- phenixbb - phenix-online.org

Molecular replacement with fixed solution
by Muhammed bashir Khan 19 Jan '15

19 Jan '15

Hi There; I want to solve the structure with molecular replacement using phaser in phenix GUI. When I get solution from the one, how I can use as it as already solution using phenix in the next run. I use the "ensamble is fixed partial solution" but seems its not working. Any suggestion will be highly appreciated. Thanks Regards -- Muhammad Bashir Khan ************************************************** Department for Structural and Computational Biology Max F. Perutz Laboratories University of Vienna Campus Vienna Biocenter 5 A-1030 Vienna Austria Austria Phone: +43(1)427752224 Fax: +43(1)42779522

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sudden increase of clashscore
by Smith Lee 19 Jan '15

19 Jan '15

Dear All, In a Phenix refinement, with refinement settings as default in the graphics interface, at 2' rsrl stage the clashscore suddenly increases to more than 50, and then gradually decreases to lower than 20. Will you please tell me why this can occur? And what its effect on the refinement? Smith

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Re: [phenixbb] questions related to Phenix refinement
by Kay Diederichs 18 Jan '15

18 Jan '15

Dear Pavel, Am 18.01.15 um 07:23 schrieb phenixbb-request(a)phenix-online.org: > Date: Sat, 17 Jan 2015 20:36:30 -0800 > From: Pavel Afonine <pafonine(a)lbl.gov> > To: Smith Lee <smith_lee123(a)yahoo.com>, "phenixbb(a)phenix-online.org" > <phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] questions related to Phenix refinement > Message-ID: <54BB384E.30602(a)lbl.gov> > Content-Type: text/plain; charset="windows-1252"; Format="flowed" > > Hello Smith, > >> > 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? > Completeness is how many reflections you have compared to theoretically > possible. So the higher completeness the better. Ideally (and it's not > that uncommon these days) you should have 100% complete data set in > d_min-inf resolution. Anything below say 80 in any resolution bin is > bad, and numbers you quote 6-60% mean something is wrong withe the dataset. > Given your standing in the community, the last sentence will lead many unexperienced people to believe that they should cut their data at the resolution where the completeness falls below "say 80"%. But that would be wrong. There is no reason to consider a completeness as "too low in a high-resolution shell" as long as the data in that shell are good. Particularly in refinement any reflection helps to improve the model, and to reduce overfitting. Of course, more complete is better! Nowadays there should be no reason _not_ to get >95% (>99% in high-symmetry spacegroups) completeness in the low resolution shells, unless people stick to the "collect minimum rotation range" paradigm, and get the starting angle (or the point group!) wrong. best, Kay

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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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