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refinement with twinning
by alexander.singer＠utoronto.ca 16 Feb '11

16 Feb '11

Hi -- I have a twinned data set -- approximate twinning fraction of 0.4. I decided to try to try twinned refinement using phenix.refine in what would seem to be the appropriate manner -- from the "All Parameters" menu, I select twinning, hit "Run Xtriage now" on my mtz file, it gives me the input to the "Twin Law", I keep the rest of the values the same (gave no Anisotropy correction), hit OK, then run 3 cycles of refinement. The only thing is that the Rwork/Rfree values are really very good, almost too good to be true -- for my 1.7 A refinement, I have values of 12.4 and 14.8%, respectively for Rwork and Rfree. Is there anything that I may be doing wrong yielding R values which are artifically too low? Thanks for your help Alex -- Dr. Alex Singer C.H. Best Institute 112 College St. Room 70 University of Toronto Toronto, Canada, M5G 1L6 416-978-4033

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how to move one domain of a protein in respect to another?
by Tatyana Sysoeva 15 Feb '11

15 Feb '11

Dear all, I am working with a protein which form homooligomeric assembly. Each subunit of the assembly consists of 2 subdomains. I would like to create chimeras with the subdomains moved with respect to each other, keeping the linkers. I am wondering what would be the easiest way to do this? Any suggestions are welcome! Sincerely, Tanya

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phenix.refine: Sorry: Inappropriate value for grid_step_factor: must be positive and non-zero.
by Francis E Reyes 15 Feb '11

15 Feb '11

Hi all Refining a low res (~ 3.5A) structure using a reference structure that was solved to 3.0A. I get the following error right when the refinement starts =============================== refinement start ============================== Sorry: Inappropriate value for grid_step_factor: must be positive and non-zero. All instances of grid_step_factor in my .def are positive and non-zero (they should be defaults b/c I never changed them). Thanks! F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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phenix.model_vs_data feature request
by Stephen Graham 15 Feb '11

15 Feb '11

Hi there, A simple feature request: Like most phenix programs, when run from the command line phenix.model_vs_data fails when it is passed an mtz file with multiple 'data' columns (i.e. Fs, F(+/-)s, Is). However, unlike say phenix.xtriage it doesn't tell you the list of possible column combinations and the correct keyword. Would it be possible to add this in? Thanks, Stephen -- Dr Stephen Graham 1851 Research Fellow Cambridge Institute for Medical Research Wellcome Trust/MRC Building Addenbrooke's Hospital, Hills Road Cambridge, CB2 0XY, UK Phone: +44 1223 762 638

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phenix.maps
by Jason 14 Feb '11

14 Feb '11

Hi everyone, I have noticed that the coefficient mtz file generated by phenix.maps can't not be loaded to coot (it can be read through the link in the GUI version once after process). I am using 1.7 version. Any suggestions? -- ====================== Jason Structural Biology Department University of Pittsburgh ======================

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Help for pdb deposition
by qiang liu 14 Feb '11

14 Feb '11

Hi,Dear all, Maybe it's a simple question for you,because I am a beginner in crystallography. Recently I deposited a structure in the pdb and got a reply bellow. "The deposited structure factor file is incomplete. We failed convert the deposited mtz file to cif format. Please send me the correct SF file including h, k, l, F, SigmaF (and/or I and SigmaI)and test flags as an attachment." The mtz file I uploaded is map_coeffs.mtz after refinement.The column lables are listed. type column lable H H H K H L F 2FOFCWT P PH2FOFCWT F 2FOFCWT_no_fill P PH2FOFCWT_no_fill F FOFCWT P PHFOFCWT So how can I get the parameters for deposition in PHENIX? Any suggestions will be appreciated! Thank you very much. Qiang Liu

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difference map
by intekhab alam 11 Feb '11

11 Feb '11

Hi i am trying to calculate a difference map ( ligand-native ) using isomorphous difference map program in phenix. I used the reflection files of ligand and native and phase information of ligand derived data. But the difference map donot fits the ligand, and appears as a circular chunk of density at sigma level 5. I calculated an omit map that clearly showed the presence of my ligand at the specific position. Is there anything wrong in my calculation. What alternate ways are there to improve my difference map. -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL

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'python' received an X Window System error.
by Rongjin 10 Feb '11

10 Feb '11

Hello, when I was running Phenix for model building, I encountered some error. Is this a bug? Thanks Rongjin Guan close failed in file object destructor: The program 'python' received an X Window System error. This probably reflects a bug in the program. The error was 'BadIDChoice (invalid resource ID chosen for this connection)'. (Details: serial 1812949 error_code 14 request_code 53 minor_code 0) (Note to programmers: normally, X errors are reported asynchronously; that is, you will receive the error a while after causing it. To debug your program, run it with the --sync command line option to change this behavior. You can then get a meaningful backtrace from your debugger if you break on the gdk_x_error() function.) The program 'python' received an X Window System error. This probably reflects a bug in the program. The error was 'BadIDChoice (invalid resource ID chosen for this connection)'. (Details: serial 41593302 error_code 14 request_code 55 minor_code 0) (Note to programmers: normally, X errors are reported asynchronously; that is, you will receive the error a while after causing it. To debug your program, run it with the --sync command line option to change this behavior. You can then get a meaningful backtrace from your debugger if you break on the gdk_x_error() function.)

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Graduate Student Summer Internship
by Soisson, Stephen M 09 Feb '11

09 Feb '11

Hi Everyone, Merck Research Laboratories has an opening for a summer intern in the Structural Chemistry (X-ray crystallography) groups located in either Kenilworth, NJ or West Point, PA. The idea is to have someone comfortable with programming and mathematics to explore some computational ideas that can take advantage of the large parallel computing cluster at Merck (> 3000 cores). I am pasting the advertisement below - please note that the deadline is rapidly approaching. Interested applicants must apply through the link provided below. Please note that an advanced undergraduate with the appropriate cross-disciplinary skill set would also be considered for this position. Thanks- Steve Stephen M. Soisson, Ph.D. Structural Chemistry Site Lead, WP Merck Research Laboratories 770 Sumneytown Pike, WP14-1101 West Point, PA 19486 Phone: (215) 652-6185 Fax: (215) 652-9051 stephen_soisson(a)merck.com Job Description Graduate Structural Chemistry Internship 2011:CHE002969 Description Merck is a global health care leader with a diversified portfolio of prescription medicines, vaccines and consumer health products, as well as animal health products. Today, we are building a new kind of healthcare company - one that is ready to help create a healthier future for all of us. Our ability to excel depends on the integrity, knowledge, imagination, skill, diversity and teamwork of people like you. To this end, we strive to create an environment of mutual respect, encouragement and teamwork. As part of our global team, you'll have the opportunity to collaborate with talented and dedicated colleagues while developing and expanding your career. The X-ray Crystallography group of the Global Structural Chemistry Department within Merck Research Laboratories is seeking graduate interns for their summer internship program. The intern will be embedded in the Structural Chemistry/X-ray Crystallography group and will conduct research on a project relevant to drug discovery. The intern will also attend group meetings to gain a wider perspective of the role of structural chemistry within the discovery process in the pharmaceutical industry. The Global Structural Chemistry Department is an industry-leading research group with world class laboratory, synchrotron, and computational facilities. A suitable candidate has a science background with interest in x-ray crystallography and drug discovery. Not required, but a plus, would be experience in one or more of the areas of protein crystallization, X-ray diffraction theory and x-ray crystallography. Preference will be given to candidates having a strong math and/or physical science background with expertise in computers and computer programming. We are seeking graduate student with strong academic performance, communication skills, teamwork, and the ability to work in a multi-functional environment. This internship is offered at either of our research facilities in Kenilworth, NJ or West Point, PA. It is a paid 10-12 week internship targeted to start in June 2011. A weekly stipend will be provided. Housing and transportation to and from work are available for those interns meeting the housing distance guideline. **Please note when applying for this position, the candidate MUST upload a cover letter or a personal statement letter and a copy of your unofficial transcript along with your resume. Qualifications * Candidate is currently pursuing a graduate degree in a relevant field (biochemistry, biophysics, applied math, computer science, etc.). * Science background with an interest in drug discovery * Must have experience in x-ray crystallography and knowledge of programming tools such as Python, Perl or C. * Applicants must be currently enrolled in an academic program. * Applicants must be available for full-time employment for 10 - 12 weeks during the months of June - August 2011. To be considered for this position, please visit our career site at www.merck.com/careers to create a profile and submit your resume for requisition #CHE002969. Merck is an equal opportunity employer, M/F/D/V - proudly embracing diversity in all of its manifestations. Primary Location:US-NJ-Kenilworth Job Type:Intern Employee Status:Regular Number of Openings:1 Stephen M. Soisson, Ph.D. Structural Chemistry Site Lead, WP Merck Research Laboratories 770 Sumneytown Pike, WP14-1101 West Point, PA 19486 Phone: (215) 652-6185 Fax: (215) 652-9051 stephen_soisson(a)merck.com Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.

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How to locate and refine a ligand using anomalous scattering
by Jason 09 Feb '11

09 Feb '11

Hello everyone, I have a few crystals to be x-rayed next week. Before that I hope to get a clear idea about what I am doing (I am new to anomalous scattering). Facts: 1. The crystal is a protein co-crystallized with a ligand 2. The protein structure is known. 3. The ligand has a heavy atom bromide (absorption K-egde=13.47Kev) 4. Data resolution is ~3 angstrom Goals: 1. Locate the bromide position 2. Locate and refine the ligand Questions: 1. Do I need to carry out MAD experiment at 3 wavelengths or there is some other easier way since the protein structure is known (I am not expecting big change of the protein structure itself)? 2. Assuming I have the MAD data, what should I do next using phenix to achieve the two goals listed above? Here are some thoughts: - Using phenix.hyss to locate the anomalous scatterers - Using phenix.autobuild to build the protein model (which data set to use?) - Using coot to add ligands to the protein structure (Is the relative position between the protein and the ligand known based on phenix.hyss and phenix.autobuild?) - Using phenix.refine to refine the ligand+protein complex Thank you all for reading this. ====================== Jason Structural Biology Department University of Pittsburgh ======================

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