- phenixbb - phenix-online.org

HETATM automated chain assignment
by Talon Romain 15 Feb '13

15 Feb '13

Hello to the Phenix bulletin board community, I would like to know if I could find a tool to automatically assign HETATM atom (or even, water molecules) to the nearest protein chain ? In my case, I have 4 protein chains in the asymmetric unit : A, B, C and D. I would like to assign each ions and each ligands (which are numerous) with the chain letter of the nearest residue that coordinate them. Usually, I rename everything by hand but as the in-house program of the PDBe AutoDep deposition tool automatically do that... I beg your pardon if this question has just been posted here. I didn't find any tool either in the Phenix Suite or in the "Extensions" and "Calculate" menus of the Coot program (v0.7). Best regards. Romain Talon

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how to make covelent link of BME with Cys and refine
by Rajeshwer Sankhala 14 Feb '13

14 Feb '13

Hello Sabine Yah i could specify link in the pdb and also could see it in coot but when i go for refinement then bond is broken. I given pdb mtz and cif files in refinement. The only problem i feel could be that i don't have restrains for SS bond in cif file but i don't know how to generate SS-bond restrains. Thanks RAJ

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how to make covelent link of BME with Cys and refine
by Rajeshwer Sankhala 14 Feb '13

14 Feb '13

Thanks Nigel, I am using phenix 1168 but when i type intra_chain = True command with phenix.refine it gives error message as "intra_chain = True is unknown command". The actual command i used was " phenix.refine .pdb .mtz .cif intra_chain = True". can you please explain how to resolve it. Raj

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Re: [phenixbb] how to make covelent link of BME with Cys and refine
by Ed. Pozharski 13 Feb '13

13 Feb '13

Excellent point. The difference between using bme and cme is rather ideological. I would say that incorporating cme implies that your protein was somehow synthesized with non-canonical amino acid. Usind bme seems more in line with what actually happens - betamercaptoethanol forming disulfide bond with a cysteine. In practical sense, both things work. Until IUCr comes up with a convention, one is free to ignore ideological considerations :) -------- Original message -------- From: Abhinav Kumar <abhinavk(a)slac.stanford.edu> Date: To: phenixbb(a)phenix-online.org Subject: Re: [phenixbb] how to make covelent link of BME with Cys and refine How about using residue CME which is the CYS and BME linked together. CME is included in the CCP4 monomer library, and so Phenix should accept it without a dictionary file. Thanks, Abhinav JCSG@SSRL, SLAC (650) 926-2992 On 02/13/2013 01:02 PM, Nigel Moriarty wrote: Raj In the more recent versions of PHENIX, phenix.refine can found and link atoms closer than 3 angstrom if you specify intra_chain=True. In the older versions, you can use phenix.ligand_linking to generate the needed files. Nigel PS PHENIX does not read SSBOND or LINK records but there is a script to generate the link files from the LINK records. On Tue, Feb 12, 2013 at 11:56 PM, Sabine Schneider <sabine.schneider(a)mytum.de> wrote: Hello Raj, do you have the link specified in you PDB file? Here is an example for an disulphide bond. Usually the link is the line above the CRYST1 card. SSBOND 1 CYS A 123 CYS A 123 1555 8555 2.12 Best, Sabine On 02/12/2013 11:21 PM, Rajeshwer Sankhala wrote: Hello, I can see additional density just next to Cys residues in my protein structure and it looks like BME is covalently linked to cys. I could form a disulfide bond between BME and Cys in "Refmac 5 review restrain" but when i subject it for refinement BME is thrown away (no disulfide bond). I also given Cif file in refinement but it didnot help. I have a feel that i am missing something in cif file. Can anyone suggest step by step starting from adding BME to making a link with BME (Cys-BME) and then refinement? Raj _______________________________________________ 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 -- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division 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

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how to make covelent link of BME with Cys and refine
by Rajeshwer Sankhala 13 Feb '13

13 Feb '13

Hello, I can see additional density just next to Cys residues in my protein structure and it looks like BME is covalently linked to cys. I could form a disulfide bond between BME and Cys in "Refmac 5 review restrain" but when i subject it for refinement BME is thrown away (no disulfide bond). I also given Cif file in refinement but it didnot help. I have a feel that i am missing something in cif file. Can anyone suggest step by step starting from adding BME to making a link with BME (Cys-BME) and then refinement? Raj

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How to export difference patterson map in PHENIX
by 李翔 12 Feb '13

12 Feb '13

Hi everyone, I got a native and derivative dataset (by soaking) of my crystal and want to do MIR in phenix. I am wondering whether there is a way for me to export the difference Patterson map so I could have a better idea that whether the heavy atom is really in the crystal? Cheers, Frank

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fwd: WCPCW 21 - Abstract due...
by Nathaniel Echols 11 Feb '13

11 Feb '13

---------- Forwarded message ---------- From: "Williams, John Charles" <jwilliams(a)coh.org> To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> Date: Mon, 11 Feb 2013 12:47:21 -0800 Subject: WCPCW 21 - Abstract due... Dear All, March 17th is coming up soon. Looks like we have a great crowd and some really good abstracts. Those who havent submitted their abstracts are encourged to do so now. We will start to select talks shortly there after. Those who would like to still attend are encouraged to sign up - we still have space. Looking for to seeing you on St. Patty's day! Best, John

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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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Problem getting Phenix and Rosetta working together
by Dale Tronrud 01 Feb '13

01 Feb '13

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

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Seats are still available for RapiData - the deadline is in 4 days for our course on Data Collection and Structure Solving at the NSLS.
by Robert Sweet 01 Feb '13

01 Feb '13

We will present RapiData 2013, the fifteenth offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement The course will be held 21-26 April 2013: http://www.bnl.gov/RapiData/. Students could be at any level from advanced undergraduate to full professor. The course should accommodate 48 students total. We encourage all students to bring their own specimens for data collection, and to bring old data for the data-reduction and structure-solving tutorials. Please read the Course Announcement at http://www.bnl.gov/RapiData/. You'll see that many experts in the field will be available for lectures and tutorials. You'll find the application materials on the Course Application tab at this site. For the eleventh time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 21 April. The body of the RapiData course really requires that students have a healthy knowledge of crystallography. For potential students who have some experience but are shaky about fundamentals, this course will help. There will be a small additional fee for the fundamentals course, to pay for Saturday night accomodations and food on Sunday morning and noon. Latin American Scientists: Several scholarships are available, from the International Union of Crystallography, to pay partial travel and subsistence costs for Latin-American students and junior faculty (under 40 yrs). Please apply for the course, and then contact R. Sweet (sweet(a)bnl.gov) if you are interested in applying for a scholarship. In accordance with the standards of the International Union of Crystallography, we observe the basic policy of non-discrimination, affirming the right and freedom of scientists to associate in international scientific activity without regard to such factors as citizenship, religion, creed, political stance, ethnic origin, race, colour, language, age, or gender, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist beyond the application procedure that would prevent the participation of bona fide scientists. Please apply or send your students to our course, Bob Sweet, Sonya Kiss, and Alex Soares Course Announcement at http://www.bnl.gov/RapiData/ ========================================================================= Robert M. Sweet E-Dress: sweet(a)bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLS not 1) http://px.nsls.bnl.gov/ Photon Sciences and Biology Dept Mail Stop, Bldg 463 Brookhaven Nat'l Lab. Phones: Upton, NY 11973 631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =========================================================================

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dzp
by Fumiaki Yumoto 31 Jan '13

31 Jan '13

Sent by iPhone

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January 2013 Computational Crystallography Newsletter
by Nigel Moriarty 31 Jan '13

31 Jan '13

Folks The latest edition of the Computational Crystallography Newsletter is available at http://phenix-online.org/newsletter The table of contents is listed below. Articles cctbx tools for transparent parallel job execution in Python. I. Foundations cctbx tools for transparent parallel job execution in Python. II. Convenience functions for the impatient. Short communications Phenix / MolProbity Hydrogen Parameter Update PSI SBKB Technology Portal: A Web Resource for Structural Biologists Fitting tips #5 - What’s with water FAQ - I'm seeing a lot of CIF files. Are they all restraints? Cheers Nigel -- Nigel W. Moriarty, PhD Building 64R0246B, Physical Biosciences Division 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

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Hirshfeld (rigid bond) test
by amakal＠chem.uw.edu.pl 31 Jan '13

31 Jan '13

Good Morning, I have a question concering ADP-s analysis and validation. Thanks to the recent discussion on this list I learned about the tools for general ADP-s statistics and average B-factor plotting in PHENIX. Has anyone ever tried to similarly document/visualize the values of the Hirshfeld's rigid bond test for macromolecules, using phenix/cctbx tools? I know the Hirshfeld's can be calculated during phenix refinement (there is this rigid_bond_test keyword), but I would like to analyze the values for the final model... With regards, Anna Makal

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phenix.refine command line
by Simon Kolstoe 30 Jan '13

30 Jan '13

Hi guys, I'm just trying to install phenix on a students new macbook pro running OS10.8.2, and want to get phenix.refine working on the command line. I've put in: alias setphenix="source /Applications/PHENIX-1.8.1-1168/Contents/phenix-1.8.1-1168/phenix_env.sh" in the .bashrc which seems to execute OK (and already pointed the .bash_profile to .bashrc) however whenever I then type phenix.refine I get command not found. As this is the same setup that I have running on my own machine I am a bit confused as to what is happening! Thanks! Simon

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Phaser with fixed solution
by Ursula Schulze-Gahmen 30 Jan '13

30 Jan '13

I am trying to solve a structure by molecular replacement in phaser using 2 model fragments. I think I may have placed the 1st fragment correctly. I don't quite understand how to best proceed with a fixed ensemble searching for the second fragment in phaser-MR. If I select "use partial solution from previous job", do I still need to read in the coordinates of that previous solution for one ensemble? And If I do, should I read in the starting coordinates or the placed output from this 1st molecular replacement? The second question is about how to relax the restraints fr the packing. In the "other settings" sub window is a section for packing. Could someone explain to me what the different options in this packing section mean? Which of them should I change to allow for more close contacts? Thanks Ursula -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220

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2013 workshop on Neutron Scattering Applications in Structural Biology
by Meilleur, Flora 30 Jan '13

30 Jan '13

Fourth Workshop on Neutron Scattering Applications in Structural Biology Oak Ridge, TN. June 24 - June 28, 2013 Application deadline: April 22, 2013 The workshop on Neutron Scattering Applications in Structural Biology aims at enabling structural biologist to fully exploit the latest instrumentation and software development at the SNS and HFIR facilities at Oak Ridge National Laboratory. Attendees will participate in lectures and tutorials focusing exclusively on neutron techniques applied in structural biology. The workshop is designed for graduate students, post-doctoral fellows and faculty new to or with limited experience of neutron scattering. Travel and accommodation expenses are supported for selected participants from the United States. International applications are welcome. However the course organization may not be able to offer travel or accommodation support. The number of participants will be limited to 15. There is no registration fees for all selected participants. The application package consisting of 1) Information form, 2) CV, 3) Applicant motivation letter (1/2 to 1 page), 4) Principal Investigator letter of support (for graduate students only; 1/2 to 1 page), should be sent electronically to meilleurf(a)ornl.gov<mailto:[email protected]> before April 22, 2013. Detailed information can be found on the course web page: http://neutrons.ornl.gov/conf/gcnb2012/ (gcnb2013 in construction). Best Regards, Flora Meilleur, Ph. D Assistant Professor, Molecular and Structural Biochemistry North Carolina State University Neutron Sciences Directorate Oak Ridge National Laboratory Phone: 865-242-5747

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