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Rosetta compile problem
by miyatake 13 Nov '14

13 Nov '14

Dear all, I tried to compile Rosetta for rosetta_refinement, on Mac OX10.10. I run " /rosetta_2014.22.56873_bundle/main/source] user% sudo scons.py But it was in failure, showing the following message: g++-4.2 -o build/external/debug/macos/14.0/64/x86/gcc/4.2/default/dbio/cppdb/atomic_counter.os -c -isystem external/boost_1_55_0/ -isystem external/include/ -isystem external/dbio/ -pipe -ffor-scope -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -m64 -march=nocona -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_SUFFIX=\".dylib\" -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_DISABLE_SHARED_OBJECT_LOADING -DCPPDB_DISABLE_THREAD_SAFETY -DCPPDB_SOVERSION=\"0\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -Ibuild/external/debug/macos/14.0/64/x86/gcc/4.2/default/dbio/sqlite3 -Iexternal/dbio/sqlite3 -Iexternal/boost_1_55_0 -Iexternal/dbio -I/usr/include -I/usr/local/include external/dbio/cppdb/atomic_counter.cpp sh: g++-4.2: command not found scons: *** [build/external/debug/macos/14.0/64/x86/gcc/4.2/default/dbio/cppdb/atomic_counter.os] Error 127 scons: building terminated because of errors. How can I resolve that? Best regards, H. Miyatake

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simulated annealing omit map
by Singh, Bishal 13 Nov '14

13 Nov '14

Hello everybody, I am generating figures showing the electron density map around the ligands. I deleted the ligands from final co-ordinate file and then performed refinement with identical parameters as before while keeping simulated annealing=true. I shall be thankful if someone could suggest me whether I consider mFo-DFc map or 2mFo-DFc map or both. Kindly also tell me the minimum acceptable contour level required for showing difference map. All structures are at 1.4 - 2.0 angstrom resolutions. Regards, Bishal

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Settings-Directories of MR-Rosetta wizard is altered when phenix-GUI is restarted?
by Martin Moche 13 Nov '14

13 Nov '14

Dear colleagues, When restarting phenix followed by opening the "MR-Rosetta(beta)" the Settings-Directories need to be reset each time? How can I set Rosetta binary directory name: Rosetta binary name: Rosetta script directory name: Rosetta database directory name: in Settings-Directories of "MR-Rosetta(beta)" wizard (or elsewhere) so that they do not change each time I restart the phenix-GUI? These settings are not changed: Base output folder: Rosetta path: Likely "Rosetta path" does not change between phenix-GUI restarts since PHENIX_ROSETTA_PATH is set in the shell as: echo $PHENIX_ROSETTA_PATH /software/apps/rosetta/2014.35/gcc01/rosetta_2014.35.57232_bundle The "Path to Rosetta" in "Phenix preferences - Wizards" is currently left blank since $PHENIX_ROSETTA_PATH is set in the shell. I have by accident started a few jobs with mixed (new and old) settings and phenix-GUI starts without error messages and all processors are running 100% CPU, however likely in some infinite loop since no work is performed beyond "place model"... Best regards, Martin Martin Moche, Ph.D. Head of Protein Crystallography Karolinska Institutet MBB/PSF Scheeles väg 2 171 77 Stockholm Sweden phone: +46-8-524 868 43 mobile: +46-73-322 93 27 fax: +46-8-524 868 68 email: Martin.Moche(a)ki.se

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fix atoms during refinement
by CPMAS Chen 10 Nov '14

10 Nov '14

Dear All Phenix Users, Is there a way to fix certain atoms position during refinement? I have some heavy atoms identified with MR-SAD, but when I build the whole molecule and have phenix to refine its position, the heavy atom's position is shifted from the anomalous signal. Therefore I would like to have these heavy atoms positions fixed during refinement. Thanks! Charles -- *************************************************** Charles Chen Research Associate University of Pittsburgh School of Medicine Department of Anesthesiology ******************************************************

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Ringer
by Ivan IVANOV 10 Nov '14

10 Nov '14

Dear All, I am trying to use ringer with a model I have. I followed the tutorial for Calmodulin and it worked very well for my protein. (http://bl831.als.lbl.gov/ringer/ringer/Tutorial/tutorial.htm). Now I have all files sigma vs chi angles for the residues I want and also the list of peaks identified above the sigma cutoff I selected. I am struggling to analyse the outputs as it is shown on the calmodulin exemple. I found this website (http://bl831.als.lbl.gov/ringer/ringer/Documentation/ringerManual.htm#Userp…) which is explaining very briefly how to plot all different conformation vs chi angles and how to show all selected amino acid conformation in the electron density (4.4 Plotting Accessory). I have to admit that this is not straigthforward for me to plot all outputs in a comprehensive way. Does anyone of you have a script to run with ringer outputs and get the final figures as it is shown on both websites ?? Kind regards, Ivan -- Ivan Ivanov, PhD PostDoctoral fellow at EMBL, European Molecular Biology Laboratory, Structural biology of RNA-protein complexes, Dr. Stephen Cusack, EMBL 71, avenue des Martyrs CS 90181 38042 Grenoble Cedex 9 T: +33 (0)4 76 20 7630 T(lab): +33 (0)4 76 20 7014 Email: ivanov(a)embl.fr Url: http://www.embl.fr

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"Femtosecond crystallography of membrane proteins in lipidic cubic phase (LCP)” Webinar
by Angela Criswell 04 Nov '14

04 Nov '14

Dear colleagues, I would like to draw your attention to an upcoming free, educational webinar to be presented by Dr. Wei Liu titled “Femtosecond crystallography of membrane proteins in lipidic cubic phase (LCP).” Despite recent technological advances in heterologous expression, stabilization and crystallization of membrane proteins, structural studies remain difficult. Wei’s presentation will describe the use of serial femtosecond crystallography of membrane proteins in LCP and how this approach holds promise to interrogate this difficult, yet important, class of proteins. This webinar is scheduled to occur on Thursday, November 13th at 11:00 AM CST (9:00 AM PST / 5:00 PM GMT). You can find an abstract and registration link for this webinar at: http://www.rigaku.com/webinars. We hope you will join us for the event. Best regards, Angela Criswell -- Angela Criswell VP, Life Science X-ray Products Rigaku Americas Corporation 9009 New Trails Drive The Woodlands, TX 77381 USA Ph: +1 281 362 2300 ext. 216 Fax: +1 281 364 3628 Email: angela.criswell(a)rigaku.com URL: http://www.rigaku.com Subscribe to Rigaku eNewsletters<http://www.rigaku.com/subscribe>

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green ball in aspartate
by Murpholino Peligro 31 Oct '14

31 Oct '14

Hi Everybody. Does anybody knows what could this be? Blue map at 1rmsd Green and red map at 3.5 rmsd Purple map (FEM map) at 1rmsd Conditions 100mM sodium acetate, NaCl 10% w/v, cryo=glycerol 30 % v/v; protein is hen egg white lysozyme (usual condition, usual protein and ohh..almost forget it.. ascorbic acid at 0.5 M) A water molecule overlaps with the oxygen atom (OD1) of the aspartate residue. So it is not a water molecule. Any ideas? (In coot -> validate-> difference map peaks and holes-> its the only one at 7.7 rmsd) Thanks

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[ot]: nedit on Mac 10.10 yosemite
by Sebastiano Pasqualato 29 Oct '14

29 Oct '14

Hi folks, sorry for the off-topic and slightly ‘demodée’ question, but, since I updated to Yosemite on my Mac, "nedit" does not work any more. Here’s the error message: Seba@host041:~> nedit dyld: Library not loaded: /usr/X11R6/lib/libXp.6.dylib Referenced from: /Applications/nedit/nedit Reason: image not found Trace/BPT trap: 5 Seba@host041:~> Anybody knows if there is a fix for that? Thanks in advance, S -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990 web http://is.gd/IEO_XtalUnit

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Fwd: Postdoc position in acoustic crystal preparation and high throughput screening at NSLS II
by Nathaniel Echols 28 Oct '14

28 Oct '14

---------- Forwarded message ---------- From: "Soares, Alexei" <soares(a)bnl.gov> To: "CCP4BB(a)JISCMAIL.AC.UK" <CCP4BB(a)jiscmail.ac.uk>, "cnsbb(a)yahoogroups.com" <cnsbb(a)yahoogroups.com>, "pdb-l(a)rcsb.org" <pdb-l(a)rcsb.org>, " phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org>, " x-plor(a)net.bio.net" <x-plor(a)magpie.bio.indiana.edu>, "xtal-log(a)net.bio.net" <xtal-log(a)magpie.bio.indiana.edu> Cc: Date: Tue, 28 Oct 2014 14:44:30 +0000 Subject: Postdoc position in acoustic crystal preparation and high throughput screening at NSLS II *Postdoctoral Research Associate – Macromolecular Crystal Preparation for NSLS-II* *2-year Term Position* *BNL Overview:* Brookhaven National Laboratory is a nonprofit research and development institution whose purpose is to advance ideas and knowledge through a multidisciplinary program of basic and applied research. *Project Overview:* A postdoctoral position is available to develop new crystal-preparation technologies to advance the use of serial macromolecular crystallography (MX) at NSLS-II. This new synchrotron will soon begin operation at Brookhaven National Laboratory. The individual will develop technologies for crystallization, drug discovery, and crystal handling to make serial crystallography possible, using various technologies, including acoustic droplet ejection (ADE). The project will provide the capability for experimenters to employ nanoliter quantities of material to produce specimens for diffraction studies with a large number of discrete experiments in a small area. This will exploit the micro-beam capabilities of NSLS-II MX beamlines; both room temperature and cryogenic serial crystallography strategies will be explored. High-throughput screening will be used for different types of structural biology projects (crystallization conditions, fragment binding, etc). The individual will work closely with a broad technology-development team. Our team members have different areas of expertise, from 3D labware design to research on medically relevant expressed proteins. No experience with ADE is necessary. *Essential Duties and Responsibilities:* The successful candidate will assist in the development and implementation of procedures and computer algorithms that leverage the Echo 550 instrument for macromolecular crystallography applications for serial crystallography applications in the few-nanoliter regime. The candidate will also develop novel technologies as well as improve existing technologies, and will have opportunities to participate in other related projects in a large and diverse group. *Required Knowledge, Skills and Abilities:* - Ph.D. in an appropriate chemistry, biology, or physics discipline; structural biology, crystallography, or a related field will have preference - Demonstrated experience (preferably including publications) in innovative experimentation and/or methods development with crystallography or drug discovery - Experience with conventional crystallization, and familiarity with micro crystallization and handling of micro crystals will be valuable - Experience in computer programming - The candidate must have a demonstrated ability to work with a team. *Other Information:* BNL policy states that Research Associate appointments may be made to those who have received their doctoral degrees within the past five years. *Please apply to Job # 137 on our jobs website:* *http://www.bnl.gov/HR/careers/ <http://www.bnl.gov/HR/careers/> * At Brookhaven National Laboratory we believe that a comprehensive employee benefits program is an important and meaningful part of the compensation employees receive. Our benefits program includes but is not limited to: - Medical Plans - Vacation - Holidays - Dental Plans - Life Insurance - 401(k) Plan - On-site Child Development Center, Swimming Pool, Weight room Tennis Courts, and many other employee perks and benefits.

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R/R free reported values
by Cedric 28 Oct '14

28 Oct '14

Hi Phenix and CCP4 community, (sorry for the cross posting). I was looking at a PDB file. The http://www.rcsb.org/ website page gives the following values: R-Value: 0.103 (work) R-Free: 0.134 The actual PDB file gives the following: R :0.110 FREE R VALUE : 0.170 I was wondering why the difference. The structure is 1.0A resolution 2CWS. Thank you, ____________________________________________________________ FREE ONLINE PHOTOSHARING - Share your photos online with your friends and family! Visit http://www.inbox.com/photosharing to find out more!

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