- phenixbb - phenix-online.org

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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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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using reference model for low resolution refinement
by crystallogrphy 07 Feb '11

07 Feb '11

Hi, I am refining a hexamer model using low resolution data (4.7A). I want to use a high resolution model (2.4A) which is a dimer as the reference model. The sequence identity is 100%. Does anyone know how to select the residue range from the reference model for my refinement? Thanks!

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is new phenix.refine (1.7-650) comaptible with twinning refinement?
by fulvio saccoccia 04 Feb '11

04 Feb '11

Dear all, I have installed the new phenix version 1.7-650, but I have a doubt: is the real-space refinement within phenix.refine now compatible with twinning refinement?

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ICSG 2011 Abstract Deadline Feb 28, 2011: International Conference on Structural Genomics
by Thomas C. Terwilliger 04 Feb '11

04 Feb '11

Dear Colleagues, We hope that you are planning to attend the International Conference on Structural Genomics 2011, which will be held in Toronto, Canada on May 10-14, 2011. The meeting is designed to serve as a forum to discuss the most recent developments in structural genomics, structural/chemical biology, and their impact on research in biology, medicine and disease. There are many speaking slots still open that will be chosen from submitted poster abstracts. We invite you to submit your abstract by February 28, 2011. Please visit http://www.icsg2011.org for ICSG 2011 meeting and workshop registration details and to submit your abstract. In addition to the main ICSG meeting, there will be a whole day of free concurrent satellite workshops (May 10, 2011), including: Small Molecule Screening Workshop- This hands-on workshop will allow participants to screen a protein of their choice for binding of selected compounds, using thermal shift assays. Eukaryotic Gene Expression Systems Workshop - This workshop will provide participants with a detailed understanding of the state-of-the-art for production of eukaryotic proteins destined for biochemical, biophysical, and structural analyses. iSee: Interactive 3D Documents for the Dissemination of Structural Biology This hands-on workshop will familiarize participants with the iSEE 3D graphical software which allows interactive viewing of 3 dimensional molecular structures and is currently used by journals such as Nature Structural & Molecular Biology and PLoS Biology and PLoS ONE. Workshop on NMR Methods for Structural Biology- This workshop will survey technologies for structure/function investigations of proteins, developed in (or in collaboration with) structural genomics projects, that are ready for widespread use by the wider biological community. Phenix Crystallography Software Workshop This workshop will introduce the PHENIX software for macromolecular structure determination and the core algorithms that it uses. It will provide hands-on tutorials for crystallographers of all levels. We hope to see you there! Best regards, Cheryl Arrowsmith ICSG 2011 Organizer Ted Baker Stephen Burley Dino Moras Joel Sussman Shigeyuki Yokoyama Tom Terwilliger ISGO Executive Committee

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Phenix version 1.7-650 and Pymol
by Leonid Flaks 04 Feb '11

04 Feb '11

>On Tue, Feb 1, 2011 at 5:49 AM, Leonid Flaks<flaks at bnl.gov <http://phenix-online.org/mailman/listinfo/phenixbb>> wrote: >>/ Nat, As I reported minutes ago coot issue is solved. Now I clicked on pymol />>/ button - got an error: />>/ />/> /usr/local/crys/64/phenix-1.7-650/pymol/pymol.exe: error while loading />/> shared libraries: libXmu.so.6: cannot open shared object file: No such file />>/ or directory /> >That's a system library, and not something we distribute or otherwise >interfere with. Does PyMOL even work on the command line? > >thanks, >Nat Nat, pymol is installed as rpm binary and works fine from command line. The library in question is also installed from rpm: dunkin:/home/pxuser 104: rpm -qf /usr/lib64/libXmu.so.6 libXmu-1.0.5-2.fc13.x86_64 dunkin:/home/pxuser 105: rpm -q pymol pymol-1.3-3.20100705svn3911.fc14.x86_64 Could it be something like LD_LIBRARY_PATH or similar? To tell the truth my users are happy to have coot working but don't care too much about the pymol at the moment, so I would not put very high priority on this problem. By the way, I never received you reply - had to cut-and-paste from the web interface. I am subscribed to digest, which has not showed up yet. Thanks, Leon -- Leonid Flaks Phone: (631) 344-2682 Fax : (631) 344-2741

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Phenix version 1.7-650 and Pymol
by Leonid Flaks 01 Feb '11

01 Feb '11

On 02/01/2011 04:20 AM, phenixbb-request(a)phenix-online.org wrote: > Message: 11 > Date: Mon, 31 Jan 2011 16:37:14 -0800 > From: Nathaniel Echols<nechols(a)lbl.gov> > To: PHENIX user mailing list<phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] Phenix version 1.7-650 and coot > Message-ID: > <AANLkTim6ux3V6FcfhXr_0vhNf2P9GWXfBh3aexbZcZ41(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > On Fri, Jan 28, 2011 at 8:00 AM, Leonid Flaks<flaks(a)bnl.gov> wrote: >> > Hi! >> > I just installed phenix version 1.7-650 on fedora 14 64-bit and noticed that >> > if I start coot from within phenix interface, most of the icons on the right >> > hand side of the coot window are not displayed. >> > There is a lot of messages like this: >> > >> > Error loading icon: Couldn't recognize the image file format for file >> > '/usr/share/coot/pixmaps/residue-info.png' > Okay, apparently we missed an important environment variable in the > script that launches Coot from Phenix - several library paths need to > be cleansed to prevent conflicting with the libraries we distribute. > The one we didn't know about (because it never caused problems before) > appears to be XDG_DATA_DIRS. The crude fix for this is to edit > $PHENIX/phenix/phenix/command_line/start_coot.sh and add this line at > the end of a list of "unset" commands: > > unset XDG_DATA_DIRS > > It'll be fixed in the next build too. If this doesn't totally solve > the problem, let me know - I'm going to unset several other paths too, > but those didn't appear to have any effect on our Fedora 14 machine. > > -Nat Nat, As I reported minutes ago coot issue is solved. Now I clicked on pymol button - got an error: /usr/local/crys/64/phenix-1.7-650/pymol/pymol.exe: error while loading shared libraries: libXmu.so.6: cannot open shared object file: No such file or directory So, looks like we need to unset more variables indeed ;-) Meanwhile I'll just keep clicking on buttons... All the best, Leon -- Leonid Flaks Phone: (631) 344-2682 Fax : (631) 344-2741

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AutoBuild fails using NFS on Snow Leopard
by Chris Richardson 01 Feb '11

01 Feb '11

I've been having a problem running AutoBuild jobs in NFS-mounted project directories on Snow Leopard. The jobs start ok, but typically fail in a build cycle with the error "File exists". The problem is reproducible, but the exact details of the failure are not - the point at which the error occurs changes from run to run. Identical jobs run to completion if the project directory is on a local disk or an AFP-mounted volume. My guess is that it's a file locking issue, or maybe some sort of race condition in file creation. Has anybody else experienced this and if so, is there a solution? The details are: OS X 10.6.6, mounting volumes by NFS from a variety of machines (Ubuntu 10.0.4, OS X 10.6.6 & 10.4), Phenix 1.7-650. Regards, Chris -----%<----{ Log Extract }----- Sorry, a subprocess has failed... END OF LOG FILE /work/nedu/foop/phenix_nedu_nfs/AutoBuild_run_3_/TEMP0/RUN_FILE_3.log : rd desired_run_number=self.desired_run_number) File "/common/app/phenix-1.7-650/phenix/phenix/autosol/wizard_command_line.py", line 132, in __init__ overwrite_defaults=False,desired_run_number=desired_run_number) File "/common/app/phenix-1.7-650/phenix/phenix/wizards/AutoBuild.py", line 83, in __init__ init_OutputDir=init_OutputDir,init_RunInstance=init_RunInstance) File "/common/app/phenix-1.7-650/phenix/phenix/autosol/AutoBaseExtend.py", line 613, in local_init quiet=self.quiet,OutputDir=self.OutputDir) #032107 OutputDir File "/common/app/phenix-1.7-650/phenix/phenix/autosol/RunWizardPDS.py", line 65, in __init__ self.ScriptPDS=ScriptPDS(workspace=workspace) File "/common/app/phenix-1.7-650/phenix/phenix/pds/ScriptPDS.py", line 29, in __init__ PhenixDataStorage.__init__(self, dirname) File "/common/app/phenix-1.7-650/phenix/phenix/pds/PDS.py", line 233, in __init__ os.mkdir(self.dirname) OSError: [Errno 17] File exists: 'PDS/AutoBuild_run_1_' Possibly this subprocess is run on a machine with different architecture than the main process? -- Dr Chris Richardson :: Sysadmin, structural biology, icr.ac.uk 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.

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Re: [phenixbb] Phenix version 1.7-650 and coot - SOLVED!
by Leonid Flaks 01 Feb '11

01 Feb '11

On 02/01/2011 04:20 AM, phenixbb-request(a)phenix-online.org wrote: > Message: 11 > Date: Mon, 31 Jan 2011 16:37:14 -0800 > From: Nathaniel Echols<nechols(a)lbl.gov> > To: PHENIX user mailing list<phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] Phenix version 1.7-650 and coot > Message-ID: > <AANLkTim6ux3V6FcfhXr_0vhNf2P9GWXfBh3aexbZcZ41(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > On Fri, Jan 28, 2011 at 8:00 AM, Leonid Flaks<flaks(a)bnl.gov> wrote: >> > Hi! >> > I just installed phenix version 1.7-650 on fedora 14 64-bit and noticed that >> > if I start coot from within phenix interface, most of the icons on the right >> > hand side of the coot window are not displayed. >> > There is a lot of messages like this: >> > >> > Error loading icon: Couldn't recognize the image file format for file >> > '/usr/share/coot/pixmaps/residue-info.png' > Okay, apparently we missed an important environment variable in the > script that launches Coot from Phenix - several library paths need to > be cleansed to prevent conflicting with the libraries we distribute. > The one we didn't know about (because it never caused problems before) > appears to be XDG_DATA_DIRS. The crude fix for this is to edit > $PHENIX/phenix/phenix/command_line/start_coot.sh and add this line at > the end of a list of "unset" commands: > > unset XDG_DATA_DIRS > > It'll be fixed in the next build too. If this doesn't totally solve > the problem, let me know - I'm going to unset several other paths too, > but those didn't appear to have any effect on our Fedora 14 machine. > > -Nat Nat, Just to confirm - your fix worked! Thank you very much, Leon -- Leonid Flaks Phone: (631) 344-2682 Fax : (631) 344-2741

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(no subject)
by Shuchi 01 Feb '11

01 Feb '11

hello, i have solved one structure and after solving the average B factor of the model is 107 and average B factor from wilson plot of DATA is 85.5 . is this fine or i did some wrong while fitting and refinement. resolution is 3.0 Angstroms . -- vandana kukshal CSIR-senior research fellow X ray lab ,MSB division central drug research institute lucknow

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Phenix version 1.7-650 and coot
by Leonid Flaks 01 Feb '11

01 Feb '11

Hi! I just installed phenix version 1.7-650 on fedora 14 64-bit and noticed that if I start coot from within phenix interface, most of the icons on the right hand side of the coot window are not displayed. There is a lot of messages like this: Error loading icon: Couldn't recognize the image file format for file '/usr/share/coot/pixmaps/residue-info.png' for png and svg files in the console window. I can see all of the icons if I start coot directly. I am using coot version 1.6.2-pre1 rev 3213 which is installed on 64-bit fedora 14 as a rpm file. I did not see this issue on a phenix version 1.6.4-476 with the same version of coot. Thanks, Leon -- Leonid Flaks Phone: (631) 344-2682 Fax : (631) 344-2741

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phenix.mr_rosetta paths
by Ben Eisenbraun 01 Feb '11

01 Feb '11

Hi, I'm testing Rosetta 3.2+PHENIX 1.7-650, and in the phenix.mr_rosetta output, I see: Checking rosetta paths: rosetta binary: /programs/l/rosetta/3.2/rosetta_source/bin/mr_protocols.default database_dir: /programs/l/rosetta/3.2/rosetta_database script_dir: /programs/l/rosetta/3.2/rosetta_source/src/apps/public/electron_density pilot_script_dir: /programs/l/rosetta/3.2/rosetta_source/src/apps/pilot/frank/ In the script directory, the C++ files were not built along with the regular Rosetta build. Do those need to be compiled for the target platform? Also, the pilot_script_dir is empty. Is there supposed to be something in there? Thanks. -ben -- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |

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translation/rotation matrix
by Yogesh Gupta 31 Jan '11

31 Jan '11

Dear PhenixBB members, I calculated two maps one using 3 wavelengths Se to 4.2A, and 3 wavelength Ta to ~3.9A for ~100kDa protein in space group P62 with 1 molecule in A.U. These crystals are non-isomorphous. Ta MAD map is better than Se MAD map. There is no model available at this point. Is there a way to transform Se sites accurately to the Ta map? Thanks for your help. Yogesh -- -------------------------------------------------- Yogesh K. Gupta, Ph.D. Dept of Structural & Chemical Biology Mount Sinai School of Medicine Icahn Medical Institute 1 Gustave L. Levy Place, Box 1677 New York, NY, USA 10029 Tel:+1 212-659-8639 --------------------------------------------------

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Re: [phenixbb] Phenix version 1.7-650 and coot
by Leonid Flaks 31 Jan '11

31 Jan '11

On 01/29/2011 03:00 PM, phenixbb-request(a)phenix-online.org wrote: > Message: 1 > Date: Fri, 28 Jan 2011 12:09:01 -0800 > From: Nathaniel Echols<nechols(a)lbl.gov> > To: PHENIX user mailing list<phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] Phenix version 1.7-650 and coot > Message-ID: > <AANLkTini0jaSAh9KKv1xZGbtE4ABtdU2_G5KMxWP0c4p(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > On Fri, Jan 28, 2011 at 8:00 AM, Leonid Flaks<flaks(a)bnl.gov> wrote: >> I just installed phenix version 1.7-650 on fedora 14 64-bit and noticed that >> if I start coot from within phenix interface, most of the icons on the right >> hand side of the coot window are not displayed. >> There is a lot of messages like this: >> >> Error loading icon: Couldn't recognize the image file format for file >> '/usr/share/coot/pixmaps/residue-info.png' >> >> for png and svg files in the console window. I can see all of the icons if I >> start coot directly. I am using coot version 1.6.2-pre1 rev 3213 which is >> installed on 64-bit fedora 14 as a rpm file. I did not see this issue on a >> phenix version 1.6.4-476 with the same version of coot. > Could you please send me the complete console output from Coot under > these conditions: > > a) when launching from Phenix 1.7 > b) when launching from Phenix 1.6.4 > c)when launching from the command line? > > Very little has changed in the Coot-related parts of Phenix since > 1.6.4, so I'm not sure how it's possible for one to work but not the > other. In the past, errors like this were due to conflicts with the > shared libraries distributed with Phenix, but we largely reset the > environment when starting Coot to avoid the problem, and I'm pretty > sure we started that a year and a half ago. > > thanks, > Nat > Nat, first of all - my apologies for the incorrect report. It turned out this problem exists in phenix 1.6.4 under fedora 14 also - just nobody noticed it on the current setup! Fedora 14 is about 2 month old and we are coming out of the winter shutdown. We had a mixture of fedora 12 and 13 before and did not see that problem. Of course, python version has been changed to python-2.7 for Fedora 14. Console output for all 3 conditions are saved. I'll mail them to you directly - I don't want to flood the list. Thanks, Leon -- Leonid Flaks Phone: (631) 344-2682 Fax : (631) 344-2741

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cis peptides
by Timothy Springer 30 Jan '11

30 Jan '11

Is there an easy way to specify unwanted cis-peptides and remove them in refinement or with torsion dynamics or SA? Tim

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Re: [phenixbb] Global refinement parameters - use statistical model for missing atoms
by Joseph Noel 30 Jan '11

30 Jan '11

Hi Pavel! Thanks for the reply. It does seem to be working though in the current version as long as I choose advanced level in the gui. Does it make sense though that it is lowering my Free-R? Also, the upshot is that the Fo-Fc maps are much flatter. I can see waters to build but only in the 2Fo-Fc sigmaa weighted maps so it does certainly seem to be doing something. Anyway, I look forward to the docs on it when you officially release it. Seems useful! Best- 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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selection string for omit maps
by Alexandra Deaconescu 29 Jan '11

29 Jan '11

Hi: I am new to Phenix and I am currently using the GUI. I would like to compute a sa-omit map by leaving out residues 204-209 of my chain C. In the GUI, what is the proper syntax for this selection string? I tried a few obvious formats but the jobs failed. Thank you very much in advance, Alexandra ----- Original Message ----- From: phenixbb-request(a)phenix-online.org To: phenixbb(a)phenix-online.org Sent: Tue, 25 Jan 2011 15:00:01 -0500 (EST) Subject: phenixbb Digest, Vol 62, Issue 25 Send phenixbb mailing list submissions to phenixbb(a)phenix-online.org To subscribe or unsubscribe via the World Wide Web, visit http://phenix-online.org/mailman/listinfo/phenixbb or, via email, send a message with subject or body 'help' to phenixbb-request(a)phenix-online.org You can reach the person managing the list at phenixbb-owner(a)phenix-online.org When replying, please edit your Subject line so it is more specific than "Re: Contents of phenixbb digest..." Today's Topics: 1. Problem with loop fitting (Kendall Nettles) 2. Re: Problem with loop fitting (Tom Terwilliger) 3. Re: Problem with loop fitting (Kendall Nettles) 4. Ligandfit bug report (Kendall Nettles) 5. Re: Ligandfit bug report (Nigel Moriarty) 6. ADP: fix_wxu and wxu_scale (fulvio saccoccia) 7. Re: Problem with loop fitting (Tom Terwilliger) 8. Re: ADP: fix_wxu and wxu_scale (Pavel Afonine) 9. Re: adp values (Pavel Afonine) ---------------------------------------------------------------------- Message: 1 Date: Mon, 24 Jan 2011 15:47:02 -0500 From: Kendall Nettles <knettles(a)scripps.edu> To: PHENIX user mailing list <phenixbb(a)phenix-online.org> Subject: [phenixbb] Problem with loop fitting Message-ID: <C9634F76.F559%knettles(a)scripps.edu> Content-Type: text/plain; charset="iso-8859-1" Dear PHENIX developers, I am trying fit_loops for the first time and getting error message: "No suitable gap found matching residues" I'm not sure what the problem is. Best regards, Kendall Nettles knettles$ phenix.fit_loops pdb_in=Liganded_overall_best-coot-1.pdb mtz_in=cycle_best_refine_map_coeffs_1.mtz seq_file=seq.dat start=331 end=336 chain_id=A # fit_loops # # Fit loops in a PDB file with gaps # Type phenix.doc for help Input sequence file is seq.dat Reading sequence from seq.dat Fit_loops: Fit a missing loop in a model. Map from: TEMP_cycle_best_refine_map_coeffs_1.mtz using labin FP=2FOFCWT PHIB=PH2FOFCWT Model from: Liganded_overall_best-coot-1.pdb LABIN LINE: FP=2FOFCWT PHIB=PH2FOFCWT No suitable gap found matching residues 331 - 336 chain: A No final model obtained

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Global refinement parameters - use statistical model for missing atoms
by Joseph Noel 29 Jan '11

29 Jan '11

Hi All, Does it make sense that when the box for "use statistical model for missing atoms" is picked under the GUI's "Global refinement parameters options" that one might obtain "better" Free-R values? I seem to be seeing that for a 2.3 A refinement of a crystal with a monomer of 550 residues in the asymmetric unit and 68% solvent content. When I uncheck the box I get about a 3% increase in Free-R. Is there more information about what this option is actually doing and when it might be useful to employ? 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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REMINDER - EMBO 2011 Practical Course - ESRF-EMBL, Grenoble, France, 6 - 10 June 2011
by Daniele de Sanctis 28 Jan '11

28 Jan '11

Hi all, Just a reminder, as deadline is approacing DEADLINE TO APPLY FEBRUARY 28th COURSE ANNOUCEMENT EMBO 2011 Practical Course - Exploiting Anomalous Scattering in Macromolecular Structure Determination ESRF-EMBL, Grenoble, France, 6 - 10 June 2011 The EMBO 2011 Practical Course on Exploiting Anomalous Scattering in Macromolecular Structure Determination will be hosted by the ESRF in Grenoble, France from 6 to 10, June 2011. The course aims to impart the theoretical and practical basis for the 3-dimensional structure determination of bio-macromolecules using Anomalous Dispersion techniques (SAD & MAD) to young scientists who intend to apply these methods in macromolecular crystallography. Through a series of lectures, software demonstrations, practicals on the ESRF beamlines and tutorials, participants will get insights into all aspects of the structure determination process including beamline instrumentation, data collection and processing, heavy atom substructure determination, phasing and model building. There will also be sessions focusing on automated structure solution procedures and newer methods. Additional sessions will include presentations of distinguished structures solved with these techniques. The number of participants is limited to 20 and the deadline for application is February 28th, 2011. Additional information, course programme and instructions to apply to the course can be found in the course webpages: http://cwp.embo.org/pc11-03/ -- ἀρετή --------------------------------------- Daniele de Sanctis, PhD Structural Biology Group ESRF, Grenoble, France Tel 33 (0)4 76 88 2869

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Carien Dekker is out of the office.
by carien.dekker＠novartis.com 26 Jan '11

26 Jan '11

I will be out of the office starting 01/27/2011 and will not return until 01/31/2011. I will respond to your message when I return.

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Phenix version 1.7 released
by Paul Adams 26 Jan '11

26 Jan '11

The Phenix developers are pleased to announce that version 1.7 of Phenix is now available. Binary installers for Linux, and Mac OSX platforms are available at the download site: http://phenix-online.org/download/ Some of the new features in this version are: Graphical Interface ------------------- - Simplified AutoMR interface for single-component searches. - Multi-criterion validation kinemage display in KiNG. - Validation of RNA, isotropic ADPs, occupancies. - Improved project management interface, which will automatically import old projects to the new format when upgrading from a previous version of Phenix. - Integrated help browser on Mac with contextual help buttons embedded in program windows. - phenix.find_tls_groups available as part of the phenix.refine GUI. - Improved and expanded documentation for wizard and Phaser GUIs. Structure refinement -------------------- - A new fast real space refinement protocol, which can substantially improve poor starting models. - A fast method for automated identification of TLS groups (phenix.find_tls_groups). - Reference model, Ramachandran, and secondary structure restraints to improve refinement at low resolution. - Automated secondary structure restraint generation for non-Watson-Crick base pairs (using the Saenger classification). - Automatic support for D-peptides when using standard PDB residue names. Molecular Replacement --------------------- - A new command, phenix.mr_rosetta, which integrates molecular replacement, automated model building and Rosetta model rebuilding for difficult structures. - A new fast search method in Phaser for efficiently locating multiple copies of the same molecule - A new program (mr_model_preparation) for preparing models for molecular replacement, which automatically downloads related molecules based on a sequence alignment and runs sculptor. - Improvements to ensemble generation (phenix.ensembler), with an option to use secondary structure matching (using code from Eugene Krissinel). Ligand fitting -------------- - New tool for automated ligand fitting using previous structures of related protein/ligand complexes (phenix.guided_ligand_replacement). - Bug fixes and other improvements to phenix.elbow. Analysis -------- - Multi-criterion kinemages can now handle custom restraints (from a .cif file). - RNA model validation is now available on the command line (phenix.rna_validate). - Updates to phenix.model_vs_data, which now generates Sigma-A plots and more detailed ADP statistics. For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that this publication should be used to cite use of Phenix: PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010). Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Kathleen Moody [ KLMoody(a)lbl.gov ][ 1-510-495-2506 ] --

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adp values
by Agnieszka 25 Jan '11

25 Jan '11

Hello, I have 1.96 resolution structure (RNA) which I refine with individual adp factors. I found that in some cases the differences of apd between the covalently bonded atoms is quite large, for example: phosphate 24 and one of the oxygen 33; O4' - 26 and C1'-18. In extreme case for the so4 anion is: sulphate atom 63 and one of the oxygen 31. Why is it happened? I was trying refmac and the b-factors are totally different (they are much bigger). Is it because of scaling and resolution? thank you in advance, Agnieszka Kiliszek

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ADP: fix_wxu and wxu_scale
by fulvio saccoccia 25 Jan '11

25 Jan '11

Dear Phenix users and developers, I'm trying to refine a 3 A resolution structure. In order to better understand how can I use wxu_scale and fix_wxu options in phenix.refine, may you explain me their use, since I have a lot of problems with ADPs? In fact, I have big variations between atoms of the same residue. So, is it better to use wxu_scale or to impose fix_wxu to refine the ADPs? Thanks to all Fulvio Saccoccia

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Problem with loop fitting
by Kendall Nettles 25 Jan '11

25 Jan '11

Dear PHENIX developers, I am trying fit_loops for the first time and getting error message: "No suitable gap found matching residues" I'm not sure what the problem is. Best regards, Kendall Nettles knettles$ phenix.fit_loops pdb_in=Liganded_overall_best-coot-1.pdb mtz_in=cycle_best_refine_map_coeffs_1.mtz seq_file=seq.dat start=331 end=336 chain_id=A # fit_loops # # Fit loops in a PDB file with gaps # Type phenix.doc for help Input sequence file is seq.dat Reading sequence from seq.dat Fit_loops: Fit a missing loop in a model. Map from: TEMP_cycle_best_refine_map_coeffs_1.mtz using labin FP=2FOFCWT PHIB=PH2FOFCWT Model from: Liganded_overall_best-coot-1.pdb LABIN LINE: FP=2FOFCWT PHIB=PH2FOFCWT No suitable gap found matching residues 331 - 336 chain: A No final model obtained

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Ligandfit bug report
by Kendall Nettles 25 Jan '11

25 Jan '11

We are generating pdb files with chemdraw3D, which turn out to not be "real" pdb files. PHENIX.ELBOW fixes them, but leaves some of the atom ID numbers blank, such as Oxygen #2, and Carbon #18: HETATM 17 C16 LIG 1 -83.510 -0.856 0.582 1.00 20.00 C HETATM 18 O01 LIG 1 -86.640 -2.401 -0.357 1.00 20.00 O HETATM 19 O LIG 1 -75.199 2.925 2.145 1.00 20.00 O HETATM 20 C17 LIG 1 -83.058 -0.188 1.872 1.00 20.00 C HETATM 21 C LIG 1 -76.676 0.780 -1.835 1.00 20.00 C After editing it to add in the missing numbers, I re-ran elbow, and found that the resulting optimized ligand had imploded, producing altered atom connectivity. If I ran it with --final_geometry it came out OK. If you would like files to reproduce the error, I am happy to send them. Best, Kendall Nettles

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autobuild and buccaneer reference
by Bryan Lepore 21 Jan '11

21 Jan '11

1.7-629 it appears that autobuild does not have buccaneer implemented such that _buccaneer's_ reference structure method is used - N.B. i do not mean the "reference structure" as used by resolve/autobuild. any comment appreciated, thanks -Bryan

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Stereochemistry statistics
by miket＠chem.ucla.edu 20 Jan '11

20 Jan '11

Hi All, I have a very naive question, but nobody I have asked has been able to give me a confident answer. When phenix calculates the stereochemistry statistics for a model, two of the statistics given are RMS(chirality) and RMS(planarity). What specific measurements are being calculated to produce these statistics, and what are the units for the numbers given? For example, is RMS(planarity) telling me the average distance out of plane for an atom that should be in plane? If this is the case I imagine the units are angstroms? Thanks for the explanation, 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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Ten days left to apply, and many seats available, for RapiData 2011, our course on Data Collection and Structure Solving at the NSLS.
by Robert Sweet 20 Jan '11

20 Jan '11

This may be the last reminder that 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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Submitting autobuild to cluster
by Kendall Nettles 20 Jan '11

20 Jan '11

Dear PHENIX developers, I'm preparing a bunch autobuild runs. If I submit 20 autobuild jobs to our 100 node cluster, what would you recommend for nproc and nbatch? How about for 10 jobs at once? Thanks! Kendall Nettles

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Defining an Intermolecular link
by Ryan Timothy Vanderlinden 19 Jan '11

19 Jan '11

Hi, I am working on a complex of three molecules in which, I believe, there is a covalent bond between the sulfur atom of a cysteine on molecule "A" and the c-terminal carbon of molecule "C". There are other structures deposited that have a similar linkage. I have looked at these structures and included a replica description of the supposed link in my input pdb file for refinement. I have redefined this c-terminal residue as a ligand and used phenix elbow do create a .cif file for it. Even when I use the modified pdb file that describes the linkage and the cif file that describes the ligand, the intermolecular link falls apart and the ligand (c-terminal amino acid) separates from the rest of the chain. The resulting mtz file still shows density (2Fo-Fc) supporting the link but the ligand is not in the density. The fact that the ligand moves away from where I would expect it is evidence that modeling the intermolecular linkage is really incorrect or I have not included all the proper files to define this linkage and hold it together during refinement. What are all the necessary files required hold an intermolecular linkage of this nature together during refinement? Are there certain commands that I might be leaving out from my refine script that are necessary to recognize such linkages? Thanks in advance, Ryan VanderLinden University of Utah

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labelit documentation
by Bryan Lepore 19 Jan '11

19 Jan '11

in 1.7-629 (not the latest ), I cannot find any labelit documentation (however, i found some on the labelit site OK). could anyone comment on that - e.g. is there a timeframe, etc. thanks, -Bryan p.s: the interesting CCN article compelled me to look.

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Autobuild: problems with modified amino acids
by Kendall Nettles 19 Jan '11

19 Jan '11

I'm running autobuild from a molecular replacement solution and having two problems: 1. methionines are converted to MSE 2. I'd like to include a .cif file for b-mercapto-ethanol adducted cysteines: CME. The .cif file is one that works for phenix.refine (listed below). I suspect I am not writing the .eff file correctly: refinement.pdb_interpretation.apply_cif_modification { data_mod = cme residue_selection = chain A and resid 530 residue_selection = chain B and resid 381 } Thanks! Kendall Nettles # electronic Ligand Builder and Optimisation Workbench (eLBOW) # - a module of PHENIX version 1.6-289 (Mon Jan 21 12:43:00 2010) # - file written: Sat May 22 10:41:08 2010 # # Input file: /AutoBuild_run_1_/TEMP0/LIGANDS.pdb # Residue: CME # data_comp_list loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level CME CME 'Unknown ' ligand 21 10 . # data_comp_CME # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge CME N N NH2 . CME C C C1 . CME O O O . CME CA C CH1 . CME CB C CH2 . CME SG S S2 . CME SD S S2 . CME CE C CH2 . CME CZ C CH2 . CME OH O OH1 . CME H H HNH2 . CME H2 H HNH2 . CME HC1 H H . CME HA H HCH1 . CME HB2 H HCH2 . CME HB3 H HCH2 . CME HE2 H HCH2 . CME HE3 H HCH2 . CME HZ2 H HCH2 . CME HZ3 H HCH2 . CME HH1 H HOH1 . # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.type _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd CME N CA single 1.450 0.02 CME C O double 1.224 0.02 CME C CA single 1.492 0.02 CME CA CB single 1.497 0.02 CME CB SG single 1.780 0.02 CME SG SD single 2.018 0.02 CME SD CE single 1.783 0.02 CME CE CZ single 1.485 0.02 CME CZ OH single 1.374 0.02 CME H N single 0.913 0.02 CME H2 N single 0.914 0.02 CME HC1 C single 0.965 0.02 CME HA CA single 0.975 0.02 CME HB2 CB single 0.966 0.02 CME HB3 CB single 0.973 0.02 CME HE2 CE single 0.972 0.02 CME HE3 CE single 0.973 0.02 CME HZ2 CZ single 0.976 0.02 CME HZ3 CZ single 0.968 0.02 CME HH1 OH single 0.880 0.02 # loop_ _chem_comp_angle.comp_id _chem_comp_angle.atom_id_1 _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd CME C CA N 109.05 3.0 CME CB CA N 110.14 3.0 CME CB CA C 110.73 3.0 CME CA C O 119.98 3.0 CME SG CB CA 117.67 3.0 CME SD SG CB 109.52 3.0 CME CE SD SG 109.45 3.0 CME CZ CE SD 117.64 3.0 CME OH CZ CE 117.63 3.0 CME HA CA N 109.56 3.0 CME HA CA C 109.15 3.0 CME HC1 C O 120.00 3.0 CME H N CA 109.48 3.0 CME H2 N CA 109.47 3.0 CME HC1 C CA 120.00 3.0 CME HB2 CB CA 107.69 3.0 CME HB3 CB CA 107.72 3.0 CME HA CA CB 108.19 3.0 CME HB2 CB SG 107.73 3.0 CME HB3 CB SG 107.72 3.0 CME HE2 CE SD 107.78 3.0 CME HE3 CE SD 107.74 3.0 CME HZ2 CZ CE 107.71 3.0 CME HZ3 CZ CE 107.80 3.0 CME HE2 CE CZ 107.71 3.0 CME HE3 CE CZ 107.70 3.0 CME HH1 OH CZ 109.49 3.0 CME HZ2 CZ OH 107.74 3.0 CME HZ3 CZ OH 107.69 3.0 CME H2 N H 109.47 3.0 CME HB3 CB HB2 107.97 3.0 CME HE3 CE HE2 107.93 3.0 CME HZ3 CZ HZ2 107.94 3.0 # loop_ _chem_comp_tor.comp_id _chem_comp_tor.id _chem_comp_tor.atom_id_1 _chem_comp_tor.atom_id_2 _chem_comp_tor.atom_id_3 _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period CME Var_01 O C CA N 133.07 30.0 2 CME Var_02 SG CB CA N 179.49 30.0 3 CME Var_03 SG CB CA C 58.80 30.0 3 CME Var_04 CB CA C O -105.59 30.0 3 CME Var_05 SD SG CB CA 161.56 30.0 3 CME Var_06 CE SD SG CB -172.66 30.0 3 CME Var_07 CZ CE SD SG 177.33 30.0 3 CME Var_08 OH CZ CE SD 45.37 30.0 3 CME Var_09 HC1 C CA N -45.35 30.0 2 CME Var_10 HB2 CB CA N -58.63 30.0 3 CME Var_11 HB3 CB CA N 57.60 30.0 3 CME Var_12 H N CA C -165.67 30.0 3 CME Var_13 H2 N CA C -45.66 30.0 3 CME Var_14 HB2 CB CA C -179.32 30.0 3 CME Var_15 HB3 CB CA C -63.09 30.0 3 CME Var_16 HA CA C O 13.41 30.0 3 CME Var_17 H N CA CB 72.63 30.0 3 CME Var_18 H2 N CA CB -167.36 30.0 3 CME Var_19 HC1 C CA CB 75.99 30.0 2 CME Var_20 HA CA CB SG -60.78 30.0 2 CME Var_21 HE2 CE SD SG 55.43 30.0 3 CME Var_22 HE3 CE SD SG -60.81 30.0 3 CME Var_23 HB2 CB SG SD 39.69 30.0 1 CME Var_24 HB3 CB SG SD -76.55 30.0 1 CME Var_25 HZ2 CZ CE SD 167.25 30.0 3 CME Var_26 HZ3 CZ CE SD -76.51 30.0 3 CME Var_27 HH1 OH CZ CE 173.81 30.0 3 CME Var_28 HE2 CE CZ OH 167.31 30.0 3 CME Var_29 HE3 CE CZ OH -76.51 30.0 3 CME Var_30 HA CA N H -46.26 30.0 3 CME Var_31 HA CA N H2 73.74 30.0 3 CME Var_32 HA CA C HC1 -165.01 30.0 3 CME Var_33 HB2 CB CA HA 61.10 30.0 3 CME Var_34 HB3 CB CA HA 177.33 30.0 3 CME Var_35 HZ2 CZ CE HE2 -70.81 30.0 3 CME Var_36 HZ3 CZ CE HE2 45.43 30.0 3 CME Var_37 HZ2 CZ CE HE3 45.37 30.0 3 CME Var_38 HZ3 CZ CE HE3 161.61 30.0 3 CME Var_39 HH1 OH CZ HZ2 51.95 30.0 3 CME Var_40 HH1 OH CZ HZ3 -64.25 30.0 3 # loop_ _chem_comp_chir.comp_id _chem_comp_chir.id _chem_comp_chir.atom_id_centre _chem_comp_chir.atom_id_1 _chem_comp_chir.atom_id_2 _chem_comp_chir.atom_id_3 _chem_comp_chir.volume_sign CME chir_01 CA N C CB both #

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Re: [phenixbb] phenix.refine & twinning
by Nicholas Cody Sennett 19 Jan '11

19 Jan '11

Yes, it was the remark portion of the pdb. Thanks, --------------------------------------------- Nick Sennett Wood Lab, Graduate Student University of Georgia BMB Davidson Life Sciences A428 (706) 583-0303 nsennett(a)gmail.com<mailto:[email protected]> [cid:3DCE4F6D-E184-4DA2-A921-93D4311BE545] On Jan 18, 2011, at 3:00 PM, <phenixbb-request(a)phenix-online.org<mailto:[email protected]>> wrote: I can't see any reason why this wouldn't work, but you're right, it's running untwinned ML refinement despite the twin law being set correctly. However, I just tried running the twinned example included in Phenix (the porin-twin dataset, which can be set up as a tutorial from the GUI), and it worked as expected. I'm downloading the latest installer now to double-check, but I doubt it's much different. One possibility is that the REMARK section in the input PDB file is giving conflicting instructions. Could you please run this command and send me the output (off-list, unless you're certain there isn't anything secret in there)? grep "REMARK" /Users/nick/k94e_208/Refine_30M/ligand_revised2-coot-0.pdb thanks, Nat

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Post-doctoral positions at the NKI /Amsterdam to work on Autotaxin
by Anastassis Perrakis 19 Jan '11

19 Jan '11

Dear all, Post-doctoral positions are available in the Netherlands Cancer Institute in the group of Tassos Perrakis (http://xtal.nki.nl). Our group, together with that of Wouter Moolenaar and of Huib Ovaa, have a long-standing interest and lively collaboration in the function and structure of Autotaxin (ATX), a human enzyme that produces the well-established lipid mediator LPA. ATX has a very promising potential as a drug target. Together also with our collaborators at Pfizer and at Kentucky (Andrew Morris) we have recently published the structure of Autotaxin alone and in complex with our favorite inhibitor, as well as data that argue for an interaction of ATX with integrins. Structure: http://www.nature.com/nsmb/journal/vaop/ncurrent/full/nsmb.1980.html Crystals (good fun!): http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2935246/?tool=pubmed Our chemistry collaborators (Ovaa group at the NKI) have also recently published data on potent inhibitors that act in vivo, as well as an activity-based probe. Best Inhibitor: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2867685/?tool=pubmed Inhibitor design: http://pubs.acs.org/doi/abs/10.1021/jm1005012 Activity based probe: http://onlinelibrary.wiley.com/doi/10.1002/cbic.201000349/abstract;jsession… We are looking for highly motivated post-doctoral scientists to work on projects related to the function of Autotaxin, aiming to understand how Autotaxin activity regulates the production of LPA and how we can design more potent inhibitors and activity based probes. The project includes protein and mutant production, crystallographic studies and/ or cell biology analysis, and is funded by the KWF (Netherlands Cancer Fund) and the NWO (Netherlands Science Organization). The Netherlands Cancer Institute (http://www.nki.nl) is a center of excellence with a high standard of biological research and an interactive international atmosphere. It is located in Amsterdam, with all its cultural amenities, close to Schiphol airport. You will join a lively team, closely associated with that of Titia Sixma in the Department of Biochemistry and next to the NKI Protein facility. http://xtal.nki.nl/ http://proteinfacility.nki.nl/ The research teams at B8 are closely associated and have an interest in structural studies coupled to functional analysis, combined with activities in method development for structural biology. Our department also hosts the newly established "Protein Facility" with equipment that includes high throughput crystallization and automated crystal visualization robotics both for nano-drop and Fluidigm micro- fluidics experiments, an X-ray facility (with Micro-star Ultra source from Bruker and a MarDTB), Biacore surface plasmon resonance, isothermal titration calorimetry (ITC), static light scattering (MALLS) , Thermofluor, an automated protein expression testing platform, a mass-spectrometry unit, as well as facilities to express protein in E.coli, insect and mammalian cells. We are looking for enthusiastic researchers, which could have experience in protein crystallography and/or molecular biology and/or biochemistry and/or cell biology. Applicants should send an e-mail including a formal CV, a very short motivation letter for why they want to work on this project, and include the names of three referees, and send it to me. Tassos

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Computational Crystallography Newsletter Issue 2
by Paul Adams 19 Jan '11

19 Jan '11

Dear Colleagues, I am pleased to announce the publication of the second issue of the Computational Crystallography Newsletter: http://www.phenix-online.org/newsletter/ A listing of the articles and short communications is given below. Please note that the newsletter accepts articles of a general nature of interest to all crystallographers. Please send any articles to Nigel Moriarty at NWMoriarty(a)lbl.gov Articles -------- - Fuzzy space group symbols: H3 and H32 - Visualizing the raw diffraction pattern with LABELIT - Electron density illustrations - Maximum likelihood refinement for twinned structures - TLS for dummies Short communications -------------------- - Multi-criterion kinemage graphics in PHENIX - phenix.ensembler: a tool for multiple superposition - phenix.mr_rosetta: a new tool for difficult molecular replacement problems Cheers, Paul -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Kathleen Moody [ KLMoody(a)lbl.gov ][ 1-510-495-2506 ] --

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phenix.refine : desire less conservative bonds and angles in optimize_wxc = True.
by Francis E Reyes 19 Jan '11

19 Jan '11

Although I specify that I'll allow a max angle rmsd of 2.0 (angles_rmsd_max), optimize_wxc = True results in a limited range of angles.. for example my optimize_wxc output Start r_work= 0.2507 r_free= 0.2709 bonds= 0.002 angles= 0.47 r_work= 0.2558 r_free= 0.2728 bonds= 0.001 angles= 0.41 scale= 1.00 r_work= 0.2550 r_free= 0.2725 bonds= 0.001 angles= 0.41 scale= 1.40 r_work= 0.2543 r_free= 0.2724 bonds= 0.001 angles= 0.41 scale= 1.80 r_work= 0.2538 r_free= 0.2723 bonds= 0.001 angles= 0.41 scale= 2.20 r_work= 0.2533 r_free= 0.2721 bonds= 0.001 angles= 0.42 scale= 2.60 r_work= 0.2529 r_free= 0.2721 bonds= 0.001 angles= 0.42 scale= 3.00 r_work= 0.2525 r_free= 0.2721 bonds= 0.001 angles= 0.42 scale= 3.40 r_work= 0.2520 r_free= 0.2720 bonds= 0.001 angles= 0.42 scale= 3.80 r_work= 0.2516 r_free= 0.2719 bonds= 0.001 angles= 0.43 scale= 4.20 r_work= 0.2513 r_free= 0.2719 bonds= 0.001 angles= 0.43 scale= 4.60 r_work= 0.2510 r_free= 0.2718 bonds= 0.001 angles= 0.43 scale= 5.00 r_work= 0.2501 r_free= 0.2717 bonds= 0.002 angles= 0.44 scale= 6.00 r_work= 0.2494 r_free= 0.2718 bonds= 0.002 angles= 0.45 scale= 7.00 r_work= 0.2488 r_free= 0.2716 bonds= 0.002 angles= 0.46 scale= 8.00 r_work= 0.2481 r_free= 0.2715 bonds= 0.002 angles= 0.46 scale= 9.00 r_work= 0.2476 r_free= 0.2714 bonds= 0.002 angles= 0.47 scale= 10.00 r_work= 0.2561 r_free= 0.2729 bonds= 0.001 angles= 0.41 scale= 0.85 r_work= 0.2563 r_free= 0.2729 bonds= 0.001 angles= 0.41 scale= 0.70 r_work= 0.2567 r_free= 0.2730 bonds= 0.001 angles= 0.42 scale= 0.55 Final r_work= 0.2476 r_free= 0.2714 bonds= 0.002 angles= 0.47 The resolution is about 1.95A and I think the angles/bonds are a little too tight. My wxc_scale is currently set to 0.01. Does optimize_wxc use this as a starting point/does it matter what this value is set to when optimize_wxc =True ? Is the scale= result in the output really wxc_scale? 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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fwd: Reminder: Fourth annual CCP4 summer school in USA, at APS, June 7-15
by Nathaniel Echols 18 Jan '11

18 Jan '11

---------- Forwarded message ---------- From: "Sanishvili, Ruslan" <rsanishvili(a)anl.gov> To: <phenixbb(a)phenix-online.org> Date: Tue, 18 Jan 2011 12:44:58 -0600 Subject: Reminder: Fourth annual CCP4 summer school in USA, at APS, June 7-15 Dear Colleagues, This is a reminder that the on-line applications are being accepted for the 4th annual CCP4 summer school “From data collection to structure refinement and beyond”, which will take place early June, 2011 at the APS near Chicago. There is no registration fee for the school. The students will be responsible for their own travel and lodging expenses. These and other details (application process, accommodations, site access, contacts etc) can be found at the workshop website at http://www.ccp4.ac.uk/schools/APS-2011/ The school will include data collection, processing, structure solution, model building, refinement, validation, automation of many steps etc. Participants are encouraged to bring their own crystals, raw data or processed data for hands-on problem solving under the guidance of software developers and other experts. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov

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phenix.refine & twinning
by Nicholas Cody Sennett 18 Jan '11

18 Jan '11

Can phenix detwin data? I have tried to input the twinning law (l,-k,h) but phenix.refine does not create the appropriate maps and there is no appreciable change in R-factor. I have attached my xtriage and refinement logs. Thanks, Nick

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Partial charges / fractional charges
by Romain Talon 17 Jan '11

17 Jan '11

Dear Phenix bulletin board users, I would like to know if there is a way to introduce a partial or a fractional charge for a given atom in a structure subjected to a refinement with phenix.refine ? It is maybe totally useless to put a charge equal to -0.5 instead of -1 for an oxygen which is involved in a non-covalent binding with an ion but I didn't found any information about that... I thank you a lot in advance. Romain. -- ----- -------- ---------------------------------------------------------- Romain TALON Extremophile and Large Molecular Assemblies Team (E.L.M.A) Institut de Biologie Structurale 41, rue Jules Horowitz 38027 GRENOBLE Cedex 1 Tel: +33 (0)438.78.95.93 ----------------------------------------------------------

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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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