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FW: phenixbb Digest, Vol 87, Issue 3
by Phoebe A. Rice 10 Feb '13

10 Feb '13

Hi, Although its theoretically possible, I've never had 5-Br-dU cause a problem. My approach would be to pick the strand with more T's and get every T replaced with 5-Br-dU, unless the 3' nt is a T (you pay a lot more for 3' modifications). We have had issues where crystals wouldn't grow with a heavily 5-I-dU modified DNA, presumably because Iodine is significantly bigger than a the 5-methyl of T, and it annoys the protein. If you've got good footprinting data, you may be able to guess where the protein will "care" about the surface of the major groove, and avoid putting iodines in those regions. If not, its probably faster to just order several oligos and try them all. If you've got a lot of T's and are worried about locating all those heavy atoms, I'd go for one derivative with a couple of paired 5-I-dU's (in spots where you have two T's in a row) in hopes that that will give you a toehold on solving the Patterson, and then a 2nd where every T on one strand is brominated, which may provide more phasing power. Note that both of these pop off in the x-ray beam, so collect your anomalous data first and fast. Also note that if you're lucky, you can get an extra large delta f' by subtracting the last data set from the first ("radiation induced phasing"). Hope that helps! Phoebe ++++++++++++++++++++++++++++++++++++++++++ Phoebe A. Rice Dept. of Biochemistry & Molecular Biology The University of Chicago 773 834 1723; PRice(a)uchicago.edu http://bmb.bsd.uchicago.edu/Faculty_and_Research/ http://www.rsc.org/shop/books/2008/9780854042722.asp

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CeBEM-CCP4 Macromolecular Crystallography Workshop 2013 at Montevideo: Application deadline extended
by Alejandro Buschiazzo 08 Feb '13

08 Feb '13

Dear Colleagues, Due to the application deadline originally scheduled for February 10, overlapping with Summer holiday dates in several South American countries, we have decided to extend the course application deadline UNTIL FEBRUARY 17, 2013. We invite all of you interested in this workshop, especially the ones that have contacted us, to take advantage of this opportunity and send your application forms (plus CV and letter of your supervisor): last days for applications open!! Find all details about the workshop and application form in www.pasteur.edu.uy/mx2013 <http://www.pasteur.edu.uy/mx2013>- for further inquiries and applications contact mx2013(a)pasteur.edu.uy <mailto:[email protected]>! *Second Macromolecular Crystallography School 2013 *at the Institut Pasteur de Montevideo (Uruguay). *Title:* "Macromolecular Crystallography School 2013: From data processing to structure refinement and beyond" *Dates:*April 9th-17th, 2013. *Site:*Institut Pasteur de Montevideo (Montevideo), Uruguay *The workshop content:* Conceived to provide theoretical background and hands-on abilities in the use of computational tools to exploit X ray diffraction data. Through lectures, tutorials and hands-on trouble-shooting, the students will be trained in state-of-the-art macromolecular crystallography. Particular emphasis will be given to data processing, phasing/structure determination and model refinement/validation. The workshop will feature authors and experts of many modern crystallographic software packages. This workshop represents the continuation within the series started in 2010 (http://www.pasteur.edu.uy/mxcourse) on Macromolecular Crystallography. In this opportunity it is being co-organized by the Center for Structural Biology of the Mercosur CeBEM (www.cebem.org.ar <http://www.cebem.org.ar>), jointly with the Collaborative Computational Project Number 4 (CCP4 -- UK www.ccp4.ac.uk <http://www.ccp4.ac.uk>). Support from the Institut Pasteur International Network, the International Union of Crystallography and Institut Pasteur de Montevideo is also greatly acknowledged. *Applicants:* Graduate students, postdoctoral researchers and young scientists are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets so they can be used during the workshop's hands-on sessions. There is no registration fee. Support for accommodation, per diem and local transportation will be provided to all participants from abroad. Support to cover travel expenses will be considered on a case-by-case basis. Specific requests should be well-grounded as we will only be able to select a limited number. *Application:* Application *deadline has now been extended until February 17, 2013*. Application form, the program, contact info and other details can be found at www.pasteur.edu.uy/mx2013 <http://www.pasteur.edu.uy/mx2013> Please address further inquiries to mx2013(a)pasteur.edu.uy <mailto:[email protected]> Ronan Keegan and Alejandro Buschiazzo -- Alejandro Buschiazzo, PhD Research Scientist Unit of Protein Crystallography Institut Pasteur de Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +598 25220910 int. 120 Fax: +598 25224185 http://www.pasteur.edu.uy/pxf

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phaser for long thin molecule
by Ursula Schulze-Gahmen 08 Feb '13

08 Feb '13

I am doing molecular replacment for a very elongated molecule in phaser. I would like to try different values for the maximum patterson cutoff but I am not sure which parameter I need to change in the phenix version of phaser. Does somebody have experience with this? Thanks Ursula -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220

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How to model domain-wide disorder in Phenix.refine (turn off bump interactions) ?
by Phil Jeffrey 08 Feb '13

08 Feb '13

Hi, I've got a pernicious problem where the electron density for one domain appears to extensively interpenetrate another similar domain. I'm in the process of trying to work out things like: MR solution in the wrong space group courtesy of pseudo-centering. In the meanwhile I want to model it as interpenetrating domains, and need to turn off VdeW bumps at the domain (chain) level of structure. I can't just model it as a infinite list of alternate locations. I (think) I remember how to do this in CNS (constraints interaction), but is there a way to do this in phenix ? I could not track down a particularly promising section of either the manual or the .def/eff file(s). Thanks Phil Jeffrey Princeton

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Designing heavy atom positions on my DNA crystal
by Xiang Li 07 Feb '13

07 Feb '13

Hi everyone, I am trying to grow my DNA crystal with bromide derivatives. The content in one asymmetric unit is a 30 bp DNA duplex. I am considering about how many bromides modified bases should I use to ensurethe strong enough heavy atom signal. Also where to put these bromides? To my understanding, maybe I should put the heavy atoms at the most rigid places, avoiding the clashes and not too close to other heavy atoms. I have few experience on this and hope you could give me some help on the design. Thanks a lot! Sincerely, Xiang

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Phaser annoyance
by Morten Groftehauge 05 Feb '13

05 Feb '13

Hi guys, The pop-up warning from Phaser about lack of eLLG for the resolution of the data would be more informative if you added the value of eLLG so one wouldn't have to scroll back in the log to find it. It would also allow the user to see with a glance whether the warning is because eLLG is under 120 or under 60. And it seems like the 'non-simple' Phaser GUI is broken in 1.8.2-1288. At least I haven't been able to open it, neither from the main window or by opening a previous job (Ubuntu 10.04). Cheers, Morten -- Morten K Grøftehauge, PhD Pohl Group Durham University

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AUTOBUILD: sequence file for multiple chains
by Gino Cingolani 03 Feb '13

03 Feb '13

Hi All, my model contains multiple chains and I would like Autobuild to build them all. What is the correct way to give multiple sequences (in FASTA format) to Autobuild? In my 'seq.dat' file, shall I leave one (or two) spaces in between one sequence and the other? Thanks, Gino ****************************************************************************** Gino Cingolani, Ph.D. Associate Professor Thomas Jefferson University Dept. of Biochemistry & Molecular Biology 233 South 10th Street - Room 826 Philadelphia PA 19107 Office (215) 503 4573 Lab (215) 503 4595 Fax (215) 923 2117 E-mail: gino.cingolani(a)jefferson.edu Website: http://www.cingolanilab.org ****************************************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e canoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120) ________________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of Terwilliger, Thomas C [terwilliger(a)lanl.gov] Sent: Saturday, February 02, 2013 9:55 PM To: PHENIX user mailing list Subject: Re: [phenixbb] autosol MIR with more than one native? Hi Ed, Unfortunately, autosol only has a way to deal with one native, so you'd need to average them together or run 2 runs, one with each. All the best, Tom T ________________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of Edward A. Berry [BerryE(a)upstate.edu] Sent: Saturday, February 02, 2013 10:39 AM To: PHENIX user mailing list Subject: [phenixbb] autosol MIR with more than one native? Is it possible to run phenix.autosol MIR problem with two "native" datasets? And does this make sense, or would it be better to scale the two natives together to make a single dataset before running autosol? eab _______________________________________________ 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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autosol MIR with more than one native?
by Edward A. Berry 03 Feb '13

03 Feb '13

Is it possible to run phenix.autosol MIR problem with two "native" datasets? And does this make sense, or would it be better to scale the two natives together to make a single dataset before running autosol? eab

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Re: [phenixbb] Problem getting Phenix and Rosetta working together
by Nathaniel Echols 01 Feb '13

01 Feb '13

---------- Forwarded message ---------- From: Dale Tronrud <dale(a)daletronrud.com> To: phenixbb(a)phenix-online.org Cc: Date: Fri, 01 Feb 2013 08:24:53 -0800 Subject: Re: [phenixbb] Problem getting Phenix and Rosetta working together Hi Tom, I was right! The source of the problem was in the stupid/silly category. I had left the "export" out. I didn't notice the problem since my test scripts didn't include the "-f" option, like yours, so they were reading the init scripts every time. Thanks for pointing me to your scripts so I could figure this out. Dale Tronrud On 1/31/2013 2:11 PM, Terwilliger, Thomas C wrote: > > Hi Dale, > > I think the check that is giving you the error is: > > if (! $?PHENIX_ROSETTA_PATH) then > echo "Skipping phenix rosetta tests: rosetta build not available." > goto skip > > This is located in > > $PHENIX/phenix-dev-1117/phenix_regression/wizards/test_command_line_rosetta_quick.csh > > I'm puzzled how that can give you the error message you are getting unless the environment is different in the script you are running from your shell, but maybe now with the location of this file you can track it down? > > All the best, > Tom T > > > On Jan 31, 2013, at 3:01 PM, Dale Tronrud wrote: > >> Hi, >> >> I would like to get mr_rosetta running on my CentOS 6.3 64 bit >> computer but I can't seem to get them connected. I'm probably >> doing something stupid/silly but I'm stumped. >> >> I've downloaded, installed and compiled rosetta3.4 in the folder >> /usr/local/rosetta3.4. There are a bunch of files in rosetta_source/bin >> and they are executable. However, typing the following commands >> shows my problem. >> >> [dale@athena tln]$ echo $PHENIX_ROSETTA_PATH >> /usr/local/rosetta3.4 >> [dale@athena tln]$ ls -l $PHENIX_ROSETTA_PATH >> total 156 >> drwxr-xr-x. 10 root root 4096 Mar 20 2012 Antibody >> drwxr-xr-x. 3 root root 4096 Jul 26 2011 foldit-3.4 >> -rw-r--r--. 1 root root 1115 Mar 25 2012 new_apps.note >> drwxr-xr-x. 25 root root 4096 Mar 20 2012 protocol_capture >> -rw-r--r--. 1 root root 460 Mar 25 2012 README.Copyrights >> -rw-r--r--. 1 root root 12 Mar 25 2012 README.version >> -rw-r--r--. 1 root root 3345 Mar 25 2012 release.note >> drwxr-xr-x. 19 root root 106496 Mar 25 2012 rosetta3.4_user_guide >> drwxr-xr-x. 9 root root 4096 Mar 25 2012 rosetta_database >> drwxr-xr-x. 61 root root 4096 Mar 20 2012 rosetta_demos >> drwxr-xr-x. 11 root root 4096 Jan 30 15:27 rosetta_source >> drwxr-xr-x. 7 root root 4096 Mar 27 2012 rosetta_tests >> drwxr-xr-x. 13 root root 4096 Mar 20 2012 rosetta_tools >> [dale@athena tln]$ phenix_regression.wizards.test_command_line_rosetta_quick >> Skipping phenix rosetta tests: rosetta build not available. >> >> I can try "mr_rosetta" itself but it just tells me that I need to >> set PHENIX_ROSETTA_PATH. >> >> What, in particular, is Phenix looking for to determine that >> Rosetta is installed? >> >> Dale Tronrud >> _______________________________________________ >> 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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MR: Apply rotation and translation to structure factors
by Shweta Kailasan 01 Feb '13

01 Feb '13

Hello, I am trying to use a cryo-EM map as a MR model for an Xtal data set. I have calculated structure factors for my map using SFALL. And also used rotcross and trans.com (from AMORE) to determine best possible rotation and translation solutions. Is there is a program/script available that can be used to apply those rotations and translation to structure factors ? Most programs start with a coordinate file (pdb) as a model whereas my initial model is a map. I tried to use Phaser but it didnot work out. Any help would be highly appreciated. Thank you. -S <peter.ramsumair(a)credit-suisse.com>

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