55 PM, Luc Bourhis <luc_j_bourhis(a)mac.com> wrote: > > That's right. In practice I bisect the date instead; that way I can > issue the same command in all my svn source directories from sf.net and > lbl.gov. For example: > > > > svn update -r "{2014-03-08 18:00}” > > You can do that with git as well but it looks more geeky: > > git checkout `git rev-list -n 1 --before="2014-03-08 18:00” master` > > although you could easily put that in a tiny script called checkout-date > and then issue “git checkout-date”. > > In any case, git bisect is easy to run in the simple case where you know > HEAD is broken but 3c303a24 is good: > > % git bisect start HEAD 3c303a24 — > > This will checkout some version half-way through. You test and you find > it’s broken: > > % git bisect bad > > If on the contrary, you find it works fine: > > % git bisect good > > Either of those commands will again checkout some version half-way > through. Then you continue until git tells you the bisection is done. > > > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/cctbxbb >

9 years, 7 months

Re: [cctbxbb] dependency on phenix

by Roger Martin

Reminder: While looking at dev build 565 there is this dependency back on phenix; line number moved to 63 and the second file location stayed at 134 On 12/10/2014 10:33 AM, Pavel Afonine wrote: > Hi Roger, > > thanks for pointing this out. This must be an overlook. I will see > what can be done to eliminate this. > > Pavel > > On 12/10/14 5:17 AM, Roger Martin wrote: >> Hi, >> >> looking through >> http://sourceforge.net/p/cctbx/code/HEAD/tree/trunk/mmtbx/refinement/minimi… >> shows at line 61 >> from phenix.refinement import weight_xray_chem >> and >> http://sourceforge.net/p/cctbx/code/HEAD/tree/trunk/mmtbx/refinement/occupa… >> line 134 >> >> Is weight_xray_chem.py code that could move to cctbx? >> (cctbx_project/mmtbx/refinement/weight_xray_chem.py) >> >> Are there other cross dependencies? >> >> >> >> >> _______________________________________________ >> 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

10 years

[phenixbb] Call for abstracts: IUCR session on SARS-CoV-2 structural biology

by Andrea Thorn

Dear all, Gianluca Santoni and I are co-chairing a session at IUCr meeting 2021 entitled "Structural biology of coronaviruses" on the 16th of August. The subject of the session are structural and functional insights about the life cycle and virus-host interaction of SARS-CoV-2 and other coronaviruses with a particular view to integrative uses of crystallography in connection with other methods. Abstract deadline has been extended to the 15th of may. We will select 4 abstracts for a 20 minutes talk. You can submit your abstracts through the conference website: https://iucr25.org/scientific/ Please feel free to forward this to scientists who may want to contribute an abstract, including junior researchers! We are looking forward to the meeting and the abstracts, best wishes, Gian and Andrea -- Dr. Andrea Thorn | group leader andrea.thorn(a)uni-hamburg.de HARBOR (Institute for Nanostructure and Solid State Physics), Universität Hamburg Luruper Chaussee 149 / Bldg. 610 | 22761 Hamburg | Germany Tel. +49 (0)40 42838 3651 www.thorn-lab.de | www.insidecorona.de

4 years, 9 months

[phenixbb] phenix.composite_omit_map

by Dyda

Dear Phenix list, I have generated an mtz file with phenix.composite_omit_map. It has labels assigned as 2mFo-DFC for F and PH2mFo-DFC for P. Now, I would like to generate a map file. I was trying to convince phenix.maps to use this mtz file to do that, however it didn't seem to like the labels. I tried both the GUI interface of phenix.maps and also tried to force feed it through the command line with a maps.param file. Neither of these worked, so I'm obviously missing something. Btw., Coot can open the mtz file and display the map, and it does look reasonable. This is phenix-1.9-1692 running under RHEL6. Thank you for your help. Fred [32m******************************************************************************* Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular Biology Fax: 301-496-0201 DHHS/NIH/NIDDK e-mail:[email protected] Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476710(a)mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred *******************************************************************************[m

10 years, 7 months

[phenixbb] GUI parameter files

by Leonid Sazanov

Hi, I have a following problem in dev-874 version: If I restore a previous job in refine GUI, to run it with modified settings, and include a new parameter file .eff with definitinon of secondary structure restrains, these new restrains are combined with previously used restrains. How do i get rid of previous restrains? Older file is not visible in inputs, but its settings are still used. And in general, how can one be sure which parameters are used at the start of each refine run? If older settings loaded from .eff or .param file are not visible, the only way is to look through new .eff file, which takes a lot of time. Has this been solved in latest builds perhaps? Thank you, Leo -- Dr. Leonid A. Sazanov Research group leader Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-mbu.cam.ac.uk Tel: +44-1223-252910 Fax: +44-1223-252915

13 years, 10 months

[phenixbb] autobuild 'hires_file'

by Bryan W. Lepore

i have phenix 2007_08_18_1856, (and i think latest cci apps). i have a jumble of questions, i'll try step by step: [1 A] in phenix.autobuild, e.g. a SAD dataset, does the flag 'hires_file=w1.sca' (help says "Merge in hires data"), mean that phases will be extended to a high resolution limit as found in w1.sca? (vide infra) [1 B] can the labels be the same as the 'other' data (the documentation suggests this)? i have tried a few things like : phenix.autobuild data=resolve.mtz hires_file=high_resolution.mtz input_hires_labels='FPnat SIGFPnat' seq_file=seq.txt ... and i see Cell: [99.810997009277344, 99.810997009277344, 140.37300109863281, 90.0, 90.0, 90.0] New resolution: 2.20520367253 High-res file input labels: ['FPnat', 'SIGFPnat'] ... which is good, but the job promptly fails with this cryptic (to me) error message: ************************************************************ Failed to carry out AutoBuild_datafile_info_inputs: 'all_input_hires_labels' ************************************************************ ... (google:all_input_hires_labels and looking through docs quick didn't find it) -bryan

18 years, 3 months

Re: [cctbxbb] First svn commit

by Pavel Afonine

When I look at a function and do not understand what it does given it's name and list of arguments I look no more and write my own. Always. This is because my believe that if the author of that function did not bother to make the interface clear it says something about quality of the job as a whole (to me at least), and I don't have time to take chances or waste it reading more. Pavel On 4/17/13 11:02 PM, Nathaniel Echols wrote: > On Wed, Apr 17, 2013 at 10:19 PM, Richard Gildea <rgildea(a)gmail.com> wrote: >> Also, I would prefer the function arguments to be spelled out explicitly >> without using *args and **kwds, so that I can figure out what arguments it >> takes without having to read through the function source code to figure out >> that internally you are calling self.as_miller_arrays(), and then have to go >> and look up the function arguments for that. > My preference is actually the opposite (I do the same thing quite a > bit in my code), because otherwise there is no guarantee that keyword > arguments added to add_miller_arrays will also be usable with > add_miller_arrays_map. Using *args, **kwds makes the APIs explicitly > the same. (That said, I'm increasing favoring using **kwds alone in > these circumstances.) > >> My IDE (WingIDE) shows me the >> function signature in its source assistant and also provides code completion >> for function arguments and keywords. However these won't be of much use when >> functions only list *args and **kwds. > <insert generic snarky vi advocacy here> > > -Nat > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/cctbxbb

12 years, 9 months

Search results for query "look through"