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FW: question regarding Table1
by SD Y 18 Jan '15

18 Jan '15

From: ccp4_sc(a)hotmail.com To: phenixbb-request(a)phenix-online.org Subject: question regarding Table1 Date: Fri, 16 Jan 2015 20:30:47 -0600 Hi Everyone, I used phenix refined pdb, mtz and original mtz in the latest version of phenix to generate Table 1 and I felt the following was not right. I am not sure of the reason. R-merge 1.193e-17 (1.036e-17) R-meas 1.688e-17 CC1/2 1 (1) CC* 1 (1) Let me know . I appreciate your comments. Regards,SDY

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questions related to Phenix refinement
by Smith Lee 18 Jan '15

18 Jan '15

Dear All, In the X-ray statistics by resolution bin of the Phenix.refine result, there is a column "%complete". For my refinement data, I find the better the resolution (from lower resolution to the higher resolution), the lower the completeness (for example for 40-6 A, %complete is 98, for 3.1-3.0 A, %complete is 60%, for 2.2-2.1 A, %complete is 6%). Will you please tell me what does this "%complete" mean? why it decreases in the better diffraction bin? For the Ramachandran restrain in the Phenix.refine, there was a recommendation that for good resolution (I forget how much exactly, maybe 2.5 A), do not use Ramachandran restrain. But for a crystal data with resolution better than 1.5 A, in the X-ray statistics by resolution bin of the Phenix.refine result, there are more rows with resolution poorer than the defined 2.5 A (for example 40-6 A,6-3 A), although the crystal has a resolution better than 1.5 A (for example 1.4 A), can I use Ramachandran restrain in the Phenix.refine in this situation? If I use Ramachandran restrain in the Phenix.refine, I find the R-work and R-free level goes up, can we say the strategy of Ramachandran restrain in my refinement was not appropriate? I am looking forward to getting your reply. Smith

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Xray / neutron joint refinement
by Anna Makal 16 Jan '15

16 Jan '15

Hi, I have just done a joint x-ray / neutron refinement in Phenix using 5PTI structure and data from PDB. The input contains H atoms, with positions as refined against neutron dataset. In the resulting model, all H atoms ended up in 'idealized X-ray' positions (C-H distance of 0.96A), just as they would if I performed refinement against xray data only with riding model for H hydrogen atoms. Is it possible to run joint X-ray neutron refinement in such a manner that final H atoms positions are based on neutron data? Regards, Anna Makal

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Phenix - Research Scientist Position
by Paul Adams 15 Jan '15

15 Jan '15

Lawrence Berkeley Laboratory Career-track Research Scientist Job ID: 80447 Division: Physical Biosciences Date Opened: 1/14/2015 https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=en&job=80447 Summary: A research scientist position is available to work on developing new methods for macromolecular structure determination and refinement with the PHENIX software system. To learn more about Phenix visit: http://www.phenix-online.org Duties: This position will develop and maintain a powerful graphical user interface for the PHENIX system, and develop code within the Computational Crystallography Toolbox (cctbx). This position will include the development of new methods for crystallographic structure determination and completion in the context of the PHENIX program. This position also has a significant responsibility for the maintenance of PHENIX automated compilation tools, web-based interfaces for software downloads and coordinating releases of Phenix to the user community. The incumbent will work under the general direction of the Principal Investigator (PI; Paul Adams) for this project. Duties will also include testing, documentation writing, and extensive interaction with users and other developers. Qualifications: Demonstrated expertise with computational methods for protein crystallography. First-author publications in the area of macromolecular crystallography. Familiarity with software development: C++ and the Python scripting language. Advanced knowledge of Python-based or similar graphical user interface development tools. Solid interpersonal skills and the ability to work in a team environment are critical. A Ph.D. in computational crystallography, biophysics, chemistry, computer science, or related field is strongly preferred. Note that this is a multi-year position that is renewed annually on the basis on performance and continued funding. Berkeley Lab addresses the world’s most urgent scientific challenges by advancing sustainable energy, protecting human health, creating new materials, and revealing the origin and fate of the universe. Founded in 1931, Berkeley Lab’s scientific expertise has been recognized with 13 Nobel prizes. The University of California manages Berkeley Lab for the U.S. Department of Energy’s Office of Science. Berkeley Lab is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, national origin, disability, age or protected veteran status. Learn more at http://www.lbl.gov. -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 64, Room 248 Building 80, Room 247 Building 978, Room 4126 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: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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Reducing R/R-free
by George D 14 Jan '15

14 Jan '15

Hi Phenix users, I was looking at the phenix-refine manual and it mentions running optimize_mask=true optimize_xyz_weight=true optimize_adp_weight=true I was wondering what else I could try to bring the Rw/Rf down by 1-2% if possible, just wondering if there are any other strategies I could try. Thank you, George

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phenix.pdb_as_cif
by jp d 14 Jan '15

14 Jan '15

hi,of course, i should have included the versionphenix.version_1.9-1692 the pdb has done more digging and included this comment "Aside from the asym_id, there is another way we use for the mapping, _atom_site_anisotrop.id should map(for ANSIO) to _atom_site.id(for ATOM). This is one-by-one match for each atom. If you look at the file, you see that in the ATOM section, you have ATOM 99999 N3 . U . 367 ? -23.56200 29.36600 106.68800 1.000 135.52000 N ? UC ? 11964 1 ATOM 100000 C4 . U . 367 ? -23.35700 30.62600 106.16100 1.000 133.22000 C ? UC ? 11964 1 But in the ANISO section, you have 99999 N3 . U . 367 ? 2.04230 1.43260 1.67410 -0.19220 -0.28280 -0.16500 A0000 C4 . U . 367 ? 2.00150 1.41600 1.64420 -0.1 8730 -0.28010 -0.16450 i.e. the atom No. after 99999 is inconsistent between the two sections. The ANISO should use 100000. " thanksjpd

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Importing project to Phenix
by Emilia C. Arturo (Emily) 14 Jan '15

14 Jan '15

Hello, I'd like to take a phenix project (on which I've been working successfully on the Mac where I initially created the project) from one Mac to another Mac. When I tried to use the 'Import project' tool on the new computer, I got a notification that "[...] the directory must contain the PHENIX project tracking data (a sub-directory named 'phenix' or '.phenix', and associated files)." Unfortunately, I didn't see a sub-directory named 'phenix' or '.phenix' in the folder where all my project files had been created and stored, and wasn't sure what to do about it, so I proceeded with the Import anyway, to see what would happen. On the new computer, the project was imported seemingly successfully (e.g. the project history is all there), but when I tried to Run a refinement I'd configured for this project, I got an error about the missing '.phenix' file. The error is: "Cannot open file for write: [...] No such file or directory: [...]/.phenix/project_data/refine_22.eff' Can someone help me figure out how to properly move a project from one computer to another? Thank you, Emily.

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pdb_as_cif
by jp d 14 Jan '15

14 Jan '15

hi,I am making a large deposit to the pdb. To convert it to cif i usedphenix.pdb_as_cif model.pdb it looks like the ANISOU lines lose chain information.the PDB responded with this comment "The model coordinates file you output from Phenix is not complete. In the cif format file you deposited, if you look at the cif item _atom_site_anisotrop.pdbx_auth_asym_id, i.e. the column 5 of the Aniso section, you see value for every atom is dot ("."). The _atom_site_anisotrop.pdbx_auth_asym_id is just like the chain ID in the legacy PDB format, it should be consistent with the values of cif item _atom_site.auth_asym_id in the xyz section, otherwise there is no way to map between xyz Cartesian values and aniso values that are now separated in two sections." Do you reccomend another way to convert it to cif ? Thanksjpd

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map coefficients file
by Dialing Pretty 14 Jan '15

14 Jan '15

Dear All, Will you please tell me the subfixer of the map coefficients file, or which file is the map coefficients file? Dialing

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Applications for RapiData 2015 are now open
by Thomas Eriksson 13 Jan '15

13 Jan '15

The 2015 RapiData Course on Data Collection and Structure Solution will take place at the Stanford Synchrotron Radiation Lightsource (SSRL) from May 3-8 2015. The aim of the course is to educate and train scientists in data collection and processing methods at synchrotron beamlines, using state-of-the-art software and instrumentation. The course will comprise hands-on experiments at the SSRL beamlines, software tutorials, and lectures on sample preparation, data collection and reduction, phasing and complementary methods. For a more complete description of the course goals and format see http://www-ssrl.slac.stanford.edu/conferences/rapidata-2015/about.html The deadline for applications is February 23rd 2015. To apply follow this link: http://www-ssrl.slac.stanford.edu/conferences/rapidata-2015/apply.php Several scholarships are available from the International Union of Crystallography to cover partial travel and subsistence for Latin-American students, postdocs and junior faculty. Additional funds may be also be awarded to other participants (no restrictions) on a per need basis. Interested participants should apply for the course, and contact the organizers, enclosing a letter of recommendation from their supervisor. The Organizing Committee of RapiData2015 shall observe the basic policy of non-discrimination and affirms the right and freedom of scientists to associate in international scientific activity without regard to such factors as ethnic origin, religion, citizenship, language, political stance, gender, sex or age, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist which would prevent the participation of bona fide scientists. Ana Gonzalez and Clyde Smith -- ------------------------------------------- Ana Gonzalez <ana(a)slac.stanford.edu> Staff Scientist Stanford Synchrotron Radiation Lightsource 2575 Sand Hill Road, MS 99 Menlo Park CA 94025 Phone: (650) 926 8682 Fax: (650) 926 3292 -------------------------------------------

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Rosetta MR mmcif file subprocess failed
by Christian Roth 12 Jan '15

12 Jan '15

Hi phenix developers, I started a Rosetta MR run with a model pdb and the target sequence file. It seems that the initial MR run went fine and the Rebuilding Job for the best MR solution started. A sequence alignment is shown in the log file and than the job stops suddenly with the message Sorry: mmcif file must contain at least one data block. I can't even find a mmcif file in one of the folders. Any idea what might went wrong. Thanks in advance for your help. Christian

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6th workshop on Neutron Scattering Applications in Structural Biology
by Meilleur, Flora 12 Jan '15

12 Jan '15

Firth announcement 6th Workshop on Neutron Scattering Applications in Structural Biology Oak Ridge, TN. June 1 - June 5, 2015 Application deadline: April 10, 2015 The workshop on Neutron Scattering Applications in Structural Biology aims at enabling structural biologists to fully exploit the latest instrumentation and software development at the SNS and HFIR facilities at Oak Ridge National Laboratory. Attendees will participate in lectures and tutorials focusing exclusively on neutron techniques applied in structural biology. The workshop is designed for graduate students, post-doctoral fellows and faculty new to or with limited experience of neutron scattering. Travel and accommodation expenses are supported for selected participants from the United States. International applications are welcome. However the course organization is not able to support travel or accommodation. The number of participants will be limited to 15. There is no registration fee for all selected participants. The application package consisting of 1) Information form, 2) CV, 3) Applicant motivation letter (1/2 to 1 page), 4) Principal Investigator letter of support (for graduate students only; 1/2 to 1 page), should be sent electronically to meilleurf(a)ornl.gov<mailto:[email protected]> before April 10, 2015. Detailed information can be found on the workshop web page: https://public.ornl.gov/neutrons/conf/gcnb2015. Flora Meilleur, Ph. D Assistant Professor, Molecular and Structural Biochemistry North Carolina State University Neutron Sciences Directorate Oak Ridge National Laboratory Phone: 865-242-5747

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Rw/Rf -phenix - wwPDB Validation Server
by Haytham Wahba 11 Jan '15

11 Jan '15

1- after getting structure refined with phenix.refine to 0.145 , 0.164 Rw/Rf. and then you feel happy with that. then after using validation server from PDB you get 0.158 , 0.181 Rw/Rf. why this big jump for R free. why phenix.refine giving us low R free where in reality is not? 2- if i want to show kick map for metal binding site for publication, which map and how could i generate it. thank you for your help. HWUdeM

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A question related to phenix refine
by Dialing Pretty 11 Jan '15

11 Jan '15

Dear All, In a Phenix refinement process, the RMS angles fluctuates between 1.50 and 1.60, i..e., it does not decrease gradually. Can I accept the refinement result or not, and why? I am looking forward to getting a reply from you. Dialing.

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how can I merge denzo output files
by lbetts0508 . 10 Jan '15

10 Jan '15

I hope I am a dummy and I missed the obvious, but if I have a list of ".x" files from DENZO integration and want to merge and scale them as an mtz file in phenix or xds (I don't have access to scalepack) is there a pre-written program for that? Laurie Betts

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a question related to Phenix and Coot
by Dialing Pretty 10 Jan '15

10 Jan '15

Dear All, When I use WinCoot 0.8.1 to open a PDB file got by Phenix.refine, it comes, Fix Nomenclature Errors. Correct them? Asp [spec: 1 "A" 128 ""]PHE[spec: 1 "A" 134""]PHE [spec: 1 "A" 371""] But when I check the 3 residues, I cannot find any error. Will you let me know the issue? Dialing

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A question related to Phaser-MR (simple interface)
by Dialing Pretty 08 Jan '15

08 Jan '15

Dear All, When I run Phaser-MR, I met a fatal error "The composition you have entered has a protein/nucleic acidcontent of 132.513%, which is impossible. DECREASE your composition". Can you remind me in which black I fill the composition? And how to decrease it? Dialing

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advice on 'Fit rotatable H or D' refinement stage in phenix.refine
by Anna Makal 07 Jan '15

07 Jan '15

Hi, I would like to ask for advice concerning 'Fit rotatable H or D' refinement stage in phenix.refine. I am attempting to run unconstrained refinement on a certain high-resolution protein dataset: just XYZ and ADPs refinement for every single atom in the structure, with hydrogen atoms treated with individual approach. It turns out that when I set more then 3 macrocycles, the 'Fit rotatable H or D' refinement stage is activated in every macrocycle prior to 'XYZ individual' refinement stage. I am using version 1.9, release 1692 for windows. When I last worked with PHENIX, it was distribution 1342, and I am positive I have not come across such refinement stage. It seems that TARDY is involved at that stage. As I specifically do not want to introduce any kind of torsion angle dynamics in my current refinement, I would like to ask, what command/option shall I use to deactivate this stage of H-atom fitting in my refinement? With regards, Anna Makal

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Coot failed to launch in Phenix after CCP4 update
by Shun Liu 07 Jan '15

07 Jan '15

Dear all, After I updated ccp4 to a new version (ccp4-6.5), I found that coot failed to launch in phenix. /Applications/PHENIX-1.9-1692/Contents/phenix-1.9-1692/build/mac-intel-osx-x86_64/../../phenix/phenix/command_line/start_coot.sh: line 37: /Applications/ccp4-6.4.0/coot.app/Contents/MacOS/coot: No such file or directory Apparently it requires ccp4-6.4.0, which has been deleted. I tried to modify find_coot_command.py in phenix, but it didn’t work. Can anybody give me some suggestions so that I can figure this problem out? Thanks! Best, Shun

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Coot launch failure
by Shun Liu 06 Jan '15

06 Jan '15

Dear all, After I updated ccp4 to a new version (6.5), I found that coot failed to launch in phenix. Can anybody give me some suggestions to figure this problem out? Thanks! Best, Shun

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a question related to Phaser-MR
by Wind Sui 05 Jan '15

05 Jan '15

Dear All, In the Phenix Phaser-MR (simple interface, will you please tell me what should I input for the "sequence identities"? I am looking forward to getting your reply. Wind

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FEM maps
by Colin Levy 05 Jan '15

05 Jan '15

Dear All, when using FEM maps I notice that some solvent structure has clean (ish) 2Fo-Fc but not FEM density. Is this indicative of the water without FEM density being simply noise or is it more complicated than that? Many thanks, Colin Manchester Protein Structure Facility Dr. Colin W. Levy MIB G034 Tel. 0161 275 5090 Mob.07786 197 554 c.levy(a)manchester.ac.uk<mailto:[email protected]>

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phenix.refine reference?
by Ulrich Baumann 04 Jan '15

04 Jan '15

Dear colleagues, a very happy New Year 2015 to all of you! Is there a specific reference for phenix.refine, please? Or is it ok if we cite Adams et al., Acta Cryst D66, 213-221 (2010) or the 2011 paper on Phenix? What about Xtriage? Thanks you very much for your kind help! Best wishes, Ulrich

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a command on Phenix refine
by Wind Sui 04 Jan '15

04 Jan '15

Dear All, I use the graphic phenix.refine to do a refinement, and Phenix informed me I need to have a command "refinement.pdb_interpretation.clash_guard.nonbonded_distance_threshold=None". Will you please tell me by graphic phenic.refine, how can I input this command? Wind

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a question related to phenix.refine
by Wind Sui 04 Jan '15

04 Jan '15

Dear All, After I finished a refinement by Phenix.refine and I closed the Phenix software, is any method I can get the exact phenix.refine window as the moment the Phenix.refine just finished the refinement? I mean by all the documents saved automatically by the Phenix.refine after it finished a refinement, how can I get the Phenix refine window once more, for the check of Log output, Run status, Results, MolProbity, Real-space correlation, Atomic properties, and sequence check? Wind

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Fw: Reading a shelx file
by Rex Palmer 25 Dec '14

25 Dec '14

Can I read a Shelx file with Phenix and output the new pdb in Phenix format? Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://rexpalmer2010.homestead.com

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Announcement: Membrane Protein Structures 2015 Meeting (MPS 2015)
by Nagarajan Venugopalan 22 Dec '14

22 Dec '14

Posted on behalf of the organizing committee: Registration is now open for Membrane Protein Structures 2015 Meeting (MPS 2015) Location: Argonne National Laboratory, Lemont, IL, USA Dates: April 10 - 12, 2015 Accompanying workshops: Membrane Protein Technologies Location: Argonne National Laboratory, Lemont, IL, USA Date: April 9, 2015 Meeting WEBsite: http://aps.anl.gov/mps2015. _Important dates_: _Registration deadline_: February 15, 2015 (https://www.regonline.com/mps2015) _Accommodation deadline_: March 10, 2015 (http://www.aps.anl.gov/Users/Communications/User_News/2014/MPS_hotel_info.p…) Thanks Naga -- ************************************************************************ Nagarajan Venugopalan, Ph.D. GM/CA@APS, Sector 23, X-ray Science Division Bldg 436, D005 Argonne National Laboratory 9700 S Cass Ave, Argonne IL 60439 Tel: 630-252-0669 Fax: 630-252-0667 email: vnagas(a)anl.gov ************************************************************************

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29th European Crystallographic Meeting
by Igor Sabljić 22 Dec '14

22 Dec '14

Dear Phenixbb users, I am delighted to tell you the registration for the 29th European Crystallographic Meeting is open. Just to remind you ECM29 (August 23-28, 2015) is taking place in beautiful city of Rovinj in Croatia. You can find more information on our web site, and please visit, like and share our Facebook page! I hope I will see you all there! Web: http://ecm29.ecanews.org/ Facebook: https://www.facebook.com/29thEuropeanCrystallographicMeeting?ref=hl Sincerely, Igor [1] IGOR SABLJIĆ _Social networks editor_ Ruđer Bošković Institute Division of Physical Chemistry Bijenička cesta 54, 10000 Zagreb, CROATIA http://ecm29.ecanews.org [1] Facebook [2] home [3] Links: ------ [1] http://ecm29.ecanews.org [2] http://www.facebook.com/29thEuropeanCrystallographicMeeting [3] http://www.irb.hr/eng/Research/Divisions-and-Centers/Division-of-Physical-C…

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Phenix Rosetta install
by Felipe Trajtenberg 22 Dec '14

22 Dec '14

Dear all, I am trying to build the hybrid installation between Rosetta and Phenix using the rosetta.build_phenix_interface command Phenix version: phenix-1.9-1692 Rosetta version: rosetta_2014.35.57232 I have no problem in compiling rosetta alone but when I try to build the hybrid system I get the following error: False scons: Reading SConscript files ... Running versioning script ... Done. (0.0 seconds) Could not find platform independent libraries <prefix> Could not find platform dependent libraries <exec_prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] ImportError: No module named site CalledProcessError: Command '['./update_options.sh']' returned non-zero exit status 1: File "/home/Xtal/Rosetta_phenix/rosetta_2014.35.57232_bundle/main/source/SConstruct", line 172: main() File "/home/Xtal/Rosetta_phenix/rosetta_2014.35.57232_bundle/main/source/SConstruct", line 163: SConscript("SConscript", "build") File "/home/Xtal/Rosetta_phenix/rosetta_2014.35.57232_bundle/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 614: return method(*args, **kw) File "/home/Xtal/Rosetta_phenix/rosetta_2014.35.57232_bundle/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 551: return _SConscript(self.fs, *files, **subst_kw) File "/home/Xtal/Rosetta_phenix/rosetta_2014.35.57232_bundle/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 260: exec _file_ in call_stack[-1].globals File "/home/Xtal/Rosetta_phenix/rosetta_2014.35.57232_bundle/main/source/SConscript", line 28: subprocess.check_call(["./update_options.sh"]) File "/home/Xtal/Phenix/phenix-1.9-1692/build/intel-linux-2.6-x86_64/base/lib/python2.7/subprocess.py", line 540: raise CalledProcessError(retcode, cmd) thanks in advance Felipe

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Cross-validation when test set is miniscule
by Derek Logan 19 Dec '14

19 Dec '14

Hi everyone, Right now we have one of those very difficult Rfree situations where it's impossible to generate a single meaningful Rfree set. Since we're in a bit of a hurry with this structure it would be good if someone could point me in the right direction. We have crystals with 1542 non-H atoms in the asymmetric unit that diffract to only 3.6 Å in P65, which gives us a whopping 2300 reflections in total. 5% of this is only about 100 reflections. Luckily the protein is only a single point mutation of a wild type that has been solved to much better resolution, so we know what it should look like and I simply want to investigate the effect of different levels of conservatism in the refinement, e.g. NCS in xyz and B, group B-factors, reference model, Ramachandran restraints etc. However since the quality criterion for this is Rfree I'm not able to do this. I believe the correct approach is k-fold statistical cross-validation, but can someone remind me of the correct way to do this? I've done a bit of Googling without finding anything very helpful. Thanks Derek ________________________________________________________________________ Derek Logan tel: +46 46 222 1443 Associate Professor mob: +46 76 8585 707 Dept. of Biochemistry and Structural Biology www.cmps.lu.se<http://www.cmps.lu.se> Centre for Molecular Protein Science www.maxlab.lu.se/crystal Lund University, Box 124, 221 00 Lund, Sweden www.saromics.com

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Mac backwards compatability
by Katherine Sippel 19 Dec '14

19 Dec '14

Hi all, I was trying to be a good child and update to the latest nightly build, but I noticed that the Mac options for dev-1893 and -1894 are all listed as OS X 10.9 rather than OS X 10.6.7+. I attempted to use the OS X 10.9 installer just to see if it would work (it does not). Is phenix no longer supporting older Mac OSs? I know you have more than enough OSs to keep track of, so there is no judgement in that statement. I am just trying to figure out if I am going to have to cave and begrudgingly update my OS. Thanks, Katherine -- "Nil illegitimo carborundum"* - *Didactylos

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secondary restraint refinement
by CPMAS Chen 17 Dec '14

17 Dec '14

Dear Phenix Users, How do I force some residues in a non-helix conformation? I have a 3A data, and have the protein model refined. But in some region, 3~4 residues are in the helix conformation, and the density fit is good. Anyway, let me say this, I want to force these residues in a non-helix conformation. I tweaked the model a little bit and load them in VMD, and make sure they are not helix anymore. I turn on secondary-structure-restraint in phenix, take out the helix remarks for these residues in the def file. but once the refinement is done, they are still in a helix region (phenix automatically secondary structure analysis, or viewed in VMD). Is there a feasible way to keep them away from helix conformation? Thanks! Charles -- *************************************************** Charles Chen Research Associate University of Pittsburgh School of Medicine Department of Anesthesiology ******************************************************

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number of alternate conformations allowed
by Scott Horowitz 17 Dec '14

17 Dec '14

Hi all, Does anyone happen to know the upper limit on the number of alternate conformations that phenix.refine can handle at once for a residue? From playing around with it, it seems that phenix.refine recognizes both letters and numbers in that position, but not a pound sign, so that would suggest it could at least handle 36, so long as I don't crash my computer trying that many. Is this correct, from anyone's experience/knowledge? Thanks, Scott -- Scott Horowitz, Ph.D. Research Associate Howard Hughes Medical Institute University of Michigan Department of Molecular, Cellular, and Developmental Biology Bardwell lab 830 N. University Ave, Room 4007 Ann Arbor, MI 48109 phone: 734-647-6683 fax: 734-615-4226

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how to use phenix.angle command?
by 李翔 16 Dec '14

16 Dec '14

Hi, I am trying to measure the angle between two DNA duplex domains. I used phenix.angle command for calculation. However, I get a wrong answer. Can anyone talk a little bit more details on this command please? I used a single strand DNA from each duplex to calculate the angle which I thought it might be working since it is calculating the axis. Thanks for your help! Sincerely, Xiang -- Li Xiang Department of chemistry, Purdue University Email：lixiang1642(a)gmail.com

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Reliable twinning fraction estimation
by Xiao Lei 11 Dec '14

11 Dec '14

Dear All, I have a x-ray dataset of a protein-DNA complex to 2.8 A resolution with space group P312 checked by phenix xtriage for twinning. The estimated twin fraction from the output of xtriage is: 0.115 (Britton analysis); 0.119 (H test) and 0.022 (maximum likelihood method). However, the L-test graph in xtriage shows my observed data almost perfectly overlay with theoretical perfect twin data. In addition, when I tried to use phenix to do refinement with twin law -h,-k,l, the log file shows my twin fraction estimation is 0.49, which is very high and much bigger than Britton analysis and H test estimation. As far as my understanding is that if a twin fraction is lower than 15%, I still have hope to solve the structure (molecular replacement in this case) with reasonable R value, but if the twin fraction is 0.49, which is almost a perfect twin, which makes detwin impossible and refinement will stall at high R values (in my case, R free start: 0.4199; R work start: 0.4121; and R free final: 0.4038 and R work final: 0.3640 after running phenix refinement with twin law -h, -k, l). My question: which twin fraction estimation is more reliable? is my data almost perfectly twined? I attached the graphs of L test, Britton analysis and twin estimation from phenix xtriage and part of log file from phenix refine here. Many thanks in advance. Xiao

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Autobuild with "build semet residues"
by Todd Jason Green 10 Dec '14

10 Dec '14

Hello all- I have been trying to use autobuild with a semet dataset. I have checked the "build semet residues" option in the autobuild gui. At some point after the composite build, the error below is generated and the final model has been stripped of all semethionines. I am using phenix version 1.8.4-1496 on a macbook. I have now downloaded the new version. But can someone expand on my problem. My input sequence and model pdb contain Methionine but I expected the rebuild process to alter them. Should I change the one letter code for semet from m to something else. -Todd . . . . Final composite model # 1 : AutoBuild_run_11_/MULTIPLE_MODELS/model.pdb_1 Final composite mtz # 1 : AutoBuild_run_11_/MULTIPLE_MODELS/resolve_composite_map.mtz_1 AutoBuild_combine_iter AutoBuild Run 11 Wed Dec 10 14:51:18 2014 AutoBuild_combine AutoBuild Run 11 Wed Dec 10 14:51:18 2014 Done with combine finished AutoBuild Run 11 Wed Dec 10 14:51:18 2014 Finishing AutoBuild Run 11 Facts written to AutoBuild_run_11_/AutoBuild_Facts.dat Warnings: Warning from subprocess run in AutoBuild_run_11_/TEMP0/AutoBuild_run_5_: NOTE: The following residues (and similar residues) from AutoBuild_run_5_/overall_ortho_best_bchain_molrep1_refmac1_semettomet_ed.pdb are not PROTEIN or do not match the sequence and will not be part of the building process : MSE B33, MSE B45, MSE B59, MSE B63, MSE B68, MSE B194, MSE B201, MSE B210, MSE B216, MSE B256, MSE B266, MSE B308, MSE A33, MSE A45, MSE A59, MSE A63, MSE A68, MSE A194, MSE A201, MSE A210, MSE A216, MSE A256, MSE A266, MSE A308, MSE C33, MSE C45, MSE C59, MSE C63, MSE C68, MSE C194, MSE C201, MSE C210, MSE C216, MSE C256, MSE C266, MSE C308, MSE D33, MSE D45, MSE D59, MSE D63, MSE D68, MSE D194, MSE D201, MSE D210, MSE D216, MSE D256, MSE D266, MSE D308, Warning from subprocess run in AutoBuild_run_11_/TEMP0/AutoBuild_run_5_: Warning: some residues not rebuilt successfully on cycle 2: Chain 'A': 32, 44, 200, 217- 221, 280- 299, 314- 323, Chain 'C': 22- 32, 39- 44, 148- 152, 163- 167, 188- 193, 211- 215, 217- 221, 334- 336, Chain 'B': 32, 44, 118- 122, 193, 227- 231, 309- 318, Chain 'D': 12- 32, 34- 44, 46- 50, 143- 147, 158- 162, 188- 193, 334- 336 Warning from subprocess run in AutoBuild_run_11_/TEMP0/AutoBuild_run_5_: Warning: some residues not rebuilt successfully on cycle 3: Chain 'A': 32, 39- 44, 193, 217- 226, 280- 294, Chain 'C': 22- 32, 34- 44, 46- 55, 153- 162, 193, 200, 211- 215, 217- 221, 242- 246, 324- 336, Chain 'B': 32, 44, 118- 122, 193, 262- 265, 319- 323, Chain 'D': 17- 32, 34- 44, 46- 50, 143- 162, 188- 193, 200, 334- 336

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Rigid body refinement at low resolution
by Jianghai Zhu 10 Dec '14

10 Dec '14

Hi all, I recently solved a complex structure at 8 Å. There are 3 molecules per asymmetric unit and each complex contains 8 domains. I was trying to do rigid body refinement in phenix.refine. However, all the rigid body refinement gave me worse Rfree, even at ultra-low resolution, and phenix.refine reversed the result to the original model. Anyway to make this rigid body refinement more stable? Is there a dampen factor in phenix.refine so that the program only moves a domain at a fraction of what it wants to, e.g. 1/2, 1/3… ? Thanks. Best, —Jianghai

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Not Updating Waters
by Ryan Henry Gumpper 09 Dec '14

09 Dec '14

Hi all, I am having an issue during refinement when using Phenix Refine. Every time I try to "update waters" it does not place or update the waters. My structure is 2.72 A. Is the resolution not good enough for this feature? If anyone has ideas, or if I need to supply more information, I would be happy to oblige as I am fairly new to the field and still learning. Thank you in advance!

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Ramachandran maps
by PC 09 Dec '14

09 Dec '14

Hi guys, Sorry for the repost in COOT/CCP4/PHENIX. It is possible on of the users in one of these communities might know the answer I was wondering if there is a small script I can use to generate the outline of the allowed regions of Ramachandran map on to which I can superimpose my coordinates phi and psi? Something like what appears in COOT->Validate->Ramachandran Plot. How does one generate such images for publications? Thank you, Patrick ____________________________________________________________ FREE 3D EARTH SCREENSAVER - Watch the Earth right on your desktop! Check it out at http://www.inbox.com/earth

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Challenging Mol.Rep. Problem
by Mo Wong 09 Dec '14

09 Dec '14

Hi all, I’m stuck on a rather complex molecular replacement problem. The crystals are of an antigen-Fab complex totaling ~67 kDa (waiting to confirm using PAGE gel). They diffract to ~3.5A at the synchrotron and process in C2 with dimensions 220x130x230 and beta at 103 so it looks like there are round 9to12-ish copies in the ASU. The overall Rmerge is high at ~25% with I/sig cutoff ~2 and redundancy of 5; however, at 4.5A this drops to ~15%. Furthermore, processing in P1 gives similar Rmerge values too. Self-Patterson doesn’t suggest translational symmetry, but the self-rotation function (SRF) suggests high NCS (see below/attached). I’m hoping the SRF might be helpful in trying to confirm/dismiss C2 is the likely space group, and perhaps suggest a logical assembly with the ASU (I see strong 2-fold and 3-fold NCS operators suggesting to me dimeric trimers or vice versa - however, I’ve never had to really analyze SRFs in the absence of a mol. rep. solution so my interpretation could be wrong). Anyway, any help to bringing a molecular replacement solution closer to reality would be appreciated. Thanks! [image: Inline image 1]

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Re: [phenixbb] [ccp4bb] MR_ROSETTA
by Terwilliger, Thomas Charles 09 Dec '14

09 Dec '14

Hi Bashir, It is probably something very small to fix...can you send me the result of doing this: echo $PHENIX_ROSETTA_PATH echo $ROSETTA3_DB/ ls $PHENIX_ROSETTA_PATH//main/source/bin/mr_protocol* On my machine I get: [terwills-MacBook-Air:~] terwill% echo $PHENIX_ROSETTA_PATH /Users/terwill/unix/rosetta/rosetta_2014.30.57114_bundle [terwills-MacBook-Air:~] terwill% echo $ROSETTA3_DB/ /Users/terwill/unix/rosetta/rosetta_2014.30.57114_bundle/main/database/ [terwills-MacBook-Air:~] terwill% ls $PHENIX_ROSETTA_PATH//main/source/bin/mr_protocol* /Users/terwill/unix/rosetta/rosetta_2014.30.57114_bundle//main/source/bin/mr_protocols.macosclangrelease /Users/terwill/unix/rosetta/rosetta_2014.30.57114_bundle//main/source/bin/mr_protocols.python.macosclangrelease All the best, Tom T Could some body explain why I am getting the error message when running MR-Rosetta. Message is " Sorry cannot locate a binary starting with mr_protocol.default' in the directory /home/phenix/rosetta_2014.34.57213_bundle/main/source/bin I just download it and locate it in the preferences, wizard and then path to Rosetta. Thanks Bashir -- Muhammad Bashir Khan ************************************************** Department of Biochemistry University of Alberta, Canada Canada

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how to use a dimer as a search model by MRage
by fukamitka＠chugai-pharm.co.jp 09 Dec '14

09 Dec '14

Dear all, I have a dataset, there are 4 or 5 copies of two different hetero dimers (i.e. 4 different chains) in au, and I'd like to use the dimers as search models. I ran phenix.MRage with a phil file below, and it searched each chains separately, as expected. In this case, I want to search dimerA (containing chain1 and 2) and dimerB (chain3 and 4) as 2 search templates, but I couldn't find how to specify a dimer as a component. Using dimer.pdb and dimer.seq caused an error (sequence file can't contain multiple sequence). How do I write an input file? Regards, ------------------------- composition { count = 5 component { sequence = dimerA-chain1.seq stoichiometry = 1 template { pdb = dimerA-chain1.pdb } } component { sequence = dimerA-chain2.seq stoichiometry = 1 template { pdb = dimerA-chain2.pdb } } component { sequence = dimerB-chain3.seq stoichiometry = 1 template { pdb = dimerB-chain3.pdb } } component { sequence = dimerB-chain4.seq stoichiometry = 1 template { pdb = dimerB-chain4.pdb } } } ------------------------- ----- Takaaki Fukami (mailto:[email protected]) Discovery Research Dept. (Biostructure Gr.) Chugai Pharmaceutical Co.,Ltd.

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Re: [phenixbb] micro-beam?
by Edna Patricia Matta, Ms 09 Dec '14

09 Dec '14

Thanks everybody for the information, A good week to all, Edna Edna Patricia Matta, MSc. PhD Postdoctoral Fellow McGill University Goodman Cancer Centre 1160 Pine Avenue West, Room 614 Montreal, Quebec, CANADA, H3A 1A3 [http://www.med.mcgill.ca/nahum/images/tel.png] TEL: 1-514-398-7275 [http://www.med.mcgill.ca/nahum/images/fax.png] FAX: 1-514-398-1287 ________________________________ From: Jurgen Bosch [jbosch2(a)jhu.edu] Sent: Monday, December 08, 2014 11:47 AM To: Edna Patricia Matta, Ms Cc: phenixbb(a)phenix-online.org Subject: Re: [phenixbb] micro-beam? tiny is relative - for some tiny means 100 µm … APS has several beam line with 25 or 50 µm focus which are not considered microfiches but still small enough for most things. SSRL 12-2 would be another option 10µm ESRF 5µm (?) SLS 10 -50 µm Jürgen ...................... Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742<tel:%2B1-410-614-4742> Lab: +1-410-614-4894<tel:%2B1-410-614-4894> Fax: +1-410-955-2926<tel:%2B1-410-955-2926> http://lupo.jhsph.edu On Dec 8, 2014, at 11:40 AM, Edna Patricia Matta, Ms <edna.matta(a)mail.mcgill.ca<mailto:[email protected]>> wrote: Good morning everyone, I have very tiny protein crystals (verified) but I do not know what facility has micro-beam to shoot them, Any information that could help me? Thanks in advance, Best, Edna Edna Patricia Matta, MSc. PhD Postdoctoral Fellow McGill University Goodman Cancer Centre 1160 Pine Avenue West, Room 614 Montreal, Quebec, CANADA, H3A 1A3 TEL: 1-514-398-7275 FAX: 1-514-398-1287 _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/phenixbb

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compiling phenix from source error
by Maxime Cuypers 09 Dec '14

09 Dec '14

hi all, am getting the following error installing phenix from source dev-1839. (tried with source from 1.9-1692 with same error) am on latest kubuntu. any idea on how to debug? -see below report... PS: am compiling from source because i need a minor modification of the neutron scattering table which requires compilation. cheerios, .... Installing Xrender... log file is /pgmax/phenix-installer-dev-1839/install_tmp/intel-linux-2.6-x86_64/A7K/Xrender_install_log getting package xrender-0.8.3.tar.gz... using /pgmax/phenix-installer-dev-1839/gui/xrender-0.8.3.tar.gz Traceback (most recent call last): File "./bin/install.py", line 815, in <module> run(sys.argv[1:]) File "./bin/install.py", line 72, in __init__ self.install_from_source() File "./bin/install.py", line 292, in install_from_source log=out) File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 115, in __init__ self.build_cctbx_dependencies() File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 170, in build_cctbx_dependencies self.build_wxpython_dependencies() File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 440, in build_wxpython_dependencies self.build_wxpython_dependencies_linux() File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 507, in build_wxpython_dependencies_linux self.build_compiled_package_simple(pkg_name=pkg, pkg_name_label=name) File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 385, in build_compiled_package_simple log=pkg_log) File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 203, in configure_and_build self.call("./configure %s" % " ".join(list(config_args)), log=log) File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 200, in call return call(args, log=log) File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/installer_utils.py", line 53, in call raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc)) RuntimeError: Call to './configure --prefix="/usr/local/phenix-dev-1839/build/intel-linux-2.6-x86_64/base"' failed with exit code 1 max@A7K:/pgmax/phenix-installer-dev-1839$ uname -a Linux A7K 3.13.0-40-generic #69-Ubuntu SMP Thu Nov 13 17:53:56 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux -- Dr. Maxime Cuypers

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Announcement - NSLS-II Early-Science Workshop for NIH-funded beamlines
by Robert Sweet 08 Dec '14

08 Dec '14

Sent on behalf of the Workshop Organizing Committee The NIH-funded ABBIX structural biology beamlines at the NSLS-II are approaching completion, delivering two crystallography and one scattering beamline for biological sciences. The performance of these beamlines will present opportunities previously unattainable at synchrotron light sources, creating challenges for data collection and scientific discovery. The beamlines will provide a photon-beam flux density at least five orders of magnitude greater than that achievable at the NSLS, and orders of magnitude greater than that achievable today at any synchrotron light source. Participation in the first science undertaken at these beamlines represents a unique opportunity for scientists to help deliver on their potential. We are organizing a workshop at BNL, to occur on Jan. 28-29, 2015, to help define and develop further the priorities for the scientific commissioning of these beamlines and their entry into routine operation. Interested participants will be able to present and discuss their vision for the early science case for each beamline, thereby helping to shape the international scene for structural biology. Find workshop information at http://workshops.ps.bnl.gov/?w=ABBIXJan2015, including a draft agenda and an opportunity to register and submit an abstract.

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micro-beam?
by Edna Patricia Matta, Ms 08 Dec '14

08 Dec '14

Good morning everyone, I have very tiny protein crystals (verified) but I do not know what facility has micro-beam to shoot them, Any information that could help me? Thanks in advance, Best, Edna Edna Patricia Matta, MSc. PhD Postdoctoral Fellow McGill University Goodman Cancer Centre 1160 Pine Avenue West, Room 614 Montreal, Quebec, CANADA, H3A 1A3 TEL: 1-514-398-7275 FAX: 1-514-398-1287

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neighbouring residues with symmetry
by Swanand Gore 08 Dec '14

08 Dec '14

Hi All, I am sure this has been asked and answered a lot of times... Is there a python script somewhere that reads a mmcif file and for any residue in it, returns a list of residues within a certain distance of it. And it returns any symmetry-related copies of residues too within that distance. Any pointer greatly appreciated. Thanks, Swanand -- Swanand Gore, wwPDB at PDBe-EMBL-EBI, Cambridge swanand(a)ebi.ac.uk ............. http://pdbe.org

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Institut Pasteur/CCP4 Joint Macromolecular Crystallography School "From data processing to structure refinement and beyond"
by Alejandro Buschiazzo 06 Dec '14

06 Dec '14

Dear colleagues, We are pleased to announce the Workshop: Macromolecular Crystallography School "From data processing to structure refinement and beyond", to be held at the Institut Pasteur de Montevideo (Uruguay). Dates: April 6 - 16, 2015 Invited speakers: Paul Emsley, Cambridge, UK Richard Garrat, São Carlos, Brazil Ronan Keegan, Oxford, UK Eugene Krissinel, Oxford, UK Victor Lamzin, Hamburg, Germany Andrey Lebedev, Oxford, UK Andrew Leslie, Cambridge, UK Garib Murshudov, Cambridge, UK Rob Nicholls, Cambridge, UK Randy Read, Cambridge, UK William Shepard, Paris, France Pavol Skubak, Leiden, the Netherlands Clemens Vonrhein, Cambridge, UK A preliminary program, as well as the application forms and contact information, can be found in this www site <http://www.pasteur.edu.uy/index.php/es/futuroscursos>. (within the page, look for this workshop’s details) The www site will be updated regularly, so stay tuned. This activity is supported by the Reseau International des Instituts Pasteur (RIIP); the Collaborative Computational Project Nº4 (CCP4, UK) & Science and Technology Facilities Council (UK); the International Union of Crystallography (IUCr); and the Institut Pasteur de Montevideo. Organizers: Alejandro Buschiazzo, PhD. Institut Pasteur de Montevideo, Uruguay Ronan Keegan, PhD. CCP4, STFC Rutherford Appleton Laboratory, United Kingdom Applicants: 24 students will be selected among the applications. The Course will provide financial support for the students, covering registration fees, and for the case of those coming from abroad, all local expenses (lodging, per diem and local transportation). The application deadline is February 16, 2015. The results will be announced by March 6. Please address further inquiries to: mx2015(a)pasteur.edu.uy <mailto:[email protected]> Looking forward to welcoming you in Montevideo! -- Alejandro Buschiazzo, PhD Research Scientist Unit of Protein Crystallography Institut Pasteur de Montevideo Mataojo 2 020 Montevideo 11400 URUGUAY Phone: +598 25220910 int. 120 Fax: +598 25224185 http://www.pasteur.edu.uy/pxf

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neutron scattering table for specific metal isotope
by Maxime Cuypers 05 Dec '14

05 Dec '14

Hello, I would like to alter the neutron scattering table for phenix.refine so that it takes into account the correct bcoherent value for the metal isotope present in my structure. the difference is significative between the natural occurence bcoh... i have been looking around in chem_data but could not find the neutron scattering tables. does anyone have any idea where to look please? cheerios -- Dr. Maxime Cuypers

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adding hydrogens to custom peptide bonds
by Dale Kreitler 04 Dec '14

04 Dec '14

Hi All, I am trying to add riding hydrogens to a model that includes beta-3-homoglutamine (B3Q). The monomer is not in the ccp4 library but it is a PDB chemical component. So far I have used elbow to build and optimize my own version of the ligand using the atom naming convention for a beta-amino acid in the PDB (where CB is in the backbone adjacent to the amino group, so the backbone goes like C-CA-CB-N). I am using a TRANS cif link from the monomer library for the N(alpha-amino acid) to C(beta-amino acid), and I have defined my own cif link for the N(beta-amino acid) to C(alpha-amino acid). However when I run phenix.reduce I can't get hydrogens to appear on the peptide bonds between the beta-amino acid and adjacent alpha-amino acids (hydrogens appear every where else on the ligand and in the model). I realize the effect of two hydrogens on the model is inconsequential but I would like to figure out how I can get phenix.reduce to recognize the bonds to my "ligand" as standard peptide bonds and add hydrogens accordingly. Thanks, Dale -- Dale Kreitler Gellman Lab UW Madison, Department of Chemistry

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