Search results for "look through"

Re: [phenixbb] Selecting ellipsoid of data

by Morten Grøftehauge

Kay suggestion is better than mine which would have been http://www.doe-mbi.ucla.edu/~sawaya/anisoscale/ On 16 July 2010 03:16, Frank von Delft <frank.vondelft(a)sgc.ox.ac.uk> wrote: > Ah.... I was wondering about that: thanks for the pointer!! > > > > On 15/07/2010 17:38, Kay Diederichs wrote: > > Hi Frank, > > "such a tool" is at > http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Aniso_cutoff > > where it's meant to be applied to INTEGRATE.HKL which comes out of XDS. > Doing it this way has the benefit that the statistics printed out by XDS' > CORRECT (or SCALA/TRUNCATE; there are people who prefer that route) match > the data you refine agains. > > HTH, > > Kay > > Message: 1 > Date: Thu, 15 Jul 2010 06:32:40 +0100 > From: Frank von Delft<frank.vondelft(a)sgc.ox.ac.uk><frank.vondelft(a)sgc.ox.ac.uk> > To: PHENIX user mailing list<phenixbb(a)phenix-online.org><phenixbb(a)phenix-online.org> > Subject: [phenixbb] Selecting ellipsoid of data > Message-ID:<4C3E9D78.5030203(a)sgc.ox.ac.uk> <4C3E9D78.5030203(a)sgc.ox.ac.uk> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi, is there a tool in phenix that allows me to select an ellipsoid of > data -- specified e.g. by the highest resolutions in three reciprocal > lattice directions. (Yes, I'm playing with anisotropy, "playing" being > the operative word.) > > phx > > > ------------------------------ > > Message: 2 > Date: Wed, 14 Jul 2010 22:47:30 -0700 > From: "Ralf W. Grosse-Kunstleve"<rwgk(a)cci.lbl.gov> <rwgk(a)cci.lbl.gov> > To: phenixbb(a)phenix-online.org > Subject: Re: [phenixbb] Selecting ellipsoid of data > Message-ID:<201007150547.o6F5lUoL018490(a)cci.lbl.gov><201007150547.o6F5lUoL018490(a)cci.lbl.gov> > Content-Type: text/plain; charset=us-ascii > > Hi Frank, > > Hi, is there a tool in phenix that allows me to select an ellipsoid of > data -- specified e.g. by the highest resolutions in three reciprocal > lattice directions. (Yes, I'm playing with anisotropy, "playing" being > the operative word.) > > > I'm not aware of such a tool. > > Ralf > > > ------------------------------ > > Message: 3 > Date: Thu, 15 Jul 2010 07:15:58 +0100 > From: Frank von Delft<frank.vondelft(a)sgc.ox.ac.uk><frank.vondelft(a)sgc.ox.ac.uk> > To: "Ralf W. Grosse-Kunstleve"<rwgk(a)cci.lbl.gov> <rwgk(a)cci.lbl.gov>, > PHENIX user mailing > list<phenixbb(a)phenix-online.org> <phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] Selecting ellipsoid of data > Message-ID:<4C3EA79E.2030503(a)sgc.ox.ac.uk> <4C3EA79E.2030503(a)sgc.ox.ac.uk> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Ralf > > Yeah, I figured. So if I want to use cctbx, where do I start? Just a > pointer to a) package and b) function where I'll see the syntax. > > So equation for ellipsoid is x^2/a^2 + y^2/b^2 + z^2/c^2 = 1; so I > imagine I take each reflection, convert each of h,k,l to 1/reso, and > with a = 1/res(a*), I just check whether the above is< 1. > > The main thing I still need is to convert h,k,l into orthogonal > coordinates.... or do I? I suppose I don't, as what I care for is not > whether it's "really" an ellipsoid, only whether it cuts through miller > index space anisotropically. > > Hmmmm... I may be able to do it in sftools; but if you can in<1minute > give me a link to where to look to get started in cctbx, that would be > awesome. > > (Thanks for listening :) > > > > > Hi Frank, > > > Hi, is there a tool in phenix that allows me to select an ellipsoid of > data -- specified e.g. by the highest resolutions in three reciprocal > lattice directions. (Yes, I'm playing with anisotropy, "playing" being > the operative word.) > > I'm not aware of such a tool. > > Ralf > > > > _______________________________________________ > phenixbb mailing listphenixbb(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 > >

15 years, 6 months

Re: [cctbxbb] [git/cctbx] master: rename test files, remove them from run_tests (23a4a6fe4)

by Nicholas Devenish

Hi all, Plethora of additional points in support of pytest: - Classification: bootstrap dials, then run the tests. All will say "OK" but in reality only about 1/3 of them ran for various skip reasons. This is *horribly* misleading and has led to broken builds in the past. I proposed a patch a while ago to add a skip classification but this was rejected because some tests (two, I think?) in phenix classified as 'SKIP' instead of 'OK'. There is a system to classify as 'WARN', but *only* if phenix_regression is installed, it misclassifies several items in dials/cctbx (apparently OK showing as WARN is acceptable where OK as SKIP wasn't) and in any case relies on a horrible whitelist of "text that looks like warnings but shouldn't classify the test as a warning". In pytest, things like skip/warn/expected failure are easy (e.g. you can mark tests as "this is currently expected to fail" rather than leaving your CI^H^Hdaily build failing permanently) - Technical debt/NIH: It's one framework for you to learn, sure. But it's N 'frameworks' to learn for the next N developers - and since pytest is very common, there is a good chance that they'll either know it already, or the knowledge will be usefully applicable to other projects in the future. Every single new developer has to go through the WTF-laden process of learning the 'historical' idiosyncrasies. - Categorisation: A dumb 'list of tests' is okay until you have e.g. very long regression tests that don't need to be run as frequently as unit tests - Documentation: How does something work/how do you do something unfamiliar? I'll let you compare the documentation for libtbx approx_equal https://github.com/cctbx/cctbx_project/blob/master/libtbx/test_utils/__init… and pytest's approx https://docs.pytest.org/en/latest/builtin.html#pytest.approx - Maintenance/bit rot: Somebody else writes this documentation, somebody else finds and fixes the bugs, and somebody else is responsible for making things better. Something untouched for a decade that people are afraid to or prevented from improving is not a good thing. Additionally, I'd want to argue great improvements and benefits in things like locality, parametrization, granularity (separation of tests), formality, discoverability, as well as lots of other things, but I think you get my point. Basically, every possible improvement a formal testing suite could have over what is effectively a dumb list of files to run. Python's unittest would have most of these benefits, but with the disadvantage of a little more boilerplate. Pytest has less boilerplate and syntax, and for almost equivalent total functionality you only have to remember a) "call the files test_something.py and the functions test_something" b) use assert (you can even use libtbx.approx_equal if you want!). Nick On Sat, Mar 3, 2018 at 11:03 AM, <markus.gerstel(a)diamond.ac.uk> wrote: > Hi Pavel, > > pytest was suggested* by a couple of people in 2015 when I asked about > unittest. Your recommendation at that time was to go ahead, so thats what I > did - with the result that in April 2016 the pytest compatibility layer was > introduced to cctbx and pytest included in the base build, so we can use > pytests alongside libtbx tests. In our packages we have been using pytests > for well over 2 years now, and just one month ago converted xia2 to pytest > completely. > > As to "why pytest" I would like to point you to our wiki page "Why > pytest?" at https://github.com/dials/dials/wiki/Why-pytest%3F which does > make the case in more detail and includes instructions to enable pytest for > cctbx modules. However I'm more than happy to demonstrate part of it here > using your example. > > First of all, the example you gave is not quite correct. You are missing > the import for approx_equal and missed the crucial line in run_tests.py > that ensures the test is actually run. This is one of the drawbacks of > libtbx testing: there is no automatic test discovery. And this tends to > happen quite a lot, cf. https://github.com/dials/dials/issues/506 > > In pytest your example would look like this: > > import pytest > def test_that_2_times_2_is_4(): > x = 2 > result = x*x > assert result == pytest.approx(4) > > which I would argue has the exact same documentation/example value. > > > Let's change the expectation value from 4 to 5, forget everything we know > about the code, run it and compare the output: > > > $ python tst_multiply.py > approx_equal eps: 1e-06 > approx_equal multiplier: 10000000000.0 > 4.0 approx_equal ERROR > 5.0 approx_equal ERROR > > Traceback (most recent call last): > File "tst_multiply.py", line 10, in <module> > exercise() > File "tst_multiply.py", line 7, in exercise > assert approx_equal(result, 5., 1.e-6) > AssertionError > > *Something* went wrong, it has to do with 1e-06, a very large number (I > still don't understand what that means), two errors for 4.0 and 5.0, and a > function called exercise(), which tells me exactly nothing. I have to look > into the code to understand what went wrong and why. From the outset I > don't know what the code is supposed to do. > > > $ pytest > =================================== test session starts > =================================== > platform linux2 -- Python 2.7.13, pytest-3.1.3, py-1.4.34, pluggy-0.4.0 > rootdir: /dls/tmp/wra62962/directories/lh0UFeF6, inifile: > plugins: xdist-1.20.1, timeout-1.2.0, forked-0.2, cov-2.5.1 > collected 2 items > > test_multiplication.py .F > > ======================================== FAILURES > ========================================= > ___________________________ test_that_two_times_two_equals_five > ___________________________ > > def test_that_two_times_two_equals_five(): > x = 2 > result = x*x > > assert result == pytest.approx(5) > E AssertionError: assert 4 == 5 +- 5.0e-06 > E + where 5 +- 5.0e-06 = <class '_pytest.python.approx'>(5) > E + where <class '_pytest.python.approx'> = pytest.approx > > test_multiplication.py:11: AssertionError > =========================== 1 failed, 1 passed in 0.04 seconds > ============================ > > > Oh look, a test to ensure two times two equals five failed. Apparently it > compared 4 to 5 +- 5e-06. > You also see that the other test in the file that I left in (which > compares 2*2 to 4) worked. You didn't know that from the libtbx-style test > output. > > Now I can fix the test, and pytest allows me to just rerun the failed > tests, not everything. > If you want to know how, have a look at https://github.com/dials/ > dials/wiki/pytest which contains a lot more information about running > pytest and converting tests. > > If you don't want to use it that is fine, too. Thanks to the compatibility > layer you can still use libtbx.run_tests_parallel, and you will still get > the more useful assertion messages. I would encourage you to try it though. > You might find it useful. > > -Markus > > > * And rightly so; pytest requires much less boilerplate, produces cleaner > code, and is overall just better - Thank you, Luc. Thank you, Jamasi. > PS: On fable specifically: thanks to the conversion I already found and > fixed one broken test which didn't fail, and another test with race > conditions. > > ________________________________________ > From: cctbxbb-bounces(a)phenix-online.org [cctbxbb-bounces(a)phenix-online.org] > on behalf of Pavel Afonine [pafonine(a)lbl.gov] > Sent: Saturday, March 03, 2018 07:13 > To: cctbx mailing list; Winter, Graeme (DLSLtd,RAL,LSCI) > Subject: Re: [cctbxbb] [git/cctbx] master: rename test files, remove them > from run_tests (23a4a6fe4) > > I'd say at least because: > > - the first 10+ years of CCTBX did not use pytest. AFAIK, the first > attempt was by our postdoc Youval Dar back in 2015 (correct me if I'm > wrong). I feel adding different testing styles are only to make the > code-base inconsistent (very much like mixing flex and np arrays isn't > cool, in my opinion!). > > - originally tests were considered as simple usage examples for > functionalities they are testing; this is because writing and (most > importantly!) maintaining the proper documentation was not provisioned. > A simple test like > > def exercise(): > """ Make sure 2*2 is 4. """ > x=2. > result=x*x > assert approx_equal(result, 4., 1.e-6) > > if(__name__ == "__main__"): > exercise() > print "OK" > > is much easier to grasp rather than the same cluttered with the stuff > (that, to add to the trouble, one needs to learn in the first place!). > > All the best, > Pavel > > On 3/3/18 14:36, Graeme.Winter(a)diamond.ac.uk wrote: > > What’s bad about pytest? > > > > > > > >> On 3 Mar 2018, at 02:26, Pavel Afonine <pafonine(a)lbl.gov> wrote: > >> > >> Just to make sure: you are converting to use pytest this particular > codes (fable), correct? > >> Pavel > >> P.S.: I'm allergic to pytest. > >> > >> > >> On 3/3/18 07:46, CCTBX commit wrote: > >>> This in preparation for pytestification. > >> _______________________________________________ > >> 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 > > -- > 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 >

7 years, 11 months

Re: [cctbxbb] Niggli-reduced cell C++ implementation

by Ralf Grosse-Kunstleve

Hi Martin, Based on iotbx.lattice_symmetry --unit_cell="4.630811 4.630811 4.630811 90 90 90" and iotbx.lattice_symmetry --unit_cell="3.27448 5.67156 5.67156 99.5941 106.779 90" the first unit cell is (obviously) cubic, the second is only monoclinic. Even with iotbx.lattice_symmetry --unit_cell="3.27448 5.67156 5.67156 99.5941 106.779 90" --delta=20 it only comes back as orthorhombic. Is this what you expect? Ralf On Tue, Apr 24, 2012 at 10:57 AM, Martin Uhrin <martin.uhrin.10(a)ucl.ac.uk>wrote: > Dear cctbxers, > > I've finally found the time to play around with a C++ version of the KG > algorithm and I've come across a result I don't understand. I've tried > both David's C++ and the cctbx python niggli_cell() implementations and > they both give the roughly the same answer. > > I'm reducing the following cell with two, equivalent, representations (a, > b, c, alpha, beta, gamma): > > Before: > > 1: 4.630811 4.630811 4.630811 90 90 90 > 2: 3.27448 5.67156 5.67156 99.5941 106.779 90 > > After: > > 1: 4.63081 4.63081 4.63081 90 90 90 > 2: 3.27448 5.67154 5.67156 99.5941 90 106.778 > > Looking at the trace, cell 1 undergoes step 3 and finishes while cell 2 > undergoes steps 2, 3, 7 and 4. > > Does anyone know why these haven't converged to the same cell? > > Many thanks, > -Martin > > On 23 March 2012 17:12, Ralf Grosse-Kunstleve <rwgrosse-kunstleve(a)lbl.gov>wrote: > >> Hi Martin, >> Let me know if you need svn write access to check in your changes. All I >> need is your sourceforge user id. >> Ralf >> >> >> On Fri, Mar 23, 2012 at 3:35 AM, Martin Uhrin <martin.uhrin.10(a)ucl.ac.uk>wrote: >> >>> Dear David and Rolf, >>> >>> thank you for your encouragement. >>> >>> David: I'm more than happy to port your implementation to cctbx if >>> you're happy with this. Of course I don't want to step on your toes so if >>> you'd rather do it yourself (or not at all) that's cool. >>> >>> There may be some licensing issues to sort out as it looks like cctbx >>> has a custom (non viral) license but the BSD license is likely compatible. >>> >>> On first impression I think a new class would be the way to go but I'd >>> have to look at the two algorithms in greater detail to be sure. >>> >>> All the best, >>> -Martin >>> >>> >>> On 22 March 2012 22:00, Ralf Grosse-Kunstleve < >>> rwgrosse-kunstleve(a)lbl.gov> wrote: >>> >>>> Hi Martin, >>>> You're very welcome to add a C++ version of the Krivy-Gruber algorithm >>>> to cctbx if that's what you had in mind. >>>> I'm not sure what's better, generalizing the fast-minimum-reduction >>>> code, or just having an independent implementation. >>>> Ralf >>>> >>>> On Thu, Mar 22, 2012 at 2:24 PM, Martin Uhrin < >>>> martin.uhrin.10(a)ucl.ac.uk> wrote: >>>> >>>>> Dear Cctbx community, >>>>> >>>>> Firstly I'd like to say thank you to Rolf, Nicholas and Paul for their >>>>> expertly thought through implementation of the reduced cell algorithm. >>>>> I've found it to be extremely useful for my work. >>>>> >>>>> My code is all in C++ and I'd like to be able to use the Krivy-Gruber >>>>> algorithm. My understanding is that only the reduced (Buerger) unit cell >>>>> algorithm is implemented in C++ [1] which guarantees shortest lengths but >>>>> not unique angles. From my understanding the Krivy-Gruber would also >>>>> guarantee me uniqueness of unit cell angles, however this is only >>>>> implemented in Python [2]. Sorry to be so verbose, I just wanted to check >>>>> that I was on the right page. >>>>> >>>>> Would it be possible for me to implement the Krivy-Gruber in C++ by >>>>> adding in the epsilon_relative to the parameter and following the procedure >>>>> found in the python version? >>>>> >>>>> Many thanks, >>>>> -Martin >>>>> >>>>> [1] >>>>> http://cctbx.sourceforge.net/current/c_plus_plus/classcctbx_1_1uctbx_1_1fas… >>>>> [2] >>>>> http://cctbx.sourceforge.net/current/python/cctbx.uctbx.krivy_gruber_1976.h… >>>>> >>>>> >>>>> >>>>> -- >>>>> Martin Uhrin Tel: +44 >>>>> 207 679 3466 >>>>> Department of Physics & Astronomy Fax:+44 207 679 0595 >>>>> University College London >>>>> martin.uhrin.10(a)ucl.ac.uk >>>>> Gower St, London, WC1E 6BT, U.K. http://www.cmmp.ucl.ac.uk >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> >>>> >>> >>> >>> -- >>> Martin Uhrin Tel: +44 >>> 207 679 3466 >>> Department of Physics & Astronomy Fax:+44 207 679 0595 >>> University College London >>> martin.uhrin.10(a)ucl.ac.uk >>> Gower St, London, WC1E 6BT, U.K. http://www.cmmp.ucl.ac.uk >>> >>> _______________________________________________ >>> 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 >> >> > > > -- > Martin Uhrin Tel: +44 > 207 679 3466 > Department of Physics & Astronomy Fax:+44 207 679 0595 > University College London > martin.uhrin.10(a)ucl.ac.uk > Gower St, London, WC1E 6BT, U.K. http://www.cmmp.ucl.ac.uk > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/cctbxbb > >

13 years, 9 months

Re: [cctbxbb] Making branches by accident

by markus.gerstel＠diamond.ac.uk

Hi Nigel, The log (and the blame log) should show the times of the commit, regardless of whether you merge the branch into master or rebase your branch onto master at the end. When you rebase your commits you can also get the rebase time. eg. for your last rebased commit: $ git show 4fa192b0 --format=fuller The author+date pair is the person who originally wrote the code (rather: who made the original commit), the commit+date pair is set by whoever rebased/cherry-picked/etc. it last. -Markus PS: Just to clarify - if you deliberately use branches to do isolated feature development, merging is absolutely fine. ________________________________ From: cctbxbb-bounces(a)phenix-online.org [cctbxbb-bounces(a)phenix-online.org] on behalf of Nigel Moriarty [nwmoriarty(a)lbl.gov] Sent: Thursday, December 08, 2016 17:41 To: cctbx mailing list Subject: Re: [cctbxbb] Making branches by accident Markus I was a non-rebaser but I have set it to true on my second machine. So my question is regardind branches. I have made a branch, made some changes and merged the master into the branch. I will make some more changes during testing. I assume that I merge into the master at some point. Will the commits appear in the log based on the time of the merge or the time I committed in the branch? Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov<http://CCI.LBL.gov> On Thu, Dec 8, 2016 at 12:14 AM, <markus.gerstel(a)diamond.ac.uk<mailto:[email protected]>> wrote: 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<mailto:[email protected]> [cctbxbb-bounces(a)phenix-online.org<mailto:[email protected]>] on behalf of Pavel Afonine [pafonine(a)lbl.gov<mailto:[email protected]>] Sent: Wednesday, December 07, 2016 18:24 To: cctbxbb(a)phenix-online.org<mailto:[email protected]> 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]><mailto:[email protected]<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]><mailto:[email protected]<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

9 years, 2 months

Re: [phenixbb] Selecting ellipsoid of data

by Frank von Delft

Ah.... I was wondering about that: thanks for the pointer!! On 15/07/2010 17:38, Kay Diederichs wrote: > Hi Frank, > > "such a tool" is at > http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Aniso_cutoff > > where it's meant to be applied to INTEGRATE.HKL which comes out of XDS. > Doing it this way has the benefit that the statistics printed out by > XDS' CORRECT (or SCALA/TRUNCATE; there are people who prefer that > route) match the data you refine agains. > > HTH, > > Kay > >> Message: 1 >> Date: Thu, 15 Jul 2010 06:32:40 +0100 >> From: Frank von Delft<frank.vondelft(a)sgc.ox.ac.uk> >> To: PHENIX user mailing list<phenixbb(a)phenix-online.org> >> Subject: [phenixbb] Selecting ellipsoid of data >> Message-ID:<4C3E9D78.5030203(a)sgc.ox.ac.uk> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> Hi, is there a tool in phenix that allows me to select an ellipsoid of >> data -- specified e.g. by the highest resolutions in three reciprocal >> lattice directions. (Yes, I'm playing with anisotropy, "playing" being >> the operative word.) >> >> phx >> >> >> ------------------------------ >> >> Message: 2 >> Date: Wed, 14 Jul 2010 22:47:30 -0700 >> From: "Ralf W. Grosse-Kunstleve"<rwgk(a)cci.lbl.gov> >> To: phenixbb(a)phenix-online.org >> Subject: Re: [phenixbb] Selecting ellipsoid of data >> Message-ID:<201007150547.o6F5lUoL018490(a)cci.lbl.gov> >> Content-Type: text/plain; charset=us-ascii >> >> Hi Frank, >> >>> Hi, is there a tool in phenix that allows me to select an ellipsoid of >>> data -- specified e.g. by the highest resolutions in three reciprocal >>> lattice directions. (Yes, I'm playing with anisotropy, "playing" being >>> the operative word.) >> >> I'm not aware of such a tool. >> >> Ralf >> >> >> ------------------------------ >> >> Message: 3 >> Date: Thu, 15 Jul 2010 07:15:58 +0100 >> From: Frank von Delft<frank.vondelft(a)sgc.ox.ac.uk> >> To: "Ralf W. Grosse-Kunstleve"<rwgk(a)cci.lbl.gov>, PHENIX user mailing >> list<phenixbb(a)phenix-online.org> >> Subject: Re: [phenixbb] Selecting ellipsoid of data >> Message-ID:<4C3EA79E.2030503(a)sgc.ox.ac.uk> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> Hi Ralf >> >> Yeah, I figured. So if I want to use cctbx, where do I start? Just a >> pointer to a) package and b) function where I'll see the syntax. >> >> So equation for ellipsoid is x^2/a^2 + y^2/b^2 + z^2/c^2 = 1; so I >> imagine I take each reflection, convert each of h,k,l to 1/reso, and >> with a = 1/res(a*), I just check whether the above is< 1. >> >> The main thing I still need is to convert h,k,l into orthogonal >> coordinates.... or do I? I suppose I don't, as what I care for is not >> whether it's "really" an ellipsoid, only whether it cuts through miller >> index space anisotropically. >> >> Hmmmm... I may be able to do it in sftools; but if you can in<1minute >> give me a link to where to look to get started in cctbx, that would be >> awesome. >> >> (Thanks for listening :) >> >> >> >> >>> Hi Frank, >>> >>> >>>> Hi, is there a tool in phenix that allows me to select an ellipsoid of >>>> data -- specified e.g. by the highest resolutions in three reciprocal >>>> lattice directions. (Yes, I'm playing with anisotropy, "playing" >>>> being >>>> the operative word.) >>>> >>> I'm not aware of such a tool. >>> >>> Ralf > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb >

15 years, 6 months

Re: [phenixbb] phenix refinement question

by Pavel Afonine

Hi Martyn, thanks for your feedback - it is very much appreciated! > It is not strictly the case that TLS is neglected during pdb deposition. This is in-sync with my understanding of the current situation. It is really great! (Although, I should re-run my tools through the whole PDB to quickly see state-of-the-art.) > The requirement for deposition now is that full ANISOU values have to be present if TLS has been used. This is really great, too! > In which case the TLS definitions are redundant as the full description of the ADP model is provided by the ATOM and ANISOU records. No, this is not true. The TLS definitions define the model partitions into TLS groups that with the current tools cannot be recovered from just ANISOU records. > There is therefore no absolute requirement for the TLS definitions in the header to be correctly read in order for the validation to proceed. This is true in a sense that you can re-calculate the R-factor (since the complete ANISOU records corresponding to Utotal (see reference below) are present and therefore you can compute correct Fcalcs), but inability to read this information correctly should be a BIG warning sign for everyone involved. Also, leaving out TLS records will result in obvious loss of information about TLS groups (atom selection defining TLS groups). I don't see a reason why one would want to give up this information. > This aids accurate validation of the model against the provided SF data using EDS for example. Absolutely true: the ability to reproduce the reported R-factors is in close and direct relation with the ability to accurately validate the model and data. phenix.model_vs_data would do it almost unconditionally: J. Appl. Cryst. (2010). 43, 669-676 phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics P. V. Afonine, R. W. Grosse-Kunstleve, V. B. Chen, J. J. Headd, N. W. Moriarty, J. S. Richardson, D. C. Richardson, A. Urzhumtsev, P. H. Zwart and P. D. Adams > The output with and without TLS was used historically to check whether the TLS definitions had been read correctly. I see, but there are more to just having TLS hint in "REMARK 3"... The TLS records contain the information about TLS groups (atom selections, at least), that, if removed, cannot be easily guessed. > Having said that the presence of TLS definitions is still informative for users of the coordinates to check that for example a full anisotropic refinement has not been carried out. Well, "TLS refinement" = "Constrained anisotropic refinement", so I don't really understand what is "full anisotropic refinement". Also, what about performing TLS refinement on top of treating each atom moving anisotropically: see p. 24-31: http://www.phenix-online.org/newsletter/CCN_2010_07.pdf for some overview. > PDB curation involves checking the description of the TLS groups that have been chosen. Great! Did you see my report that I sent to those who might be interested a few months ago? If not, I can re-send you the old one and meanwhile I can re-compute the most current. > So, for example, it is useful that the selection expressions do not refer to ranges of residues that do not exist (for example "RESID -99:9999" for a 1-100 residue protein), Absolutely true. This is what I pointed out in my report a few months ago. > or to overlapping ranges, for example: a chain with its TLS group 1 defined as "RESID 45:90" and its TLS group 2 is defined as "RESID 75:150". True. > Depending on the wwPDB deposition site, the validation programs may differ. Sure, the tools may vary under the requirement that the outcome must be the same. > PDBe uses an in-house version of the EDS server which uses REFMAC with TLS taken into account. RCSB and PDBj run the particular program that was used in determining the structure for validation, in addition to a validation check using SFCHECK. Can you reproduce the reported R-factors of this entry using the above described tools: 2WYX or 2R24? Let me know if not. > It is worth saying that the PDB sites are not attempting to completely reproduce the authors' Rfactors, This is very unfortunate, since there is no reason for the R-factors to be not 0.01% reproducible. IF you can't reproduce them, then there is THE problem either with the structure/data or with the software you use. Period. See: J. Appl. Cryst. (2010). 43, 669-676 phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics P. V. Afonine, R. W. Grosse-Kunstleve, V. B. Chen, J. J. Headd, N. W. Moriarty, J. S. Richardson, D. C. Richardson, A. Urzhumtsev, P. H. Zwart and P. D. Adams > but instead to check for errors in the deposition process. Well, reproducing the R-factors is the very first sanity check to do BEFORE wasting any time on checking the other lower level details. Indeed, if such gross thing as the R-factor doesn't reasonably match there is no point to validate fine details. > You can check the details of the PHENIX header format for TLS at > http://www.wwpdb.org/documentation/format32/remark3.html#Refinement%20using… Thanks! This looks great. Just a minor question: What if I specify a TLS group as "chain A or chain a and resseq 123:456 and element N" (that I potentially can do no problem in PHENIX)? All the best! Pavel.

15 years, 2 months

Re: [phenixbb] rotamers

by Pavel Afonine

Hi Kendall, we've been disusing this off-list between developers and some users... I'm going to copy-paste one of my latest comments: """ Given the poll result I guess there is no way to make everyone happy with a unique solution, so having multiple options (keep/trim/do something else) is clearly the way to go. I guess another poll (or proper research) about "what's distinguishable" (or what you call poor density) would be of help too. Because I bet once we start doing trimming there will be always someone screaming "No! you are trimming/not building at too low/high CC/sigma!" Personally, I'm not leaning towards one or another option. I believe all of them have approximately equal amount of clear advantages and disadvantages. I was just thinking of a longer term research-like solution that might (or might not) bring a novel idea... By the way, another alternative way to model them is to define a probability distribution mask around a side chain where its atoms are expected, and use that mask as a contribution to Fcalc. I guess (not 100% sure) this is what you can do in BUSTER-TNT (at least this is what advertised in their paper). That would account for these missing atoms to some degree without actually including the ATOM records for them into final PDB. One wrinkle though is that in this case you would need to deposit that mask along with your PDB file, since you will be having a mixed model - atomic model + nonatomic model. (I wonder how many users who ever used this option actually did deposit the masks? -:) ) """ All the best! Pavel. On 3/29/11 6:43 PM, Kendall Nettles wrote: > We have been doing a lot of parallel refinements where we are checking out the new options in PHENIX refinement, and one of the things we have observed is that sometimes the sidechains with no clear electron density end up in the main chain density, and distort the model. There is no clear pattern as to which options lead to this phenotype, as different combinations give different results. Until we can sort out what is causing this, it seems clear to me that it is better to delete the side chains. If you want to leave a side chain with no clear electron density, you have to make sure each one is not distorting the model. So leaving the side chains with no clear electron density requires much work, with a benefit that is not clear to me. > > Kendall Nettles > > On Mar 28, 2011, at 1:04 PM, Ed Pozharski wrote: > >> Pavel, >> >>> - what you mean by "no density", >> Lack of confidence in placement of the side chain. Everyone would have >> somewhat different take on it, but the question is more about what to >> do, not how to decide if the side chain is disordered. >> >>> Therefore this raises another item for your questionnaire: >> There is "other" option, feel free to use it >> >>> refine group >>> occupancy for these atoms (one occupancy per all atoms in question - the >>> occupancy typically will refine to something less than 0.5 or so). >> This raises an entirely different question regarding reliability of >> occupancy refinement in general due to its correlation with the >> B-factors. Another can of worms. >> >>> This trick with smearing out an atom by B-factor may only work for >>> isolated (single) atoms such as waters because they are not bonded to >>> anything through restraints. >> Certainly, presence of restraints makes the B-factor increase less >> steep. I just looked at an instance of a disordered arginine (no >> density above 1 sigma for any side chain atoms), and B-factors jump from >> 30 at the backbone to 90 at the tip of the side chain. This would >> reduce the density level ~5x, which is probably quite sufficient for >> blending it into the solvent. There could be a bit of a problem in the >> middle, where B-factors are inflated/deflated, but it does take care of >> density reduction. >> >> Things like atom-specific restraints and modified restraint target may >> be of some help, but the effect on the final model may be too small to >> validate the effort. >> >> -- >> "I'd jump in myself, if I weren't so good at whistling." >> Julian, King of Lemurs >> >> _______________________________________________ >> 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

14 years, 10 months

Re: [cctbxbb] bootstrap.py build on Ubuntu

by Billy Poon

Hi David, Actually, it looks like the lib64z1-dev package provides libz.so in /usr/lib64, so installing that package should fix your issue. It's a bit odd that the lib64z1 package does not provide that file. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org On Mon, Jun 13, 2016 at 1:53 PM, Billy Poon <bkpoon(a)lbl.gov> wrote: > Hi David, > > I don't have a fix yet, but here is a workaround. It seems like setup.py > is looking for libz.so instead of libz.so.1, so you can fix the issue by > making a symbolic link for libz.so in /usr/lib64. > > sudo ln -s /usr/lib64/libz.so.1 /usr/lib64/libz.so > > This requires root access, so that's why it's just a workaround. > > -- > Billy K. Poon > Research Scientist, Molecular Biophysics and Integrated Bioimaging > Lawrence Berkeley National Laboratory > 1 Cyclotron Road, M/S 33R0345 > Berkeley, CA 94720 > Tel: (510) 486-5709 > Fax: (510) 486-5909 > Web: https://phenix-online.org > > On Sat, Jun 11, 2016 at 5:05 PM, Billy Poon <bkpoon(a)lbl.gov> wrote: > >> Hi David, >> >> Sorry it look so long! Setting up all the virtual machines was a time >> sink and getting things to work on 32-bit CentOS 5 and Ubuntu 12.04 was a >> little tricky. >> >> It looks like Ubuntu 16.04 moved its libraries around. I used apt-get to >> install libz-dev and lib64z1 (the 64-bit library). There is a libz.so.1 >> file in /lib/x86_64-linux-gnu and in /usr/lib64. >> >> I have not gotten it to work yet, but I'm pretty sure this is the issue. >> I'll have to double-check 12.04 and 14.04. >> >> As for Pillow, I did test it a few months ago, but I remember there being >> API changes that will need to fixed. >> >> -- >> Billy K. Poon >> Research Scientist, Molecular Biophysics and Integrated Bioimaging >> Lawrence Berkeley National Laboratory >> 1 Cyclotron Road, M/S 33R0345 >> Berkeley, CA 94720 >> Tel: (510) 486-5709 >> Fax: (510) 486-5909 >> Web: https://phenix-online.org >> >> On Sat, Jun 11, 2016 at 2:04 AM, David Waterman <dgwaterman(a)gmail.com> >> wrote: >> >>> Hi Billy, >>> >>> I'm replying on this old thread because I have finally got round to >>> trying a bootstrap build for DIALS out again on Ubuntu, having waited for >>> updates to the dependencies and updating the OS to 16.04. >>> >>> The good news is, the build ran through fine. This is the first time >>> I've had a bootstrap build complete without error on Ubuntu, so thanks to >>> you and the others who have worked on improving the build in the last few >>> months! >>> >>> The bad news is I'm getting two failures in the DIALS tests: >>> >>> dials/test/command_line/tst_export_bitmaps.py >>> dials_regression/test.py >>> >>> Both are from PIL >>> >>> File >>> "/home/fcx32934/dials_test_build/base/lib/python2.7/site-packages/PIL/Image.py", >>> line 401, in _getencoder >>> raise IOError("encoder %s not available" % encoder_name) >>> IOError: encoder zip not available >>> >>> Indeed, from base_tmp/imaging_install_log it looks like PIL is not >>> configured properly >>> >>> -------------------------------------------------------------------- >>> PIL 1.1.7 SETUP SUMMARY >>> -------------------------------------------------------------------- >>> version 1.1.7 >>> platform linux2 2.7.8 (default_cci, Jun 10 2016, 16:04:32) >>> [GCC 5.3.1 20160413] >>> -------------------------------------------------------------------- >>> *** TKINTER support not available >>> *** JPEG support not available >>> *** ZLIB (PNG/ZIP) support not available >>> *** FREETYPE2 support not available >>> *** LITTLECMS support not available >>> -------------------------------------------------------------------- >>> >>> Any ideas? I have zlib headers but perhaps PIL can't find them. >>> >>> On a related note, the free version of PIL has not been updated for >>> years. The replacement Pillow has started to diverge. I first noticed this >>> when Ubuntu 16.04 gave me Pillow 3.1.2 and my cctbx build with the system >>> python produced failures because it no longer supports certain deprecated >>> methods from PIL. I worked around that in r24587, but these things are a >>> losing battle. Is it time to switch cctbx over to Pillow instead of PIL? >>> >>> Cheers >>> >>> -- David >>> >>> On 7 January 2016 at 18:12, Billy Poon <bkpoon(a)lbl.gov> wrote: >>> >>>> Hi all, >>>> >>>> Since wxPython was updated to 3.0.2, I have been thinking about >>>> updating the other GUI-related packages to more recent versions. I would >>>> probably update to the latest, stable version that does not involve major >>>> changes to the API so that backwards compatibility is preserved. Let me >>>> know if that would be helpful and I can prioritize the migration and >>>> testing. >>>> >>>> -- >>>> Billy K. Poon >>>> Research Scientist, Molecular Biophysics and Integrated Bioimaging >>>> Lawrence Berkeley National Laboratory >>>> 1 Cyclotron Road, M/S 33R0345 >>>> Berkeley, CA 94720 >>>> Tel: (510) 486-5709 >>>> Fax: (510) 486-5909 >>>> Web: https://phenix-online.org >>>> >>>> On Thu, Jan 7, 2016 at 9:30 AM, Nicholas Sauter <nksauter(a)lbl.gov> >>>> wrote: >>>> >>>>> David, >>>>> >>>>> I notice that the Pango version, 1.16.1, was released in 2007, so >>>>> perhaps it is no surprise that the latest Ubuntu does not support it. >>>>> Maybe this calls for stepping forward the Pango version until you find one >>>>> that works. I see that the latest stable release is 1.39. >>>>> >>>>> This would be valuable information for us..Billy Poon in the Phenix >>>>> group is supporting the Phenix GUI, so it might be advisable for him to >>>>> update the Pango version in the base installer. >>>>> >>>>> Nick >>>>> >>>>> 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 Thu, Jan 7, 2016 at 8:54 AM, David Waterman <dgwaterman(a)gmail.com> >>>>> wrote: >>>>> >>>>>> Hi again >>>>>> >>>>>> Another data point: I just tried this on a different Ubuntu machine, >>>>>> this time running 14.04. In this case pango installed just fine. In fact >>>>>> all other packages installed too and the machine is now compiling cctbx. >>>>>> >>>>>> I might have enough for comparison between the potentially working >>>>>> 14.04 and failed 15.04 builds to figure out what is wrong in the second >>>>>> case. >>>>>> >>>>>> Cheers >>>>>> >>>>>> -- David >>>>>> >>>>>> On 7 January 2016 at 09:56, David Waterman <dgwaterman(a)gmail.com> >>>>>> wrote: >>>>>> >>>>>>> Hi folks >>>>>>> >>>>>>> I recently tried building cctbx+dials on Ubuntu 15.04 following the >>>>>>> instructions here: >>>>>>> http://dials.github.io/documentation/installation_developer.html >>>>>>> >>>>>>> This failed during installation of pango-1.16.1. Looking >>>>>>> at pango_install_log, I see the command that failed was as follows: >>>>>>> >>>>>>> gcc -DHAVE_CONFIG_H -I. -I. -I../.. >>>>>>> -DSYSCONFDIR=\"/home/fcx32934/sw/dials_bootstrap_test/base/etc\" >>>>>>> -DLIBDIR=\"/home/fcx32934/sw/dials_bootstrap_test/base/lib\" >>>>>>> -DG_DISABLE_CAST_CHECKS -I../.. -DG_DISABLE_DEPRECATED >>>>>>> -I/home/fcx32934/sw/dials_bootstrap_test/base/include >>>>>>> -I/home/fcx32934/sw/dials_bootstrap_test/base/include/freetype2 -g -O2 >>>>>>> -Wall -MT fribidi.lo -MD -MP -MF .deps/fribidi.Tpo -c fribidi.c -fPIC >>>>>>> -DPIC -o .libs/fribidi.o >>>>>>> In file included from fribidi.h:31:0, >>>>>>> from fribidi.c:28: >>>>>>> fribidi_config.h:1:18: fatal error: glib.h: No such file or directory >>>>>>> >>>>>>> The file glib.h appears to be in base/include/glib-2.0/, however >>>>>>> this directory was not explicitly included in the command above, only its >>>>>>> parent. This suggests a configuration failure in pango to me. Taking a look >>>>>>> at base_tmp/pango-1.16.1/config.log, I see what look like the relevant >>>>>>> lines: >>>>>>> >>>>>>> configure:22227: checking for GLIB >>>>>>> configure:22235: $PKG_CONFIG --exists --print-errors "$GLIB_MODULES" >>>>>>> configure:22238: $? = 0 >>>>>>> configure:22253: $PKG_CONFIG --exists --print-errors "$GLIB_MODULES" >>>>>>> configure:22256: $? = 0 >>>>>>> configure:22304: result: yes >>>>>>> >>>>>>> but this doesn't tell me very much. Does anyone have any suggestions >>>>>>> as to how I might proceed? >>>>>>> >>>>>>> Many thanks >>>>>>> >>>>>>> -- David >>>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>>> >>>> >>> >>> _______________________________________________ >>> cctbxbb mailing list >>> cctbxbb(a)phenix-online.org >>> http://phenix-online.org/mailman/listinfo/cctbxbb >>> >>> >> >

9 years, 7 months

[phenixbb] POSITION AVAILABLE: Visiting Research Specialist Position at the University of Illinois at Chicago

by Yury Polikanov

*Visiting Research Specialist Position Available in the Polikanov Lab <https://sites.google.com/view/polikanovlab>Department of Biological Sciences, University of Illinois at Chicago* *The Polikanov Laboratory <https://sites.google.com/view/polikanovlab> in the Department of Biological Sciences at the University of Illinois at Chicago is looking for a talented, skillful, and highly motivated researcher to fill the Visiting Research Scientist position to study the structure and function of the bacterial ribosome.* For full consideration, please submit your application along with a Cover Letter, CV, and three references by May 31, 2025. Cover letter should describe previous research accomplishments and scientific interests as well as how these fit within the scope of the research in the Polikanov lab. Questions can be addressed to Yury Polikanov at yuryp(a)uic.edu. Visiting Research Specialist- UIC Department of Biological Sciences, Polikanov Lab Hiring Department: Biological Sciences Location: Chicago, IL USA Requisition ID: 1033622 Posting Close Date: 05/31/2025 Link to Apply: https://uic.csod.com/ux/ats/careersite/1/home/requisition/14681?c=uic *Position Summary:* The Polikanov Lab is seeking a Visiting Research Specialist. Successful candidate will conduct research by using X-ray crystallography and cryo-EM techniques to obtain a structural basis for various functions of the bacterial ribosome and its inhibition by different small-molecule inhibitors. The successful candidate should have a strong theoretical background in standard biochemical, molecular biology, and biophysical methods, as well as practical skills in the most standard methods currently used in molecular biology and biochemistry (such as protein expression, purification, etc.). Knowledge in X-ray crystallography or other structural techniques is desired but not required. The successful candidate would conduct research and assist with training laboratory personnel in various techniques, experiments, and the appropriate use of research equipment. He/She would also perform data analysis and manage, document, and help with the dissemination of research activities for publication and outreach. *Duties & Responsibilities:* - Record keeping: log and track inventory of chemicals, reagents, and lab supplies - Maintain accurate records of experiments, procedures, and results - Keep the laboratory clean, organized, and free of contaminants - Glassware & Equipment Maintenance - Prepare culture media, buffers, and reagents according to protocols - Assist other researchers in the lab in conducting experiments - Purify bacterial ribosomes and all additional components necessary for the experiments, such as recombinant proteins, tRNAs - Train undergraduate and graduate students in research methods, use of equipment, record keeping, and laboratory database entry *Minimum Qualifications :* - Bachelor’s degree in biology, chemistry, biochemistry, biophysics, or related field required. Master’s degree in science preferred. - A minimum of 3 years of related research experience. - Strong background in biochemistry and molecular biology - Practical skills with the most standard methods currently used in molecular biology, and biochemistry (such as protein expression, purification) *Salary:* The budgeted salary range for the position is $48,000 to $60,000. The pay offered to the selected candidate will be determined based on factors including (but not limited to) the experience and qualifications of the selected candidate, including equivalent years in rank, training, and field or discipline; internal equity; and external market pay for comparable jobs. *About the University of Illinois Chicago* UIC is among the nation’s preeminent urban public research universities, a Carnegie RU/VH research institution, and the largest university in Chicago. UIC serves over 34,000 students, comprising one of the most diverse student bodies in the nation and is designated as a Minority Serving Institution (MSI), an Asian American and Native American Pacific Islander Serving Institution (AANAPSI) and a Hispanic Serving Institution (HSI). Through its 16 colleges, UIC produces nationally and internationally recognized multidisciplinary academic programs in concert with civic, corporate and community partners worldwide, including a full complement of health sciences colleges. By emphasizing cutting-edge and transformational research along with a commitment to the success of all students, UIC embodies the dynamic, vibrant and engaged urban university. Recent “Best Colleges” rankings published by U.S. News & World Report, found UIC climbed up in its rankings among top public schools in the nation and among all national universities. UIC has over 300,000 alumni, and is one of the largest employers in the city of Chicago. Benefits eligible positions include a comprehensive benefits package which offers: Health, Dental, Vision, Life, Disability & AD&D insurance; a defined benefit pension plan; paid leaves such as Vacation, Holiday and Sick; tuition waivers for employees and dependents. Click for a complete list of *Employee Benefits <https://www.hr.uillinois.edu/benefits/>*. *Final authorization of the position is subject to availability of funding.* *UIC is an EOE including Disability/Vets.* *The University of Illinois may conduct background checks on all job candidates upon acceptance of a contingent offer. Background checks will be performed in compliance with the Fair Credit Reporting Act* *The University of Illinois System requires candidates selected for hire to disclose any documented finding of sexual misconduct or sexual harassment and to authorize inquiries to current and former employers regarding findings of sexual misconduct or sexual harassment. For more information, visit **https://www.hr.uillinois.edu/cms/One.aspx?portalId=4292&pageId=1411899 <https://www.hr.uillinois.edu/cms/One.aspx?portalId=4292&pageId=1411899>*

9 months, 1 week

Re: [phenixbb] alternatives to RMSD

by Pavel Afonine

Hi Ed, yes, this makes sense, sure: having models to be superposed appropriately to begin with certainly is a good idea. My point was that coordinate-based rmsd does not account for B-factors and occupancy that is a problem if you are comparing flexible molecules. A possible solution may be to use a more generous (=more information rich) representation of atomic model such as electron density map that would 'automatically' take care of disorder. Pavel On 7/5/14, 9:37 AM, Edward A. Berry wrote: > I agree that would be useful as an alternative to RMSD, > but if I understand the original post, the problem > with RMSD is that the two secondary structure elements > are connected by a variable turn so that they cannot be superimposed > simultaneously. That could still be a problem, comparing maps. > > What you can do is report the change in angle between them, > and the residues making up the hinge. > A program called dyndom (dynamic domains) is good for this, > Or you can superimpose each "domain" separately, view the > superimposed molecules, and see haw far into the turn > from each side thesuperposition is good > > To get the change in angle between the two parts, > first superimpose model A on model B using only residues > in domain 1 (say, the helix). > Save that reoriented model A, and now superimpose it on model B > using only residues in domain 2 (the strand). > The angle involved in this second rotation is the chang in interdomain > angle. > > (You could also report RMSD for superposition of the individual domain, > but helix-on-helix or strand-on-strand are likely to be pretty good fits > and not very informative.) > eab > > On 07/05/2014 10:22 AM, PC wrote: >> Hi Pavel, >> >> Thank you very much, this sounds very interesting. >> >> I have used ccp4, coot and phenix but I am no expert but I am >> definitely interested in trying this method if you could give more >> information. >> >> Thank you, >> Patrick. >> >> >> -----Original Message----- >> *From:* pafonine(a)lbl.gov >> *Sent:* Fri, 04 Jul 2014 20:34:33 -0700 >> *To:* patrick.cossins(a)inbox.com, phenixbb(a)phenix-online.org >> *Subject:* Re: [phenixbb] alternatives to RMSD >> >> Hi Patrick, >> >> RMSD is a poor measure in this case as it does not account for >> B-factors, occupancies, alternative conformations and so on >> information a crystal structure model may make available. >> Macromolecules are not a bunch of points in space. >> >> While I'm sure more thorough methods exist, I would vote for the >> simplest, most direct and obvious one. You can calculate electron >> density map using a Gaussian approximation from model A and B (yes, >> electron density map - not a Fourier image of it!). That will >> naturally account for all: B-factors, occupancies, other disorder. >> Then you can calculate a map similarity measure, such as map >> correlation, for instance. After all, why use a cannon to kill a fly?! >> >> If you are interested to follow this route I can explain the >> details. >> >> All the best, >> Pavel >> >>> Hi Phenix users, >>> >>> I am not a crystallographer but I though you guys might be a >>> good place to ask this question. >>> >>> I have 2 super secondary structures, A and B and they consist of >>> Helix-turn-Strand >>> >>> Due to the turn the two structures have a poor RMSD because the >>> two flanking fragments of Helix and Strand are far from each other >>> but when I superimpose the two fragments individually(helixA with >>> helix B and standA with strandB in Pymol they align very well). >>> >>> Now, is there a way to express this instead of using the RMSD? >>> When the two structures align well the RMSD is very good but a >>> slight movement and the RMSD is awful. >>> But looking at the two structures I can see they follow the same >>> path through space. >>> >>> Thank you, >>> Patrick >> >> ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ >> >> Protect your computer files with professional cloud backup. Get PCRx >> Backup and upload unlimited files automatically. >> <http://backup.pcrx.com/mail> >> >> >> _______________________________________________ >> 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

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