- phenixbb - phenix-online.org

Restraints generation for TaBr
by Rebecca Oot 05 Nov '13

05 Nov '13

Hello all, I am trying to create a restraints file for hexatantlum dodecabromide (TaBr or TBR) and using Elbow, I get an error message saying that the program does not deal with heavy atom clusters. Does anyone have any advice on which program would be suitable to use? Thanks very much in advance Rebecca

3 2

Re: [phenixbb] Phenix.Rosetta_refine on Ubuntu 12.04 LTS
by Jan Gebauer 05 Nov '13

05 Nov '13

Hi David, hi all, I now managed to at least get a test refinement working. What I mostly changed was the Ubuntu version. I have no idea why, but I managed to get it to work on Ubuntu 10.04. In principle I installed 10.04 freshly in a virtualbox and from their it worked rather straight-forward. Here is how I proceeded in detail for those of you who are interested: 1) Setting up a Virtualbox 4.3.2 r90405 on Ubuntu 12.04.3. 2) Installing the 64bit version of Ubuntu 10.04 in a virtualbox (4 processors / 90% speed cap / 4GB Ram /VT-x enabled) 3) Install VBoxAdditions 4) Update ubuntu (sudo apt-get update) 5) Installing g++ and zlib library (sudo apt-get install g++ zlib1g-dev) 6) Installing binary version of phenix-dev-1525 to /usr/local/science/phenix-dev-1525 (sudo ./install --prefix=/usr/local/science) 7) Unpack rosetta_2013_wk42_bundle to /usr/local/science/rosetta_2013_wk42_bundle 8) set rossetta variables by inserting them at the start of /usr/local/science/pheninx-dev-1525/phenix_env.sh (just in line 3ff): export PHENIX_ROSETTA_PATH=/usr/local/science/rosetta_2013wk42_bundle export ROSETTA3_DB=/usr/local/science/rosetta_2013wk42_bundle/main/database export PATH=$PATH:/usr/local/science/rosetta_2013wk42_bundle/main/source/bin 9) assign ownership to active user (sudo chown gebauer:gebauer /usr/local/science/ -R) 10) Compile it (phenix.build_phenix_interface nproc=4) It should run without problems Testing: 1) Create a new directory (mkdir test && cd test) 2) Download testset (suggested by Nat: phenix.fetch_pdb --mtz 1yjp) 3) Run rosetta_refine (phenix.rosetta_refine 1yjp.pdb 1yjp.mtz nproc=4) In my case rFree dropped from 18.21 to 14.90. It's not a low resolution dataset, but it show that it general works and lowRes would potentially take to long for a mere testing My real data are still being processed so I have no idea how well it will works... only thing I found out already: 4.5 GB RAM for 4 processes calculating ~500Aa via rosetta seems not to be enough. I thereby reduced my "real run" to only one processor... Regards, Jan Am 01.11.2013 08:39, schrieb David Goldstone: > Hi Jan, > > I followed the same procedure. The only differences being that I have > installed it to my home directory to keep it separate from our > standard install of phenix and rosetta and I run the phenix_env.sh > separately from the exports. I had to remove our default init.sh > script from my .bashrc (this is our setup script for all programs ccp4 > etc) and now manually source a different version to ensure it points > to the correct version of phenix. > > I originally had trouble with the python shared libraries but Nat has > fixed this by building them into the binary installer. > > Sorry I can't be more help > > David > > > ---- > Dr David Goldstone > Senior Lecturer > University of Auckland > New Zealand > Ph +64 9 3737599 x84607 <tel:+64%209%203737599;84607> > > On 1/11/2013, at 8:30 PM, Jan Gebauer <jan.gebauer(a)uni-koeln.de > <mailto:[email protected]>> wrote: > >> Dear David, >> >> thanks for your remark. Indeed my paths are wrong in the mail; >> however, this is due to lazy typing... I do set the Rosetta_DB3 path >> corretly... >> I'm still interested to know, how you managed to install build it. >> Have you done the same procedure as described by me? (only with >> different releases?) >> Or did you do something differently? >> >> Regards, >> Jan >> >> Am Donnerstag, 31. Oktober 2013 23:11:42 schrieb David Goldstone: >>> Dear Jan, >>> >>> I have recently installed phenix with rosetta refine on Ubuntu 10.04 >>> using phenix-dev-1515 and rosetta_wk40_bundle. >>> >>> This install also appears to run on an Ubuntu 12 install. >>> >>> I think you export commands are not correct mine are as follows >>> >>> export >>> PHENIX_ROSETTA_PATH=/mnt/home/dgol002/programs/rosetta_2013wk40_bundle >>> export >>> ROSETTA3_DB=/mnt/home/dgol002/programs/rosetta_2013wk40_bundle/main/database >>> export >>> PATH=$PATH:/mnt/home/dgol002/programs/rosetta_2013wk40_bundle/main/source/bin >>> >>> ie you are exporting ROSETTA_BIN twice rather than ROSETTA3_DB. >>> >>> Hope this helps >>> >>> David >>> >>> >>> >>> On 1/11/2013 4:48 a.m., Jan Gebauer wrote: >>>> Dear all, >>>> >>>> I'm trying to get rosetta_refine working on ubuntu 12.04 LTS. >>>> >>>> This was the (latest) way I tried it: >>>> >>>> 1) Downloaded phenix-dev-1523 binary & installed it via installer in >>>> /usr/local/science/phenix4rosetta/phenix-dev-1523 >>>> 2) Downloaded rosetta 2031wk42 and extracted it in >>>> /usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle >>>> 3) Inserted into phenix_env.sh >>>> export >>>> ROSETTA_BIN=/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/source/bin >>>> export >>>> PHENIX_ROSETTA_PATH=/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/ >>>> export >>>> ROSETTA_BIN=/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/database >>>> 4) sources phenix_env.sh >>>> 5) build the interface via >>>> rosetta.build_phenix_interface nproc=4 >>>> 6) exceute the refinement via phenix.rosetta_refine phasermodel.pdb >>>> data.mtz nproc=4 >>>> >>>> The programm runs fine, up to the point where it should generate >>>> models via rosetta, it then stops and crashes. >>>> I have attached some logfiles >>>> >>>> Has anyone managed to run rosetta_refine on Ubuntu? Which phenix and >>>> rosetta versions did you use? Ist there anything wrong on my above >>>> mentioned build protocol? >>>> >>>> I'm thankful for any help. >>>> >>>> Regards, >>>> Jan Gebauer >>>> >>>> >>>> >>>> -- >>>> Dr. Jan Gebauer >>>> AG Prof. Baumann >>>> Institut für Biochemie / Uni-Köln >>>> Otto-Fischer-Str. 12-14 / 50674 Köln >>>> Fon: +49 (221) 470 3212 >>>> Fax: +49 (221) 470 5066 >>>> >>>> http://px.uni-koeln.de/ >>>> >>>> >>>> _______________________________________________ >>>> phenixbb mailing list >>>> phenixbb(a)phenix-online.org <mailto:[email protected]> >>>> http://phenix-online.org/mailman/listinfo/phenixbb >>> >>> >>> -- >>> Dr David Goldstone >>> Senior Lecturer & Rutherford Discovery Fellow >>> Structural Biology >>> University of Auckland >>> New Zealand >>> Ph +64 9 3737599 x84607 -- Dr. Jan Gebauer AG Prof. Baumann Institut für Biochemie / Uni-Köln Otto-Fischer-Str. 12-14 / 50674 Köln Fon: +49 (221) 470 3212 Fax: +49 (221) 470 5066 http://px.uni-koeln.de/

2 1

Post-doctoral Fellowships at the University of Texas
by Gabrielle Rudenko 04 Nov '13

04 Nov '13

*Macromolecular Crystallography, Biophysics and Biochemistry* Two post-doctoral fellowship positions are available at the University of Texas Medical Branch (UTMB) located in the greater Houston area in the research team of Dr. Gabrielle Rudenko. We study molecules that mediate the formation, maintenance and plasticity of synapses, the contact and communication point between neurons. Our proteins of interest organize and regulate protein interaction networks in the synaptic cleft and impact how neurons communicate with each other at synapses. Many of the proteins we study are implicated in neurological disease and serve as potential novel therapeutic targets. We are looking for highly motivated, enthusiastic, hard working individuals who are interested in combining the fields of structural biology and neuroscience. Research projects involve protein over-expression and purification, x-ray crystallography, biochemical and biophysical techniques, proteomics, chemical biology and in collaboration electron microscopy and NMR. Our laboratory is joining the endowed Sealy Center for Structural Biology and Molecular Biophysics and the Department of Pharmacology/Toxicology at UTMB. The Sealy Center provides access to exceptional facilities, training and experimental assistance. *X-ray facilities* include a high-brilliance FR-E Superbright x-ray generator, a Rigaku R-AXIS-IV dual 30cm Imaging Plate detector, a Bruker SMART 2K CCD and a Rigaku BioSAXS-1000 2D-Kratky camera (for solution scattering data). *Biophysics facilities* include equipment for analytical ultracentrifugation, fluorescence, MALDI-TOF mass spectrometry, dynamic light scattering, surface plasmon resonance, titration micro-calorimetry, and high throughput screening with the ThermoFluor HTS apparatus. In addition, the *Electron Microscopy facilities*house three modern JEOL cryo-electron microscopes (a 200 keV JEOL 2200FS cryo-EM with in-column electron energy filter and field emission gun, a 200 keV JEOL 2100 EM, and a 120 keV JEM1400 microscope) and the *NMR facilities*include three NMR spectrometers (Bruker Avance III 800, 750 and 600 MHz with cryoprobes). See http://www.scsb.utmb.edu/resources/ UTMB is part of the Texas Medical Center, the world’s largest medical center located in greater Houston. UTMB is situated on Galveston Island offering a pleasant subtropical climate and miles of relaxing beaches. UTMB is located within commuting distance of Houston, the fourth largest city in the United States and a leader in the arts, education, and health care. *Qualifications:* Applicants should have received a Ph.D. degree in a field relevant to structural biology in the past three years and have a strong publication record. Applicants with experience in cloning, bacterial/insect cell culture, protein purification and crystallization, and macromolecular structure determination are preferred. However, recent graduates with a strong background in protein over-expression and purification, and an exceptional interest in learning crystallography are also encouraged to apply. Good written and oral communication skills in English are essential as well as the ability and desire to work as part of a highly motivated, collaborative team. To apply please e-mail the following to *rudenkolab.application(a)gmail.com*<rudenkolab.application(a)gmail.com>: CV, contact information for three references (address, phone and e-mail), a list of your experimental expertise and skills relevant to this position, and a research statement describing your past research experience and future goals (1-2 pages). Visa sponsorship is available for non-US nationals. For questions please contact Dr. Gabrielle Rudenko at <https://web.mail.umich.edu/blue/imp/message.php?mailbox=INBOX&index=111546> *rudenko(a)umich.edu* <rudenkolab.application(a)gmail.com>. For more information please visit http://www.lsi.umich.edu/facultyresearch/labs/rudenko. The University of Texas is a non-discriminatory, affirmative action employer. -- Gabrielle Rudenko PhD Life Sciences Institute and the Dept. of Pharmacology University of Michigan Medical School 210 Washtenaw Ave Rm 3163A Ann Arbor, Michigan 48109-2216 734 - 615 9323 rudenko(a)umich.edu www.lsi.umich.edu/facultyresearch/labs/rudenko

1 0

Re: [phenixbb] Appropriate number of reflections for FreeR
by Edward Berry 03 Nov '13

03 Nov '13

Looking at it from the other side- suppose we say for a robust refinement we need a certain number of reflections- say 4 times the number of atoms, maybe less, I don't know. Any more than that is not really going to affect the structure, So if you have high resolution you can afford to use a large percentage of free reflections, and the cross-validation and maximum liklihood will go really well, even with thin shells. On the other hand at low resolution, well, sorry, you really can't spare any reflections for cross-validation. (I have no idea whether this makes sense or not, but it would be another way of looking at it). >>> Mark van Raaij 11/01/13 7:39 PM >>> the limit of 2000 reflections I guess is just because it would be a waste to "throw away" more reflections for refinement, once the statistical minima for calculating a reliable Rfree have been met. I.e. if you have 100.000 reflections, it would be a waste to use 5 or 10% of the reflections instead of just 2%. I'd rather use as many as possible reflections for refinement. On 31 Oct 2013, at 20:21, Pavel Afonine wrote: > Hi Joe, > > flags should be selected such that there is enough of them in each relatively thin resolution shell (thin enough so ML target parameters can be considered constant in each such shell). Lower end is about 50 reflections per shell. All in all this usually translates into about 10% overall. > > Yes, there is a limit parameter set to 2000 by default. I don't know what's the rationale for having it, may be someone can explain. > > Pavel > > On 10/31/13 12:10 PM, Joseph Noel wrote: >> Hi All. I think I have asked this before but forgot. Old age. What is >> the appropriate number / percentage of reflections to flag for a >> statistically appropriate Free-R calculation? If I am correct, the >> reflection file editor in Phenix chooses by default either 10% of the >> measured reflections or 2000 whichever comes first. >> ______________________________________________________________________________________ >> Joseph P. Noel, Ph.D. >> Arthur and Julie Woodrow Chair >> Investigator, Howard Hughes Medical Institute >> Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics >> The Salk Institute for Biological Studies >> 10010 North Torrey Pines Road >> La Jolla, CA 92037 USA >> >> Phone: (858) 453-4100 extension 1442 >> Cell: (858) 349-4700 >> Fax: (858) 597-0855 >> E-mail: noel(a)salk.edu >> >> Publications & Citations: >> http://scholar.google.com/citations?user=xiL1lscAAAAJ >> >> Homepage Salk: http://www.salk.edu/faculty/noel.html >> Homepage HHMI: http://hhmi.org/research/investigators/noel.html >> ______________________________________________________________________________________ >> >> >> >> _______________________________________________ >> 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 _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb

1 0

Appropriate number of reflections for FreeR
by Joseph Noel 03 Nov '13

03 Nov '13

Hi All. I think I have asked this before but forgot. Old age. What is the appropriate number / percentage of reflections to flag for a statistically appropriate Free-R calculation? If I am correct, the reflection file editor in Phenix chooses by default either 10% of the measured reflections or 2000 whichever comes first. ______________________________________________________________________________________ Joseph P. Noel, Ph.D. Arthur and Julie Woodrow Chair Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Publications & Citations: http://scholar.google.com/citations?user=xiL1lscAAAAJ Homepage Salk: http://www.salk.edu/faculty/noel.html Homepage HHMI: http://hhmi.org/research/investigators/noel.html ______________________________________________________________________________________

4 3

Re: [phenixbb] Appropriate number of reflections for FreeR
by Pavel Afonine 02 Nov '13

02 Nov '13

Hi Rongjin, it's not really waste: test reflections are used not only in Rfree calculations, but in ML refinement target parameters estimations, so more test reflections you use better these estimations are, and so better refinement target is. I still believe that 10% is a good number, and any capping the amount of test reflections is NOT necessary: it's not about getting a statistically meaningful amount of them overall, but rather it's about getting the right spread of them across the whole resolution range, and the right amount across all of the thin slices of resolution. I imagine by capping them at a particular number you may end up having a couple of test reflections per certain bin, which isn't great. Pavel On 11/1/13 9:18 PM, Rongjin Guan wrote: > Thank you, Nat and Pavel. I just came back and saw replies from both of > you. Thanks a lot. > I have an impression that free_R set has max 2000 reflections, and more > importantly, each resolution shell has at least > 50 reflections, so I feel >4500 in the free_R set / 150 each shell kind > of luxury ("waste"), and if I have more reflections in the refinement > set, I could have better data/parameters ratio. But this may not make > much difference. > Best, and have a great weekend. > Rongjin > > > On Fri, Nov 1, 2013 at 3:18 PM, Nathaniel Echols <nechols(a)lbl.gov > <mailto:[email protected]>> wrote: > > On Fri, Nov 1, 2013 at 12:13 PM, rjguan <rjguan(a)gmail.com > <mailto:[email protected]>> wrote: > > I solved a structure with 2.7 A Se-Met data set, with 10% > reflections in free_R set. > > Now I have 2.0 A native data set, and extended free_R to 2.0A. > Now I have >4500 reflections > > in free_R set, each resolution shell has >150 reflections. Kind > of too much, right? > > I don't think it's necessarily too much, but it is probably more > than you need. > > > > What is the best way to reduce the number of reflections in the > free_R set, say, to 5%? > > I already built and refined model at 2.7 A, but do not want to > redo autobuild. > > Use the reflection file editor in the GUI - click "More options" in > the section for R-free flags, and check the box "Adjust test set > size to specified fraction". > > > Another question: now I have 2.0A data set, shall I use phases > from 2.7 A data in refinement? > > I compared, without using the phases I got lower R/R_free (about > 1% lower). > > is this because the 2.0 A data is more accurate than the 2.7 A > phases, and I should continue > > to refine at 2.0A without the phases from 2.7 A data? > > It's difficult to reach a conclusion by comparing R-factors alone; > maybe you simply need to run more cycles of refinement with phases > to get the same result. Alternately, if the crystals aren't truly > isomorphous, the phases may be inappropriate for the native > structure. But I think with 2.0Å data and a complete model, it is > perfectly valid to use the amplitudes-only ML refinement target. > > -Nat > >

2 2

Phenix.Rosetta_refine on Ubuntu 12.04 LTS
by Jan Gebauer 31 Oct '13

31 Oct '13

Dear all, I'm trying to get rosetta_refine working on ubuntu 12.04 LTS. This was the (latest) way I tried it: 1) Downloaded phenix-dev-1523 binary & installed it via installer in /usr/local/science/phenix4rosetta/phenix-dev-1523 2) Downloaded rosetta 2031wk42 and extracted it in /usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle 3) Inserted into phenix_env.sh export ROSETTA_BIN=/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/source/bin export PHENIX_ROSETTA_PATH=/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/ export ROSETTA_BIN=/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/database 4) sources phenix_env.sh 5) build the interface via rosetta.build_phenix_interface nproc=4 6) exceute the refinement via phenix.rosetta_refine phasermodel.pdb data.mtz nproc=4 The programm runs fine, up to the point where it should generate models via rosetta, it then stops and crashes. I have attached some logfiles Has anyone managed to run rosetta_refine on Ubuntu? Which phenix and rosetta versions did you use? Ist there anything wrong on my above mentioned build protocol? I'm thankful for any help. Regards, Jan Gebauer -- Dr. Jan Gebauer AG Prof. Baumann Institut für Biochemie / Uni-Köln Otto-Fischer-Str. 12-14 / 50674 Köln Fon: +49 (221) 470 3212 Fax: +49 (221) 470 5066 http://px.uni-koeln.de/

2 1

warning: do not upgrade Mac OS yet!
by Nathaniel Echols 30 Oct '13

30 Oct '13

There is some kind of strange issue with wxPython on the new Mac OS ("Mavericks"), which for at least the 1.8.4 version prevents Phenix application windows (but not the main GUI) from opening. It is also printing out an extraordinary number of warning messages about fonts to the console. I'm hoping there is a simple solution (which seems likely, since 1.8.2 is mostly okay despite using the same version of wxPython), but until we figure out what is causing this, I recommend leaving your Macs unmolested if you want to use the Phenix GUI. Updates to follow if-and-when I fix this. thanks, Nat

5 9

Using phenix_rosetta_refine
by Jan Gebauer 29 Oct '13

29 Oct '13

Dear all, I tried to install phenix.rosetta_refine for a recently solved structure, which only diffracts up to 3.5-4.0 Angstrom (anisotropic). However, I was unable to get the programs correctly set up. I first tried to compile phenix 1.8.4-1496 from source according to this documentation : http://www.phenix-online.org/version_docs/dev-1500/rosetta_refine.htm. The build process failed during GTK2 building, without an obvious explanation (error code 1, no missing libraries ...) I then realised that the developer version are potentially more suitable, as they seem to be prepared for this. I installed the binary from 1523 and tried to start the building process from there with rosetta.build_phenix_interface nproc=X Unfortunatelly Rosetta 3.5 seems to have a different folder structure. There is no main subfolder, instead there are "rosetta_sources", "rosetta_tools" and so one. After a fast "cp rosetta_sources main/source/" it worked a bit but still exited with: scons: *** Error converting option: extras Invalid value(s) for option: python File ..... /setup.py, line 72, in setup_build_options I have the following questions: 1) Am I right to assume that I do NOT have to recompile the dev 1523 (1520 states "Python shared library for linux) on Linux? 2) Which rosetta version do I have to use? Does 3.5 work? There is no 3.6 on rosettacommons... (or is it hidden?) Regards, Jan -- Dr. Jan Gebauer AG Prof. Baumann Institut für Biochemie / Uni-Köln Otto-Fischer-Str. 12-14 / 50674 Köln Fon: +49 (221) 470 3212 Fax: +49 (221) 470 5066 http://px.uni-koeln.de/

2 2

Need help with atom selection for anisotropic refinement
by Dr. Mark Mayer 27 Oct '13

27 Oct '13

Hi, I'm trying to do a mixed individual isotropic anisotropic refinement b factor refinement and can't get my atom selections to be accepted by phenix.refine. For the atoms I want to do isotropic refinement I used optional (element H or element D or resname HOH or chain E or chain F or chain A or chain B) for the anisotropic selection I used chain A and chain B and not (element H or element D or resname HOH or chain E or chain F or chain A resseq 5:11 or chain A resseq 66:72 or chain A resseq 117:138 or chain A resseq 152:184 or chain A resseq 196:210 or chain A resseq 249:251 or chain B resseq 3:6 or chain B resseq 66:72 or chain B resseq 166:210 or chain B resseq 249:251) I've tried various combuinations, but so far all have given the error message: Selection string results in empty selection. Thanks for your help Mark --

2 1

Alternative Conformation, Restraints
by Moritz Machelett 27 Oct '13

27 Oct '13

Hello everyone, I am in the final rounds of refining my protein at high resolution and currently trying to model an alternative conformation of a Chl /a/-phytol chain. I inserted a second phytol chain with coot - worked out well so far (alternate chain identifiers A and B for both phytol chains). After using phenix.refine, however, the occupancy of the second phytol chain was refined to 0. When splitting the whole Chl molecule the occupancy refines to sensible values (0.34 and 0.66). We would prefer to only model the phytol chain in alternate conformation as the macrocycle superpose perfectly. Any suggestions regarding the occupancy problem? Another issue concerns restraints. We tried to turn of specific nonbonded restraints and found a phenixbb message from 2007: http://www.phenix-online.org/pipermail/phenixbb/2007-September/011734.html Are there any news/updates on this matter? Any help appreciated! Thanks, Moritz -- Moritz M. Machelett Ruhr University Bochum Protein Crystallography, Department of Biophysics, ND04/396 44780 Bochum Tel: +49-(0)234/32-25754

2 1

fem map
by nih\mayerm 27 Oct '13

27 Oct '13

Hi, I'm trying to make a fem amp using phenix-1.8.4-1496 using my refined structure and mtz with map coefficients as input: phenix.development.fem 3222_Glu_refine_78.mtz 3222_Glu_refine_78.pdb coot 0.7.0-1 fails to generate a map when fem.mtz is opened, either in auto or manual mode mtzdmp for fem.mtz gives: Col Sort Min Max Num % Mean Mean Resolution Type Column num order Missing complete abs. Low High label 1 NONE -37 35 0 100.00 -5.0 14.2 61.69 1.21 H H 2 NONE 0 101 0 100.00 38.0 38.0 61.69 1.21 H K 3 NONE 0 44 0 100.00 16.8 16.8 61.69 1.21 H L 4 NONE 0.0 1796.7 25825 84.81 84.67 84.67 31.87 1.21 F 2mFoDFc 5 NONE -180.0 180.0 25825 84.81 1.07 90.28 31.87 1.21 P PHI2mFoDFc 6 NONE 0.0 2750.2 0 100.00 144.76 144.76 61.69 1.21 F 2mFoDFc_FilSharp 7 NONE -180.0 180.0 0 100.00 1.26 90.34 61.69 1.21 P PHI2mFoDFc_FilSharp 8 NONE 0.2 24426.8 0 100.00 235.27 235.27 61.69 1.21 F KICK 9 NONE -180.0 180.0 0 100.00 0.02 89.63 61.69 1.21 P PHIKICK 10 NONE 0.2 9283.0 0 100.00 132.01 132.01 61.69 1.21 F FEM 11 NONE -180.0 180.0 0 100.00 0.23 90.34 61.69 1.21 P PHIFEM

3 2

Using experimental phases in refinement
by Joseph Noel 26 Oct '13

26 Oct '13

Hi Folks, I am wondering if anyone can recommend some good reference(s) of structure refinements that employed experimental phases. We are attempting to collect experimental phases for a series of structures for which we have refined the structure already. I assume we can easily use initial model phases (space group doesn't change) to locate anomalous scatters and calculate experimental phases from the elucidation of the heavy atom arrangement. Most of the structures range from 1.7 to 2.4 A resolution. Would also appreciate any advice on the most efficient and accurate set of steps to accomplish this. If anyone thinks that this will not add much to the refinement of these structures would also appreciate some critiques. The protein in question crystallizes with 68% solvent content and one monomer per assymetric unit. We are employing ensemble refinement as the protein in question displays local conformational changes depending on the type of ligand(s) bound and also pH and similar but distinct crystallization conditions. We are carrying this out on ~400 mutants to do a very large scale comparison. Sorry for the long email but since we want to try and understand even minor conformational changes I thought phased-refinement would be much more powerful then refining just against the Fs. Thanks again in advance, Joe ______________________________________________________________________________________ Joseph P. Noel, Ph.D. Arthur and Julie Woodrow Chair Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Publications & Citations: http://scholar.google.com/citations?user=xiL1lscAAAAJ Homepage Salk: http://www.salk.edu/faculty/noel.html Homepage HHMI: http://hhmi.org/research/investigators/noel.html ______________________________________________________________________________________

2 1

protein-ligand complex structure
by Wei Shi 25 Oct '13

25 Oct '13

Hi all, I am working on a structure of protein-ligand complex. Four ligands are placed for the dimer protein and the density for the two ligands of the first monomer is better than the density for the other two ligands of the second monomer. Ligand is moved to fit density better in Coot (and for two ligands of the first monomer, they fits the density almost perfectly), but after a refinement in phenix (default settings + NCS restraints + Secondary structural restraints + Optimize X-ray/stereochemistry weight +Optimize X-ray/ADP weight), some part of the ligand which fits density good before moved out of the density again...Besides, it always shows green density in Coot for the ligand region even in places where the ligand is in density... Any suggestions or ideas about how to fit the ligand better and why the density for ligands of the second monomer is worse than that for the first monomer and why the ligands would move out of density after refinement? Is it because the protein model is not good enough to get the ligand density good? There is a conformational change upon ligand binding, and I rebuilt some part of the protein manually, and the density for a region of about 30 residues is not very good, and I tried to mutate those to alanies and refine, but it didn't help me see the density better... Any suggestions or ideas on how to improve this protein-complex structural model? Thank you so much! The statistics for the current best model is as follows, and the resolution of the dataset is 2.8Å. start final ------------------------------ ---------------- R-work: 0.3359 0.2993 R-free: 0.3619 0.3558 RMS(angles): 1.03 1.55 RMS(bonds): 0.006 0.007 MolProbity validation Ramachandran outliers: 4.7% (Goal: < 0.2%) Ramachandran favored: 85.3% (Goal: > 98%) Rotamer outliers: 4.5% (Goal: 1%) C-beta outliers: 0 (Goal: 0) Clashscore: 7.43 Overall score: 2.56 Thank you so much! Best, Wei

5 6

Diffraction pattern from structure factors
by Bala Venkatakrishnan 25 Oct '13

25 Oct '13

Hi Are there programs available to generate a diffraction pattern from structure factors? Purely for learning purposes. -- Bala -- Balasubramanian Venkatakrishnan, Ph.D. Post-doctoral Fellow Molecular and Cellular Biochemistry Dept. 212 S Hawthorne Dr Simon Hall Room 213 Bloomington, IN 47405-7003 Indiana University Tel.:(812) 856-1874

2 1

DEN refinement using CC instead of Rfree
by Morten Grøftehauge 25 Oct '13

25 Oct '13

Hi guys, Is there any way to do a DEN refinement run where it looks for the best map-model CC instead of the best Rfree? Even more useful would be map-model CC of selected residues... Or can I run DEN refinement on only part of the structure? That should in theory be faster. And since the Rfree values for the correct parts of the structure would be then fixed then I should get rid of the problem of Phenix selecting the refinement weights that result in the structure most like the input structure. Does that make sense? Cheers, Morten -- Morten K Grøftehauge, PhD Pohl Group Durham University

3 3

job numbers
by SD Y 24 Oct '13

24 Oct '13

Hi, I am using latest version of Phenix. Since last week, I noticed that that two jobs having same number (not always). So, I cant open the recent job in GUI, though I could see results in folder. Is there any fix for this? ThanksSDY

2 1

autobuild mistake
by Heather L Condurso 23 Oct '13

23 Oct '13

So I was running autobuild on the command line with: phenix.autobuild data=data.mtz model=model.pdb rebuild_in_place=False acceptable_r=0.2 I have a model from another data set that is missing some loops and new data sets which I would like to use autobuild to see if the model can be extended. I am using 1.8.4-1496 on a mac with osx 10.6.8. I was an idiot and when looking in the directory to check out one of the RUN_FILE_#.log files, I accidentally clicked on the RUN_FILE executable which started another AutoBuild subprocess. Since then all the other subprocesses had finished, but overall run stalled at: Splitting work into 4 jobs and running with 1 processors using sh background=False in ./AutoBuild_run_6_/TEMP0 Final job will be run with sh with background=True Starting job 1...Log will be: ./AutoBuild_run_6_/TEMP0/RUN_FILE_8.log Starting job 2...Log will be: ./AutoBuild_run_6_/TEMP0/RUN_FILE_9.log Starting job 3...Log will be: ./AutoBuild_run_6_/TEMP0/RUN_FILE_10.log Starting job 4...Log will be: ./AutoBuild_run_6_/TEMP0/RUN_FILE_11.log And the combine and extend didn't happen. I saw a post about combining models from autobuild but it was for rebuild_in_place=True and the post mentioned that the models needed to have identical sequences for it to work. Is there a way to save my mistake without starting over? The run I had restarted had yielded Rs=999.9 so If there is a way to maybe combine just 3 of the 4 that may be helpful as well. Thanks, Heather Condurso condurso(a)bc.edu

2 1

No working nightlies since 1.8.4-1496?
by Ben Eisenbraun 23 Oct '13

23 Oct '13

Hi All, I don't see any nightlies listed since then, and trolling the build pages, it looks like things are in a state of flux right now with quite a few broken builds. I don't actually care about the nightlies per se; I have a user that wants to try PHENIX with Rosetta refinement, and per an older thread, we need a Rosetta nightly release for that to work. Do we also need a PHENIX nightly? Or should 1.8.4 work for this purpose? Thanks. -ben -- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |

2 1

Postdoctoral Position in Protein Biochemistry / X-ray Crystallography (funded by Cancer Research UK) at ICR
by Sebastian Guettler 22 Oct '13

22 Oct '13

Dear PHENIX Community, We are currently looking for a postdoctoral fellow to join our research programme on the regulation and functions of ADP-ribosyltransferases. Please see the job description for the position and instructions on how to apply below. Best wishes, Sebastian Post-doctoral Training Fellow: Protein Biochemistry / X-ray Crystallography (funded by Cancer Research UK) We seek to appoint a Post-doctoral Training Fellow to a new team led by Dr Sebastian Guettler in the Divisions of Structural and Cancer Biology. The post is funded by Cancer Research UK. The successful applicant will undertake biochemical, crystallographic and functional studies on members of the ADP-ribosyltransferase (or “PARP”) family of proteins and their regulators. Our goal is to gain insight into the control and cellular roles of these enzymes with a specific interest in ADP-ribosyltransferase-dependent signalling processes linked to cancer. Applicants should possess a PhD (or equivalent) in biochemistry or molecular biology. Experience with recombinant DNA techniques, high-quality protein expression and purification, protein characterisation (such as protein-protein interaction analyses and enzymology) as well as protein crystallography is essential. Experience in protein production in insect cells would be of advantage. Appointment will be on a Fixed Term Contract for 3 years in the first instance, with a starting salary in the range of £28,425 to £34,944 p.a. inclusive (based on previous post-doctoral experience). For further details and instructions on how to apply, please refer to our online vacancy and recruitment site at http://www.icr.ac.uk/jobsearch, quoting job reference number 1376940 for this position. Closing date: 22nd November 2013 While applications need to be placed via our online system, informal inquiries can be sent to Dr Sebastian Guettler at sebastian.guettler(a)icr.ac.uk<mailto:[email protected]>. Research in the Divisions of Structural and Cancer Biology focuses on the functional, biochemical, and structural characterisation of cellular processes relevant to cancer and cancer therapy. The Division of Structural Biology has managed facilities for protein crystallography (crystallisation robots, Bruker Microstar and CCD detector), cryo-electron microscopy (FEI Tecnai F20 and T12), and protein production with expertise in multi-subunit expression (insect cell, yeast and bacterial expression, including a 60-litre fermentor). The Division is also well equipped with instrumentation for biophysical analysis (e.g. ITC, fluorescence, multi-angle light scattering). The Division of Cancer Biology provides a state-of-the-art infrastructure for mammalian cell culture, imaging, mammalian genetics, chemical biology and proteomics. The Institute of Cancer Research (ICR) is one of the world’s most influential cancer research institutes. Our mission is to make the discoveries that defeat cancer. We have a long and distinguished history of research with a major impact on the outcome for cancer patients. Our unique partnership with The Royal Marsden NHS Foundation Trust (RMH) makes us the largest comprehensive cancer centre in Europe, performing high quality original basic research and translational studies. Under the leadership of Chief Executive Professor Alan Ashworth FRS, we are committed to attracting, developing and retaining the best minds in the world. The ICR was ranked as the UK’s top academic research centre in the 2008 Higher Education Funding Council Research Assessment Exercise. Based on our publication record, citations and impact we rank among the world’s leading cancer research centres. Sebastian Guettler, PhD | Team Leader The Institute of Cancer Research | 237 Fulham Road | London | SW3 6JB | United Kingdom Lab: room 6S8 | Office: room 6S23.2 T (office) +44-(0)20-7153-5122 | T (lab) x5180 | Fax x5457 | E sebastian.guettler(a)icr.ac.uk<mailto:[email protected]> W http://www.icr.ac.uk/research/team_leaders/Guettler_Sebastian/index.shtml<http://www.icr.ac.uk/> | Twitter @ICRnews<https://twitter.com/ICRnews> Making the discoveries that defeat cancer [cid:[email protected]] The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.

1 0

Autobuild error
by Nora Cronin 21 Oct '13

21 Oct '13

Whilst running Autobuild SA omit map using 40 segments one OMIT region fail and the program quits. Error as follow: Can you help? Summary of output files for Solution 1 from rebuild cycle 2 --- Model (PDB file) --- pdb_file: /local/ncronin/phenix/APC4/Autobuild_20131018/AutoBuild_run_2_/TEMP0/AutoBuild_run_5_/overall_best.pdb --- Data for refinement FP SIGFP PHIM FOMM HLAM HLBM HLCM HLDM FreeR_flag --- refine_data: /local/ncronin/phenix/APC4/Autobuild_20131018/AutoBuild_run_2_/TEMP0/AutoBuild_run_5_/overall_best_refine_data.mtz AutoBuild_build_cycle AutoBuild Run 5 Fri Oct 18 13:30:32 2013 Ending these rebuild cycles as the limit is reached All done with build cycles in this region AutoBuild_set_up_build AutoBuild Run 5 Fri Oct 18 13:30:32 2013 Traceback (most recent call last): File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/autosol/AutoBaseExtend.py", line 989, in DoNextMethod self.CarryOutBest() # to be obtained after it is finished File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/autosol/AutoBaseExtend.py", line 2146, in CarryOutBest getattr(self,str(self.application_method))() # call this fn File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/wizards/AutoBuild.py", line 1832, in AutoBuild_set_up_build self.AutoBuild_finish_current_region() File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/wizards/AutoBuild.py", line 1909, in AutoBuild_finish_current_region self.AutoBuild_update_ncs() File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/wizards/AutoBuild.py", line 5567, in AutoBuild_update_ncs ],quiet=True,out=f) File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/command_line/find_ncs.py", line 324, in __init__ self.read_ncs_as_file(params,out=out) File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/command_line/find_ncs.py", line 511, in read_ncs_as_file quiet=self.quiet,log=null_out()) File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/command_line/simple_ncs_from_pdb.py", line 546, in __init__ starting_residue_numbers) File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/command_line/simple_ncs_from_pdb.py", line 1326, in find_invariant_groups minimum_size=min_size) File "/common/app/phenix/phenix-1.8.4-1496/cctbx_project/mmtbx/invariant_domain.py", line 35, in __init__ minimum_size=minimum_size) File "/common/app/phenix/phenix-1.8.4-1496/cctbx_project/mmtbx/invariant_domain.py", line 70, in process size, index = self.find_largest( matches, used ) File "/common/app/phenix/phenix-1.8.4-1496/cctbx_project/mmtbx/invariant_domain.py", line 168, in find_largest max_size = flex.max( sizes ) RuntimeError: unidentifiable C++ exception Traceback (most recent call last): File "/common/app/phenix/phenix-1.8.4-1496/build/mac-intel-osx-x86_64/../../phenix/phenix/command_line/autobuild.py", line 230, in <module> run_autobuild=run_autobuild(args=sys.argv[1:]) File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/autosol/wizard_command_line.py", line 564, in __init__ self.RunWizard() File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/autosol/wizard_command_line.py", line 1000, in RunWizard self.runWizard.run() File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/autosol/wizard_command_line.py", line 137, in run self.Wizard.Run(info='script') File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/autosol/AutoBaseExtend.py", line 838, in Run self.DoNextMethod() File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/autosol/AutoBaseExtend.py", line 1003, in DoNextMethod raise AssertionError, line AssertionError: Traceback (most recent call last): File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/autosol/AutoBaseExtend.py", line 989, in DoNextMethod self.CarryOutBest() # to be obtained after it is finished File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/autosol/AutoBaseExtend.py", line 2146, in CarryOutBest getattr(self,str(self.application_method))() # call this fn File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/wizards/AutoBuild.py", line 1832, in AutoBuild_set_up_build self.AutoBuild_finish_current_region() File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/wizards/AutoBuild.py", line 1909, in AutoBuild_finish_current_region self.AutoBuild_update_ncs() File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/wizards/AutoBuild.py", line 5567, in AutoBuild_update_ncs ],quiet=True,out=f) File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/command_line/find_ncs.py", line 324, in __init__ self.read_ncs_as_file(params,out=out) File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/command_line/find_ncs.py", line 511, in read_ncs_as_file quiet=self.quiet,log=null_out()) File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/command_line/simple_ncs_from_pdb.py", line 546, in __init__ starting_residue_numbers) File "/common/app/phenix/phenix-1.8.4-1496/phenix/phenix/command_line/simple_ncs_from_pdb.py", line 1326, in find_invariant_groups minimum_size=min_size) File "/common/app/phenix/phenix-1.8.4-1496/cctbx_project/mmtbx/invariant_domain.py", line 35, in __init__ minimum_size=minimum_size) File "/common/app/phenix/phenix-1.8.4-1496/cctbx_project/mmtbx/invariant_domain.py", line 70, in process size, index = self.find_largest( matches, used ) File "/common/app/phenix/phenix-1.8.4-1496/cctbx_project/mmtbx/invariant_domain.py", line 168, in find_largest max_size = flex.max( sizes ) RuntimeError: unidentifiable C++ exception Best regards Nora Dr N B Cronin X-Ray Laboratory Manager Tel. (+44) 020 7153 5445 Section of Structural Biology Fax. (+44) 020 7153 5456 Chester Beatty Laboratories mobile: (+44) 07787554059 The Institute of Cancer Research 237 Fulham Road London SW3 6JB The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.

3 2

anisotropic refinement based on B values
by Yarrow Madrona 20 Oct '13

20 Oct '13

I'm sure that this has probably already been covered but I am having some problem finding out how to tell phenix to make a decision whether to refine isotropically or anisotropically based on B factor values. Is this something you can do with a python script? Thanks. -Yarrow -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

3 2

Re: [phenixbb] increasing NCS restraints
by Mark van Raaij 17 Oct '13

17 Oct '13

Oops, 1 vote for making phenixbb default reply to sender only.... Mark van Raaij <mjvanraaij(a)cnb.csic.es> wrote: >Dont worry about it, we are alli diots...even without commuting 4 hrs a day > >Yarrow Madrona <amadrona(a)uci.edu> wrote: > >>Hi Dale, >> >>That is right! And that is what I concluded yesterday yet I somehow forgot >>all that overnight. Starting a new job and commuting 4 hours a day has >>taken a toll on my brain. I am an idiot. >> >>-Yarrow >> >>> >>> I'm puzzled. Didn't you say that the translation of your ncs >>> two-fold was not equal to half the "a" cell edge? If it is not >>> a translation of 1/2 (in fractional coordinates) then it cannot >>> be a crystallographic symmetry element and your space group cannot >>> be P212121. Unless this condition is met, the similarity of your >>> molecules is unimportant. >>> >>> Dale Tronrud >>> >>> On 10/17/2013 12:48 PM, Yarrow Madrona wrote: >>>> I am doing restrained NCS refinement and would like to know how to set >>>> the >>>> target weight of the cartesian restraint in the command line? I also >>>> found >>>> a sigma value in the GUI. I read that I can decrease it in order to >>>> increase the NCS restraints. However, I have seen this under Torsional >>>> restraints. Does this also apply to cartesian restraints? >>>> >>>> I am doing this so that I can look at the differences in position and >>>> B-factors of two molecules in the ASU that I am trying to determine are >>>> related by a perfect or imperfect 2(1) screw axis. (I posted a question >>>> about this on the CCP4 bullitan board.) If the values between molecules >>>> are exactly the same then presumably the space group is actually P212121 >>>> with 1molecule in the asu instead of P21 with two molecules. I already >>>> know that the P21 dimer superimposes almost exactly on the P212121 >>>> monomer >>>> and it's symmetry mate. I just don't know how "perfectly" they align and >>>> I >>>> am hoping this approach will tell me. I hope this makes some sense. >>>> >>>> -Yarrow >>>> >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://phenix-online.org/mailman/listinfo/phenixbb >>> >>> >> >> >>-- >>Yarrow Madrona >> >>Graduate Student >>Molecular Biology and Biochemistry Dept. >>University of California, Irvine >>Natural Sciences I, Rm 2403 >>Irvine, CA 92697 >> >> >> >>_______________________________________________ >>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

1 0

Re: [phenixbb] increasing NCS restraints
by Mark van Raaij 17 Oct '13

17 Oct '13

Dont worry about it, we are alli diots...even without commuting 4 hrs a day Yarrow Madrona <amadrona(a)uci.edu> wrote: >Hi Dale, > >That is right! And that is what I concluded yesterday yet I somehow forgot >all that overnight. Starting a new job and commuting 4 hours a day has >taken a toll on my brain. I am an idiot. > >-Yarrow > >> >> I'm puzzled. Didn't you say that the translation of your ncs >> two-fold was not equal to half the "a" cell edge? If it is not >> a translation of 1/2 (in fractional coordinates) then it cannot >> be a crystallographic symmetry element and your space group cannot >> be P212121. Unless this condition is met, the similarity of your >> molecules is unimportant. >> >> Dale Tronrud >> >> On 10/17/2013 12:48 PM, Yarrow Madrona wrote: >>> I am doing restrained NCS refinement and would like to know how to set >>> the >>> target weight of the cartesian restraint in the command line? I also >>> found >>> a sigma value in the GUI. I read that I can decrease it in order to >>> increase the NCS restraints. However, I have seen this under Torsional >>> restraints. Does this also apply to cartesian restraints? >>> >>> I am doing this so that I can look at the differences in position and >>> B-factors of two molecules in the ASU that I am trying to determine are >>> related by a perfect or imperfect 2(1) screw axis. (I posted a question >>> about this on the CCP4 bullitan board.) If the values between molecules >>> are exactly the same then presumably the space group is actually P212121 >>> with 1molecule in the asu instead of P21 with two molecules. I already >>> know that the P21 dimer superimposes almost exactly on the P212121 >>> monomer >>> and it's symmetry mate. I just don't know how "perfectly" they align and >>> I >>> am hoping this approach will tell me. I hope this makes some sense. >>> >>> -Yarrow >>> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> >> > > >-- >Yarrow Madrona > >Graduate Student >Molecular Biology and Biochemistry Dept. >University of California, Irvine >Natural Sciences I, Rm 2403 >Irvine, CA 92697 > > > >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://phenix-online.org/mailman/listinfo/phenixbb

1 0

increasing NCS restraints
by Yarrow Madrona 17 Oct '13

17 Oct '13

I am doing restrained NCS refinement and would like to know how to set the target weight of the cartesian restraint in the command line? I also found a sigma value in the GUI. I read that I can decrease it in order to increase the NCS restraints. However, I have seen this under Torsional restraints. Does this also apply to cartesian restraints? I am doing this so that I can look at the differences in position and B-factors of two molecules in the ASU that I am trying to determine are related by a perfect or imperfect 2(1) screw axis. (I posted a question about this on the CCP4 bullitan board.) If the values between molecules are exactly the same then presumably the space group is actually P212121 with 1molecule in the asu instead of P21 with two molecules. I already know that the P21 dimer superimposes almost exactly on the P212121 monomer and it's symmetry mate. I just don't know how "perfectly" they align and I am hoping this approach will tell me. I hope this makes some sense. -Yarrow -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

2 2