- phenixbb - phenix-online.org

Barely two weeks left to apply, and many seats available, for RapiData 2011, our course on Data Collection and Structure Solving at the NSLS.
by Robert Sweet 14 Jan '11

14 Jan '11

We are offering RapiData 2011, the thirteenth 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 3-8 April 2011. Students could be at any level from advanced undergraduate to full professor. The course should accommodate 48 students total. All students are encouraged 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 ninth time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 3 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, Sal Sclafani, 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/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973 631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =========================================================================

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Re: [phenixbb] Refinement Problem
by Kay Diederichs 13 Jan '11

13 Jan '11

> Date: Wed, 12 Jan 2011 17:12:04 -0500 (EST) > From: Christopher W Davies<cdavies(a)purdue.edu> > To: phenixbb(a)phenix-online.org > Subject: [phenixbb] Refinement Problem > > > I am having an issue with refining my structure. I have a 2.36 A resolution dataset. I have found a solution by molecular replacement in the space group P3221. I have been refining the structure, however, my Rfactor/Rfree are not decreasing even though I have good density. My current Rfactor/Rfree values are .40/.43. Can anyone help me? > > > Thanks. > > Chris Chris, there is a collection of things to think about at http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Refinement#R-fa… HTH, Kay

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Refinement Problem
by Christopher W Davies 13 Jan '11

13 Jan '11

I am having an issue with refining my structure. I have a 2.36 A resolution dataset. I have found a solution by molecular replacement in the space group P3221. I have been refining the structure, however, my Rfactor/Rfree are not decreasing even though I have good density. My current Rfactor/Rfree values are .40/.43. Can anyone help me? Thanks. Chris

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Problem with Autobuild
by Claudia Scotti 12 Jan '11

12 Jan '11

Dear List, Sorry fo r the easy question, but I have a problem with Autobuild. I'm trying to rebuild a scFv, composed of two domains linked by a linker. I've managed to find an MR solution with a polyalanine model deprived of the loops, which is my starting model for rebuilding. I've given Autobuild three input files: the mtz, the model coordinates and the sequence of the scFv, asking to model only the beta strands and helices. Problem is that in the final model Autobuild seems to guess incorrectly the density of two beta-strands, inserting the linker there instead of the expected side chains. Any suggestions on how to correct this? Shall I manually rebuild this part to avoid problems? Or is it crucial to prevent errors, for example, that the model and the sequence are numbered so that they are in register? Thanks in advance, Claudia Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673 _________________________________________________________________ Hotmail: Trusted email with powerful SPAM protection. https://signup.live.com/signup.aspx?id=60969

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2 quesions: 1. bond and vdw restraints; 2. cif file for BeF3-
by YoungJin 11 Jan '11

11 Jan '11

Dear Phenix users, Let me ask 2 questions and, as always, thank you whoever responses. 1. First general question is regarding bond distance or van der Waals distance in the crystal structure. As I freeze the crystals as themselves , I often see those distances are much shorter than what I normally expect in the refined structure. So how far they are acceptable or do we have any reference for bonds restraints in the crystal although ccp4 library should deal with these... 2. I was trying to model BeF3-. When I tried to get restraint file from the ReadySet, it always makes BeF3 instead of BeF3-. Is there any way I can fix the charge of the molecule? Also, I would expect it should be in the library as a kind of common inorganic molecule to mimic the phosphorus group. If so, could you let me know how I can get and use it? Thanks in advance, Young-Jin

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B-Factor issue
by Hasan Demirci 11 Jan '11

11 Jan '11

Hi, I am trying to refine a structure with a bound ligand "PAR". Unfortunately, input b-factor of the ligand and output values are matching exactly even tough I copied the ligand from a different structure. I manually changed the occupancy of the ligand to see if it changes the b-factor but again B-factor didn't change. Can someone help me to solve this issue? Below, I attached the first four lines of the pdb after occupancy change. input "HETATM51786 C11 PAR V 1 140.982 67.469 10.830 1.00 58.13 C HETATM51787 O11 PAR V 1 140.549 68.782 10.389 1.00 58.13 O HETATM51788 C21 PAR V 1 139.714 66.811 11.362 1.00 58.13 C HETATM51789 N21 PAR V 1 138.632 66.819 10.352 1.00 58.13 N " output "HETATM51828 C11 PAR V 1 157.285 114.375 -64.249 0.80 58.13 C HETATM51829 O11 PAR V 1 157.335 115.251 -65.379 0.80 58.13 O HETATM51830 C21 PAR V 1 158.559 113.509 -64.364 0.80 58.13 C HETATM51831 N21 PAR V 1 159.738 114.342 -64.677 0.80 58.13 N" Thanks. -- Hasan DeMirci, Ph.D. Postdoctoral Fellow Department of Molecular Biology, Cellular Biology & Biochemistry Brown University 185 Meeting Street Providence, RI 02912 (401) 863-3652 lab (SFH) (401) 863-6124 lab (ship st) (401) 226-7852 cell Hasan_DeMirci(a)Brown.edu demircha99(a)gmail.com

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The phenix autobuilder does not find buccaneer
by Pietro Roversi 10 Jan '11

10 Jan '11

Dear all, I have Buccaneer 1.5.0: partyring:~/Projects/Japanin/autoBUSTER> $CBIN/cbuccaneer <B><FONT COLOR='#FF0000'> <html>  <hr> <pre> ############################################################### ############################################################### ############################################################### ### CCP4 6.1: cbuccaneer version 1.5.0 : 28/05/10## ############################################################### User: pietro Run date: 10/ 1/2011 Run time: 17:18:57 and yet the phenix autobuilder fails - saying I need 1.3.0 or higher (see below) What environment variable is being checked and what should I set for the phenix autobuilder to be able to detect buccaneer? Thanks Regards Pietro **************************************** AutoBuild Input failed Sorry, the necessary version of BUCCANEER does not seem to be available.. For BUCCANEER model building you need CCP4 version 6.1.2 or higher and BUCCANEER version 1.3.0 or higher **************************************** ________________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] On Behalf Of Pavel Afonine [pafonine(a)lbl.gov] Sent: 07 September 2010 17:56 To: PHENIX user mailing list Subject: Re: [phenixbb] will phenix.fmodel automatically generates and takes into account the TLS B by reading the TLS REMARK from pdb? Hi Hailiang, > For the pdb file generated by refmac which contains only the residual-B, > will phenix.fmodel automatically generates and takes into account the TLS > B by reading the TLS REMARK from pdb? Thanks a lot! phenix.tls is the tool to convert between total and residual ADPs. It can recognize Refmac and phenix.refine formats of TLS records. phenix.model_vs_data does this internally to compute correct R-factors and ADP statistics. phenix.fmodel takes the PDB file as is, so it is your responsibility to provide the correct input B-factors. Pavel. _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb

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Displaying electron density in PyMol
by Michael Thompson 10 Jan '11

10 Jan '11

Hi All, Does phenix have a utility that will allow me to produce an electron density map that can be opened in PyMol, similar to the "FFT" utility in ccp4? Thanks for the help, Mike Thompson -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles miket(a)chem.ucla.edu

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autobuild
by Page, Rebecca 09 Jan '11

09 Jan '11

Dear phenix community. We would like to 'fix' the residues of our current protein model, and use Autobuild (perhaps via rebuild-in-place=false, which is what we've been trying) to add missing residues to our current model . However, our efforts thus far have only resulted in models that get rebuilt from scratch. Is it possible to just 'add' residues to a current structure using Autobuild? If so, is someone could share the correct command with us, we'd be very appreciative. We can't seem to find it. Thanks in advance, Rebecca

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Accessing the CCP4 monomer library in Coot opened from Phenix
by Joseph Noel 09 Jan '11

09 Jan '11

Hi All, Having trouble getting Coot loaded by Phenix to access monomers such as DTT, glycerol, etc I assume through the CCP4 monomer library. If I insert the following in the phenix file, start_coot.sh: DYLD_LIBRARY_PATH=/Applications/ccp4-6.1.13/lib:$DYLD_LIBRARY_PATH export DYLD_LIBRARY_PATH will Coot now access the monomer library? Thanks! Joe ___________________________________________________________ Joseph P. Noel, Ph.D. 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 Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________

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