- phenixbb - phenix-online.org

Rebuild fails in Rosetta-MR
by Rhys Grinter 23 Feb '16

23 Feb '16

Dear all, I'm currently trying to improve an model for a difficult MR problem using Rosetta-MR, When the program gets to the Rebuild stage it fails with the following message: *Error message:* child process stderr output: command: 'sh .../MR_ROSETTA_17/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_4/WORK_1/run_rebuild.sh"' .../MR_ROSETTA_17/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_4/WORK_1/run_rebuild.sh: line 5: 8996 Trace/BPT trap: 5 "/Applications/Rosetta/main/source/bin/mr_protocols.macosclangrelease" @"rebuild.flags" > "rebuild.log" 2>&1 Failed to run REBUILD Sorry: Failed to run REBUILD...see log file in .../MR_ROSETTA_17/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_4/WORK_1/rebuild.log Sorry: mr_rosetta failed... Sorry routine failed Please see log file for full error message *In the rebuild logfile:* dyld: lazy symbol binding failed: Symbol not found: ___sincos_stret Referenced from: /Applications/Rosetta/main/source/bin/mr_protocols.macosclangrelease Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___sincos_stret Referenced from: /Applications/Rosetta/main/source/bin/mr_protocols.macosclangrelease Expected in: /usr/lib/libSystem.B.dylib Has anyones experienced this error? Cheers, Rhys -- Dr Rhys Grinter Sir Henry Wellcome Fellow Monash University +61 (0)3 9902 9213 +61 (0)403 896 767

4 4

Problem refining structure, error message
by Natalia Ketaren 22 Feb '16

22 Feb '16

Hello, I’m building a structure at the moment, and I have since removed lithium ions from structure. However, when I go to refine using phenix, I get the error message: “No atom selected: name LI and Chain F and rename LI resseq 8” I’ve tried using earlier files, prior to my addition of lithium ions and I still get the same error message. I’m using Phenix version 1.10.1-2155-000 Could anyone help me overcome this error message? Cheers, Nat _____________________________ Natalia E. Ketaren, PhD Research Associate Rout Laboratory Box 213 The Rockefeller University 1230 York Avenue New York, NY 10065 Tel: (212) 327-8136 Fax: (212) 327-7193 Natalia.Ketaren(a)rockefeller.edu<mailto:[email protected]> website: http://lab.rockefeller.edu/rout/ NCDIR: http://www.ncdir.org/

6 7

different occupancies for same molecule; optimize final model question
by Georg Mlynek 22 Feb '16

22 Feb '16

On 02/21/2016 11:33 PM, Georg Mlynek wrote: > Dear scientific community, > > 1. > > if I put in the gui under Modify selections for: Occupancies / simple > occupancy refinement > > resname SO4 > resname GOL > > > > phenix outputs different occupancies for each of the elements in the > molecule. > > > > Is the atom selection syntax wrong or is it a bug? (Ready set is also > not flagging or correcting this, would be nice is this can be implemented) > > 2. I used phenix optimize final model and I wonder why it refines K > anisotropic but not NA and CL. > (I would be very nice, if the program could summarize at the end which > settings and strategies were finally used, so this can be added to the > publication: I know it is under development) > > > adp { > individual { > isotropic = not (element K) > anisotropic = (element K) > } > > } > occupancies { > individual = resname NA or resname K or resname CL > remove_selection = None > constrained_group { > selection = None > } > > > I am using ubuntu 15.10 > > phenix version dev-2313-000 > > Many thanks in advance, best regards Georg.

2 1

Fwd: Alternative method to Phenix_mr_rosetta
by Henry Fang 19 Feb '16

19 Feb '16

Hi All, Our group is working on an ab initial density modification method to solve the phase problem. Last year, I applied the methods to the cases with a initial template which has already been correctly placed in the unit cell. I tried several cases in the Terwilliger, T. C., et al. (2012). "phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta". Starting from the templates provided in the http://www.phenix-online.org/phenix_data/terwilliger/rosetta_2011/ I can get a initial density map, then apply our method to reduce the phase difference to around 50° in the highest experiment data resolution. Now, I might want to try more blind cases with our methods. If we can solve more structures, that would be more convincing. Do you have some suggestions? Where could I find some more unsolved structures? I might need structures with placed template and high solvent content (at least above 50%). Thanks, Henry

2 1

Fwd: Generate difference electron density maps for residues with multiple conformations
by Alejandro Virrueta 18 Feb '16

18 Feb '16

Hello all, I am trying to get the difference electron density maps for residues with multiple conformations after I set the occupancy of their atoms to 0. My main goal is to visualize the green positive density peaks that should appear for the atoms whose occupancy I set to 0. However, when I run the phenix.refine command (doing all of this via cli, not gui), the output pdb file I will try to illustrate my process and problem with an example that works fine and one that doesn't, side by side, step by step. 1. I generate a pdb file that has a chosen residue set to occupancy 0. See 'pdb_1agy_res_SER_resID_120_del.pdb' and 'pdb_1agy_res_SER_resID_129_del.pdb'. As you can see, the former has SER 120 set to 0 occupancy and has one conformation, and the latter has SER 129 set to 0 occupancy for BOTH of its conformations. Both files are correct up to this point. 2. I then execute the following command: phenix.refine *pdb_del_file* *mtz_file* main.number_of_macro_cycles=5 output.write_eff_file=False output.write_geo_file=False output.write_def_file=False refinement.input.xray_data.r_free_flags.generate=True --overwrite - with *mtz_file *set to '1agy.mtz' (from the PDB) and *pdb_del_file* set to either 'pdb_1agy_res_SER_resID_120_del.pdb' and 'pdb_1agy_res_SER_resID_129_del.pdb'. - This results in 2 files pdb_1agy_res_SER_resID_XXX_del_refine_001.mtz and pdb_1agy_res_SER_resID_XXX_del_refine_001.pdb. Comparing these pdb files, you can see that the occupancy for SER 120 remains set to 0 (which is what I want), but the occupancies for the 2 conformers for SER 129 have been filled in by phenix (not what I want) somewhere during the refinement process. As a result, I get the desired difference peaks for SER 120, but not for SER 129 (which seems to be averaged out). Other than deleting the 2nd conformation for SER 129, is there a way to solve this problem, preferably via command line arguments/flags? Thanks, Alex

2 5

correct space group for phenix.merging_statistics?
by Murpholino Peligro 18 Feb '16

18 Feb '16

Hi. Is it really important to have the correct space group in the mtz (or XDS_ASCII.HKL) file which will be the input for phenix.merging_statistics? I have space group= 89 And I know it is space group=96 Thanks

3 5

Fwd: Sorry: Fatal problems interpreting model file
by Alejandro Virrueta 17 Feb '16

17 Feb '16

Hello, How can I successfully execute the following command: phenix.refine pdb_1jbe_res_ALA_resID_101_del.pdb 1jbe.mtz main.number_of_macro_cycles=5 output.write_eff_file=False output.write_geo_file=False output.write_def_file=False refinement.input.xray_data.r_free_flags.generate=True --overwrite Currently, I am getting the following error: Sorry: Fatal problems interpreting model file: Number of atoms with unknown nonbonded energy type symbols: 8 Please edit the model file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary. I'm not a crystallographer, so I don't fully understand the error. I'm simply trying to automate this procedure for many PDBs, and this particular error has come up quite a few times. Can I resolve this issue by providing additional files or command line flags? Other files I have available are 1jbe.cif and 1jbe-sf.cif. File 'pdb_1jbe_res_ALA_resID_101_del.pdb' is similar to 1jbe.pdb, except that the occupancies for ALA 101 are set to 0. Thanks, Alex

2 1

Using phenix.real_space_refine with mmcif model?
by Oliver Clarke 16 Feb '16

16 Feb '16

Hello, Is it possible to use phenix.real_space_refine with mmcif input? When I attempt to run as "phenix.real_space_refine model.mmcif map.mrc" or "phenix.real_space_refine model.cif map.mrc" I get the error "Sorry: PDB file is needed", and looking at the documentation I cannot see how to explicitly specify the model (there is not "model" keyword or similar). Anybody have a way around this? Or is there a keyword I am missing? phenix.refine generally works fine with mmcif, but maybe real_space_refine has not been configured to do so yet? Would be helpful for large structures which break the regular pdb format if so. Cheers, Oli

2 1

Re: [phenixbb] Using PyMOL-1.8 with PHENIX-dev-2306
by acyang 16 Feb '16

16 Feb '16

Hi Billy Thanks for your reply. I installed phenix from source (phenix-installer-dev-2306-source.tar.gz). And I used scientific linux 7.1 for my workstation. I noticed that SCONS is adopted in the installation of phenix, and phenix will download a modified version of python (python_2.7.8_cci). I think the problem can be solved by adding a flag "--enable-unicode=ucs4" in configuring Python-2.7.8_cci. I'd appreciate if you can tell me how to modify the SCONS script file. by A.C. 2016-02-12 16:52 GMT+08:00 Billy Poon <bkpoon(a)lbl.gov>: > Hi, > > Are you installing phenix from source or from a binary distribution? And > which operating system are you using? I can give you the flags (in addition > to the --prefix flag for installing into the base directory) for the > configure step for either OS X or Linux. > > You can basically install Phenix normally, and then recompile our Python > from scratch with our regular flags and your extra flag. > > -- > Billy K. Poon > Research Scientist, Molecular Biophysics and Integrated Bioimaging > Lawrence Berkeley National Laboratory > 1 Cyclotron Road, M/S 33R0345 > Berkeley, CA 94720 > Tel: (510) 486-5709 > Fax: (510) 486-5909 > Web: https://phenix-online.org > > On Wed, Feb 3, 2016 at 3:05 AM, acyang <acyang0903(a)gmail.com> wrote: > >> Hi everyone >> >> I've installed pymol and phenix on my scientific linux7.1 workstation. >> I can launch pymol via the launching script($PYMOL_HOME/pymol) normally. >> But when I launched pymol in phenix GUI, I got some error as followed: >> >> ********************************************************************************************************************************* >> Traceback (most recent call last): >> File "/opt/PyMOL/modules/pymol/__init__.py", line 71, in <module> >> import pymol >> File "/opt/PyMOL/modules/pymol/__init__.py", line 521, in <module> >> import pymol._cmd >> ImportError: /opt/PyMOL/modules/pymol/_cmd.so: undefined symbol: >> PyUnicodeUCS4_SetDefaultEncoding >> >> ********************************************************************************************************************************* >> After STFW*, *I knew the problem is about unicode variant (UCS2, UCS4). >> I also checked the configuration of two python. >> For /bin/python (adopted by pymol) >> >> >>> import sys>>> print sys.maxunicode1114111 >> >> And for $PHENIX_HOME/base/bin/python (adopted by phenix) >> >>> import sys >> >>> print sys.maxunicode >> 65535 >> >> My question is : How do I add the flag --enable-unicode=ucs4 in configuring Python-2.7.8_cci. >> >> >> I'd appreciate if any reply on this. >> >> acyang >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> Unsubscribe: phenixbb-leave(a)phenix-online.org >> > >

2 2

Specify space group with phenix.map_to_structure_factors?
by Oliver Clarke 16 Feb '16

16 Feb '16

Hi, I frequently use phenix.map_to_structure_factors to generate mtz files from EM maps for use in Coot - it is by far the best tool I have found for this purpose. For convenience (so I can easily build and refine one protomer of a four-fold symmetric entity), I often convert these mtz files from the default P1 to P4 spacegroup using CCP4, and I wonder if it would be possible to include an option to specify the output spacegroup directly in map_to_structure_factors (or perhaps it is there and I have missed it?)? Even better would be if there were a way to check the symmetry and refine the orientation of the input volume such that the map is centered in the unit cell and the symmetry axis of the volume is appropriately aligned - often I have aligned the input volume to another reference volume in Chimera, and if the alignment is not perfect the symmetry axis of the volume might be slightly misaligned from what would become the fourfold axis of the output. Cheers, Oli.

2 1

Update: Check for radiation-induced reduction of a disulfide bond
by Ezequiel Noguera 15 Feb '16

15 Feb '16

Sorry, my previous email was incomplete. My structure has negative density in the center of some disulfides (the magnitude of this effect vary between different monomers in the ASU). I'd like to refine the structure in an "artificial reduced form", where cysteines involved in disulfides are treated in reduced form, but repulsions originating from neighboring sulfur atoms are turned-off, to monitor distances (I expect that SG atoms remain close to 2 A), guided only by data. Thank you, Ezequiel

4 5

ensemble refinement
by George Kontopidis 15 Feb '16

15 Feb '16

Does ensemble refinement run on Phenix version 1.10.1-2155 (for windows) If yes can it run from GUI or only using command line? George

4 7

REASONS UNKNOWN
by Almudena Ponce Salvatierra 15 Feb '16

15 Feb '16

-- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany

1 1

Re: [phenixbb] Arg, Glu, etc. naming conventions
by Mark A Saper 15 Feb '16

15 Feb '16

Apparently a torsion angle of –180° is considered very different from 0° because of the NH1.NH2 names. And the phenix convention is now different from coot. Mark _______________________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry, U-M Medical School New location: Room 3220B, MSRB III | saper(a)umich.edu | +1 (734) 764-3353 On Feb 14, 2016, at 4:07 PM, Eckhard Hofmann <eckhard.hofmann(a)bph.ruhr-uni-bochum.de> wrote: > Dear Mark, > I think Oleg is in the process of writing a little routine to fix problems in pdbs with regard to order of atoms in residues and such. Maybe fixing naming conventions could/will be included. > Cheers, > Eckhard > > > Am 14.02.2016 um 19:37 schrieb Mark A Saper: >> Phenix 1.10.1 is flagging several of my Arg residues with bad dihedral angles. Phenix is much more strict about NH1, NH2 naming conventions then 6 months ago. Can these be fixed with PDB Tools? How? Many thanks in advance. >> -Mark >> _________________________________ >> Mark A. Saper, Ph.D. >> Associate Professor of Biological Chemistry, University of Michigan >> Ann Arbor MI 48109-1055 U.S.A. >> saper(a)umich.edu phone (734) 764-3353 fax (734) 764-3323 >> >> >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> Unsubscribe: phenixbb-leave(a)phenix-online.org >> > > -- > Prof. Dr. Eckhard Hofmann <eckhard.hofmann(a)bph.ruhr-uni-bochum.de> > Ruhr-Uni Bochum > AG Proteinkristallographie, LS Biophysik, ND04/318 > 44780 Bochum > Tel: +49-(0)234/32-24463, Sekr. -24461, FAX: -14762 > ORCID: 0000-0003-4874-372X

2 1

Arg, Glu, etc. naming conventions
by Mark A Saper 14 Feb '16

14 Feb '16

Phenix 1.10.1 is flagging several of my Arg residues with bad dihedral angles. Phenix is much more strict about NH1, NH2 naming conventions then 6 months ago. Can these be fixed with PDB Tools? How? Many thanks in advance. -Mark _________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry, University of Michigan Ann Arbor MI 48109-1055 U.S.A. saper(a)umich.edu phone (734) 764-3353 fax (734) 764-3323

2 1

Check for radiation-induced reduction of a disulfide bond
by Ezequiel Noguera 13 Feb '16

13 Feb '16

I'm working with one protein, crystallized in oxidized form, which exhibits negative density in the Fo-Fc map at the center of the disulfide bond. As a test of radiation-induced reduction during data collection, I'd like to do a trial refinement described in a previous work from literature, where SG sulfurs of involved cysteines were refined without van der Waals interactions to monitor distances of these atoms. How can I do this calculation in Phenix? Thanks in advance

2 1

Using PyMOL-1.8 with PHENIX-dev-2306
by acyang 12 Feb '16

12 Feb '16

Hi everyone I've installed pymol and phenix on my scientific linux7.1 workstation. I can launch pymol via the launching script($PYMOL_HOME/pymol) normally. But when I launched pymol in phenix GUI, I got some error as followed: ********************************************************************************************************************************* Traceback (most recent call last): File "/opt/PyMOL/modules/pymol/__init__.py", line 71, in <module> import pymol File "/opt/PyMOL/modules/pymol/__init__.py", line 521, in <module> import pymol._cmd ImportError: /opt/PyMOL/modules/pymol/_cmd.so: undefined symbol: PyUnicodeUCS4_SetDefaultEncoding ********************************************************************************************************************************* After STFW*, *I knew the problem is about unicode variant (UCS2, UCS4). I also checked the configuration of two python. For /bin/python (adopted by pymol) >>> import sys>>> print sys.maxunicode1114111 And for $PHENIX_HOME/base/bin/python (adopted by phenix) >>> import sys >>> print sys.maxunicode 65535 My question is : How do I add the flag --enable-unicode=ucs4 in configuring Python-2.7.8_cci. I'd appreciate if any reply on this. acyang

2 1

reattach jobs
by andre.stiel 12 Feb '16

12 Feb '16

Hi, how do I reattach a job to a project in the GUI. Say I took the GUI to prepare a commands file (.eff) and save it. Then I run the actual refine from the command line on another computer using the save commands file. After the job is done, how do I get the job back in the GUI. I do not find something to „load“ or „reattach“ a job. Thanks. André André C. Stiel, Ph.D. (PI) +49 (0) 89 3187 3972 Office: Building 57, Room 009 Cell Engineering Group Institute of Biological and Medical Imaging Helmholtz Zentrum Muenchen Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH) Ingolstaedter Landstr. 1 85764 Neuherberg www.helmholtz-muenchen.de Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Dr. Alfons Enhsen, Renate Schlusen (komm.) Registergericht: Amtsgericht Muenchen HRB 6466 USt-IdNr: DE 129521671

2 1

phenix install error on linux
by Min Zheng 11 Feb '16

11 Feb '16

Dear All, I am installing phenix, and get the following error: ========================================================================== Phenix Installation version: 1.10.1-2155 machine type: intel-linux-2.6-x86_64 OS version: 3.11.10-29-default destination: /home/m/m_zhen01/phenix-1.10.1-2155 # of processors: 20 ========================================================================= Configuring Phenix components... Traceback (most recent call last): File "./bin/install.py", line 262, in <module> installer(sys.argv[1:]).install() File "/nfsexp/homes/m_zhen01/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos5/lib/libtbx/auto_build/install_distribution.py", line 185, in install self.install_from_binary() File "/nfsexp/homes/m_zhen01/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos5/lib/libtbx/auto_build/install_distribution.py", line 295, in install_from_binary self.reconfigure(log=log) File "/nfsexp/homes/m_zhen01/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos5/lib/libtbx/auto_build/install_distribution.py", line 460, in reconfigure call(args=args, log=log, verbose=self.options.verbose) File "/nfsexp/homes/m_zhen01/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos5/lib/libtbx/auto_build/installer_utils.py", line 81, in call raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc)) RuntimeError: Call to '/home/m/m_zhen01/phenix-1.10.1-2155/base/bin/python /home/m/m_zhen01/phenix-1.10.1-2155/modules/cctbx_project/libtbx/configure.py --current_working_directory /home/m/m_zhen01/phenix-1.10.1-2155/build --command_version_suffix 1.10.1-2155 phenix phaser solve_resolve labelit' failed with exit code 1 m_zhen01@LIBRA:~/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos5> /home/m/m_zhen01/phenix-1.10.1-2155/base/bin/python Traceback (most recent call last): File "/usr/lib64/python2.7/site.py", line 564, in <module> main() File "/usr/lib64/python2.7/site.py", line 546, in main known_paths = addusersitepackages(known_paths) File "/usr/lib64/python2.7/site.py", line 276, in addusersitepackages user_site = getusersitepackages(kind) File "/usr/lib64/python2.7/site.py", line 244, in getusersitepackages user_base = getuserbase() # this will also set USER_BASE File "/usr/lib64/python2.7/site.py", line 230, in getuserbase from sysconfig import get_config_var File "/usr/lib64/python2.7/sysconfig.py", line 10, in <module> 'stdlib': '{base}/'+sys.lib+'/python{py_version_short}', AttributeError: 'module' object has no attribute 'lib' Thanks in advance, Min

2 1

Refinement differences?
by Mark A Saper 11 Feb '16

11 Feb '16

Hi, I used Phenix, build 2037 to refine a a new structure. I reran the refinement (with the identical parameters) in build 2155 (v1.10.1) and obtained different statistics and slightly worse geometry. Any idea why? In 2037: start final --------------------------------------- R-work: 0.2488 0.2244 R-free: 0.3003 0.2851 RMS(angles): 1.67 0.80 RMS(bonds): 0.020 0.004 Ramachandran outliers: 1.2% (Goal: < 0.2%) Ramachandran favored: 94.5% (Goal: > 98%) Rotamer outliers: 8.7% (Goal: 1%) C-beta outliers: 0 (Goal: 0) Clashscore: 3.14 Overall score: 2.19 2155 start final --------------------------------------- R-work: 0.2488 0.2331 R-free: 0.3003 0.2856 RMS(angles): 1.77 0.72 RMS(bonds): 0.020 0.004 Ramachandran outliers: 1.4% (Goal: < 0.2%) Ramachandran favored: 93.4% (Goal: > 98%) Rotamer outliers: 9.4% (Goal: 1%) C-beta outliers: 0 (Goal: 0) Clashscore: 4.10 Overall score: 2.36 _________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry, University of Michigan Ann Arbor MI 48109-1055 U.S.A. saper(a)umich.edu phone (734) 764-3353 fax (734) 764-3323

4 3

differentiate Glu/Gln and Asp/Asn from Electron Density?
by Kaushik Hatti 11 Feb '16

11 Feb '16

Hello, In continuation to my earlier thread (subject: sequence independent model building possible?), I have built model into density without knowledge of sequence for a data diffracted to 1.9A resolution. Current R/Rfree is 15/19, phaser error=16.88 degrees with no Ramachandran outliers. Is there a way we can differentiate between Glu/Gln, Asp/Asn and sometimes Thr/Val directly from density? I have considered the local environment (hydrophobic/hydrophilic/polarity pockets, possible hydrogen bonds/other interactions, buried/exposed, etc...) in choosing one over the other confusing pairs of amino acids. However, I am not absolutely certain in many places. A BLAST of this sequence against all non-redundant protein sequence database yield highest hit of 80% sequence identity. Hence, we are still not sure of sequence of the contaminant protein which got crystallised and want to decipher sequence directly from the structure. Thanks for any pointers/suggestions, Regards, Kaushik -- Stupidity is everyone’s birthright. However, only the learned exercise it! --Kaushik (28Oct2014)

2 1

Creating cyclic peptide coordinates and restraints
by A User 10 Feb '16

10 Feb '16

Hi Everyone, I am working on a 1.9A enzyme inhibitor complex. The inhibitor is a macrocyclic peptide with a non-proteinogenic amino acid that is modified at the n-terminus with a chloroacetyl-group that cyclizes via the sulfhydryl group of the next cysteine. The total lenght of the peptide is 9 amino acids. What is the most straight forward way to generate the coordinates of such macrocyclic peptide and what are the best settings in eLBOW to generate the restraints for it? Thanks for your time guys! Ben

1 0

"Use starting structure as reference" for homo-multimers
by Tristan Croll 10 Feb '16

10 Feb '16

Hi, I've noticed that when I choose the option to use the starting structure as a reference model and my structure is a homo-multimeric protein, Phenix uses only the first chain as the reference for all chains during refinement. Personally I'd much prefer it if instead it ran a true 1:1 reference throughout the structure, since I tend to use this for final very fine-scale refinement of structures where I've already identified and modelled differences between NCS copies. Others' mileage may vary, of course. Best regards, Tristan

3 2

Re: [phenixbb] Refinement differences?
by Mark A Saper 10 Feb '16

10 Feb '16

Hi Eckhard, Thanks for commenting on this. Unfortunately the data is not good, so I am cutting it off at 2.6 Å resolution. I probably won’t completely refine this structure. It does have 2 molecules in different conformations in the asymmetric unit so I could try NCS. -Mark On Feb 10, 2016, at 10:51 AM, phenixbb-request(a)phenix-online.org wrote: > From: Eckhard Hofmann <eckhard.hofmann(a)bph.ruhr-uni-bochum.de> > Subject: Re: [phenixbb] Refinement differences? > Date: February 10, 2016 at 10:51:08 AM EST > To: phenixbb(a)phenix-online.org > > > Dear Mark, > there were chances to the geometry restraints which most likely would affect your refinement. > Do you have NCS in your refinement? This has been overhauled completely, and is currently not very verbose. > Generally I would not be very concerned about the exact values, given changes in the program. And it looks to me that you are not yet at the final point of refinement anyway. > What is your resolution? > All the best, > Eckhard

1 0

Computational Crystallography Newsletter, Volume 7, Number 1
by Nigel Moriarty 09 Feb '16

09 Feb '16

I am pleased to announce the publication of the latest 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 me at NWMoriarty(a)lbl.gov noting that there is a Word Template on the website to streamline production. January 2016 <http://www.phenix-online.org/newsletter/CCN_2016_01.pdf> Short Communications - Characterization of base pair geometry <http://www.phenix-online.org/newsletter/CCN_2016_01.pdf#page=5> - Visual representations of internal coordinate restraints: Advantages and limitations <http://www.phenix-online.org/newsletter/CCN_2016_01.pdf#page=9> Fitting tips #11 – Can a helical DNA basepair be Hoogsteen? <http://www.phenix-online.org/newsletter/CCN_2016_01.pdf#page=3> Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

1 0