- phenixbb - phenix-online.org

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