- phenixbb - phenix-online.org

phenix-1.7.2-x refine error
by Christoph Parthier 25 Nov '11

25 Nov '11

Dear Phenix developers, Using the current phenix version, refinements of a 'certain structure' always stop with the error message quoted below, while the refinement of other 'similar structures' work flawlessly. In the error case the three scheduled macrocycles of refinement seem to finish (the refined PDB is there) but at there seems to be problem in finishing the job - the output MTZ file has zero byte length and the last line in refine.log is: ============================== Exporting results ============================== This occurs with several 1.7.2-x versions of phenix, I'm not sure about 1.7.1-x. Interestingly, the 'problem structure' can be refined without problems using the same input files in phenix-1.7-650. Any idea whether this is due to an installation problem or a bug? Thanks, Christoph Here's the error message: MemoryError : Traceback: File "/cryst/phenix-1.7.2-869/cctbx_project/libtbx/thread_utils.py", line 229, in run return_value = self._target(self._args, self._kwargs, self._c) File "/cryst/phenix-1.7.2-869/cctbx_project/libtbx/runtime_utils.py", line 72, in __call__ result = self.target() File "/cryst/phenix-1.7.2-869/phenix/phenix/refinement/runtime.py", line 67, in __call__ call_back_handler=callback) File "/cryst/phenix-1.7.2-869/phenix/phenix/refinement/command_line.py", line 115, in run map_manger.write_files() File "/cryst/phenix-1.7.2-869/phenix/phenix/refinement/driver.py", line 1535, in write_files map_coeff_dataset=self.write_mtz_file(), File "/cryst/phenix-1.7.2-869/phenix/phenix/refinement/driver.py", line 1524, in write_mtz_file params = self.map_params.map_coefficients) File "/cryst/phenix-1.7.2-869/cctbx_project/mmtbx/maps/__init__.py", line 502, in __init__ coeffs = map_coefficients_from_fmodel(fmodel = fmodel, params = mcp) File "/cryst/phenix-1.7.2-869/cctbx_project/mmtbx/maps/__init__.py", line 353, in map_coefficients_from_fmodel fill_mode = "dfmodel") File "/cryst/phenix-1.7.2-869/cctbx_project/mmtbx/f_model.py", line 1887, in electron_density_map fill_mode = fill_mode) File "/cryst/phenix-1.7.2-869/cctbx_project/mmtbx/map_tools.py", line 114, in __init__ update_scaling = update_scaling) File "/cryst/phenix-1.7.2-869/cctbx_project/mmtbx/f_model.py", line 1663, in fill_missing_f_obs fmodel=self, fill_mode=fill_mode, update_scaling=update_scaling) File "/cryst/phenix-1.7.2-869/cctbx_project/mmtbx/missing_reflections_handler.py", line 131, in fill_missing_f_obs fmodel = select_by_map_cc(fmodel = fmodel.deep_copy())) File "/cryst/phenix-1.7.2-869/cctbx_project/mmtbx/missing_reflections_handler.py", line 85, in select_by_map_cc fourier_coefficients = coeffs) File "/cryst/phenix-1.7.2-869/cctbx_project/cctbx/miller/__init__.py", line 3688, in __init__ conjugate_flag=True) Platform info: __FILE__ = /net/longnose/scratch2/phenix/phenix-1.7.2-869/cctbx_project/boost_adaptbx/meta_ext.cpp __DATE__ = Sep 23 2011 __TIME__ = 00:13:14 __i386__ __linux __GNUC__ = 3 __GNUC_MINOR__ = 4 __GNUC_PATCHLEVEL__ = 2 boost::python::cxxabi_cxa_demangle_is_broken(): false __GXX_WEAK__ = 1 __VERSION__ = 3.4.2 20041017 (Red Hat 3.4.2-6.fc3) FE_INEXACT = 32 FE_DIVBYZERO = 4 FE_UNDERFLOW = 16 FE_OVERFLOW = 8 FE_INVALID = 1 FE_ALL_EXCEPT = 61 BOOST_LIB_VERSION = 1_48 PY_VERSION = 2.7.2 PYTHON_API_VERSION = 1013 sizeof(bool) = 1 sizeof(short) = 2 sizeof(int) = 4 sizeof(long) = 4 sizeof(std::size_t) = 4 sizeof(void*) = 4 sizeof(long long) = 8 sizeof(float) = 4 sizeof(double) = 8 sizeof(long double) = 12 sizeof(boost::int32_t) = 4 sizeof(boost::uint32_t) = 4 sizeof(wchar_t) = 4 __PTRDIFF_TYPE__ Py_USING_UNICODE sizeof(PY_UNICODE_TYPE) = 2 gnu libc version: 2.6.1 BOOST_ADAPTBX_TYPE_ID_SIZE_T_EQ_UNSIGNED os.name: posix sys.platform: linux2 sys.byteorder: little platform.platform(): Linux-2.6.22.13-GOLIAT-0.3-bigsmp-i686-with-SuSE-10.3-i586 platform.architecture(): ('32bit', 'ELF') floating_point_exceptions.division_by_zero_trapped: False floating_point_exceptions.invalid_trapped: False floating_point_exceptions.overflow_trapped: False number of processors: 8 Memory total: 4,238,028,800 Memory free: 3,715,174,400 import thread: OK "hello" = ['h', 'e', 'l', 'l', 'o'] u"hello" = ['h', '\x00', 'e', '\x00', 'l', '\x00', 'l', '\x00', 'o', '\x00'] u"\u00C5" = ['\xc5', '\x00'] as utf-8 = ['\xc3', '\x85'] LATIN CAPITAL LETTER A WITH RING ABOVE = Ã

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回复：phenixbb Digest, Vol 72, Issue 10
by dingding830106＠sina.com 25 Nov '11

25 Nov '11

Dear Thomas: I try running phenix.autosol instead of phenix.solve, and it solve this problem. Thanks a lot! Dingwei ----- 原始邮件 ----- 发件人：phenixbb-request(a)phenix-online.org 收件人：phenixbb(a)phenix-online.org 主题：phenixbb Digest, Vol 72, Issue 10 日期：2011年11月23日 01点08分 Message: 14 Date: Tue, 22 Nov 2011 10:08:46 -0700 (MST) From: "Thomas C. Terwilliger" <terwilliger(a)lanl.gov> To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> Subject: Re: [phenixbb] solve/resolve problem Message-ID: <52791.128.165.72.7.1321981726.squirrel(a)webmail.lanl.gov> Content-Type: text/plain;charset=iso-8859-1 I'm sorry for the problem! I don't recognize this error (the message solve is giving you is just saying that it has finished, unfortunately). Can you possibly (off-list) send me your input script and the output log file and I'll have a look? Or even better, try running phenix.autosol on the data and perhaps that will solve the problem! All the best, Tom T >> >> >> Dear all >> when I use SOLVE to deal with the SAD data, it will stop with a error >> message: >> >> ???STOP at >> /net/longnose/scratch2/phenix/phenix-1.7.2-869/solve_resolve/solve/solve_2.cpp(3133)??? >> Can you tell me what happen? >> >> wding >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb

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measuring angle
by Hena Dutta 23 Nov '11

23 Nov '11

Hi, Could you please tell me how I can measure angle between two helices. Can COOT or PYMOL measure this? I have another question. In PDBSET, I can use CHAIN command in shell script to write a pdb file with a desired chain ID. What is the command in shell script to write a pdb file with a desired SEGID? As for example:- pdbset xyzin start.pdb xyzout end.pdb <<eof >& pdbset.log ROTATE [INVERT] [MATRIX] values CHAIN A end eof This will change the chain ID to A after rotation. But, I also like to give a segid in the end coordinate. Thank you in advance and have a nice THANKS GIVING WEEKEND Hena

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reference model restrain error
by Stephan Barden 23 Nov '11

23 Nov '11

Dear all, I'm facing a problem with a fresh (yesterday) installation of phenix 1.7.2-869 refining a structure with 6 molecules per ASU at 3.25 A and using a different reference structure with 1 mol/ASU at higher resolution. I wrote an additional parameter file to assign the reference model to each of the six molecules, which worked well with an older version of phenix. After the upgrade neither taking the additional parameter file, nor auto alignment worked for me. The error comming up is always: RuntimeError : Duplicate sequence number and insertion code. Traceback: File "/sw/phenix-1.7.2-869/cctbx_project/libtbx/thread_utils.py", line 229, in run return_value = self._target(self._args, self._kwargs, self._c) File "/sw/phenix-1.7.2-869/cctbx_project/libtbx/runtime_utils.py", line 72, in __call__ result = self.target() File "/sw/phenix-1.7.2-869/phenix/phenix/refinement/runtime.py", line 67, in __call__ call_back_handler=callback) File "/sw/phenix-1.7.2-869/phenix/phenix/refinement/command_line.py", line 75, in run overwrite = command_line_interpreter.command_line.options.overwrite) File "/sw/phenix-1.7.2-869/phenix/phenix/refinement/driver.py", line 209, in __init__ log=self.log) File "/sw/phenix-1.7.2-869/cctbx_project/mmtbx/torsion_restraints/reference_model.py", line 145, in __init__ self.get_reference_dihedral_proxies() File "/sw/phenix-1.7.2-869/cctbx_project/mmtbx/torsion_restraints/reference_model.py", line 611, in get_reference_dihedral_proxies log=self.log) File "/sw/phenix-1.7.2-869/cctbx_project/mmtbx/torsion_restraints/reference_model.py", line 398, in process_reference_groups raise e Has anyone observed a similar problem? Are there any suggestions? Thanks, StephanB.

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solve/resolve problem
by dingding830106＠sina.com 23 Nov '11

23 Nov '11

Dear all when I use SOLVE to deal with the SAD data, it will stop with a error message: “STOP at /net/longnose/scratch2/phenix/phenix-1.7.2-869/solve_resolve/solve/solve_2.cpp(3133)” Can you tell me what happen? wding

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How to reduce clashscore value
by CelinaSocek 22 Nov '11

22 Nov '11

Hi all, I'm now using phenix to refine a small protein about 300 residues long. The resolution of my data is about 2.9 angstrom. Currently I got a refined model with good R-factors about 23/26, RMSD very reasonable and no Ramanchandran outliers. However, I found that the clashscore is extremely high: 63!! And rotamer outliers are also a lot: 8.5%. I wonder, what kind of stretagy I can use to reduce this? Thank you very much! best, Celina

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test_hhr
by Alexander Batyuk 22 Nov '11

22 Nov '11

Dear all, The phenix_regression.wizards.test_command_line_rosetta_quick_tests command hangs at the test_hhr step in phenix-dev-910 on Mac OS X 10.6.8. What could be the reason for that? What kind of log files should I post? The firewall allowed to fetch files from the net. Best wishes, Alex -- Alex Batyuk The Plueckthun Lab www.bioc.uzh.ch/plueckthun

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Re: [phenixbb] How to reduce clashscore value
by CelinaSocek 20 Nov '11

20 Nov '11

Thank you Nat! I will try to fix as many clashes as I can in coot, and hope that I can manage to reduce it to around 20. ;) Also thank other suggestions and discussions! best, Celina > > Which version are you using? We made some changes over the summer > that improve the geometry, especially the clashscore - these are > present in version 1.7.2. If you're still using an earlier version, > this might largely fix the problem. However, if there is > conformational strain in the model, it is difficult to fix severe > clashes without further rebuilding. You should inspect the clashes in > Coot (the Phenix GUI has shortcuts for this, but Coot alone also has > this capability) and fix as many as possible yourself. It is > recommended that you use explicit hydrogen atoms when doing this, > since the reason for clashes is often not obvious if only heavy atoms > are used. (You don't necessarily need to refine with heavy atoms > though - they're just an aid to visualizing clashes.) > > The rotamer problem may be related; there isn't much you can do with > these except fix them manually, but relieving some of the clashes may > help. The dihedral angle restraints simply aren't that strong, so in > areas of weak density it can be difficult to completely prevent > outliers. > > -Nat > > > ------------------------------ > >

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multiple ligand conformations
by Leonard Thomas 20 Nov '11

20 Nov '11

Hello All, One of the groups here has run into a problem in the refinement of their structure or more specifically a ligand bound to the structure. Through a series of other experiments they know that a photo reaction occurs to the compound when exposed to high flux as found at your everyday synchrotron source. The exposure changes the bonding such that there are two conformations with a bit in between obviously. They collected 360 degrees worth of data and if the data is split you can model the two conformations depending which half of the data you use. They are trying to refine with all of the data and modeling of the ligand into the two conformations. In refmac they can model this with no problem but in Phenix the ligand adopts a chemically wrong conformation, sort of a halfway point between the two chemically relevant conformations. They have used Phenix to do similar refinements on other structures but it appears either the last release or the latest release is causing problems. They have started out with everything from 50% occupancy to shifting it towards on one conformation or the other and the ligand always ends up in the chemically wrong position. Data is in the 1.4-1.5 ang. range. Ideas? Thanks in advance. Len Leonard Thomas Ph.D. Macromolecular Crystallography Laboratory Manager University of Oklahoma Department of Chemistry and Biochemistry Stephenson Life Sciences Research Center 101 Stephenson Parkway Norman, OK 73019-5251 lmthomas(a)ou.edu http://barlywine.chem.ou.edu Office: (405)325-1126 Lab: (405)325-7571

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multiple ligand conformations
by Yuri 20 Nov '11

20 Nov '11

Hi, When you say "wrong postion", what does it mean? are the 2 ligands you are trying to refine being "pushed away" from each other? If that is the case first thing I would check is the ALTLOC comlumn of their pdb file entries. Make sure one is ALTLOC A and the other ALTLOC B. I have refined with ligands in four different positions before using phenix before and got satisfactory results... Hope this helps, -- Yuri Pompeu

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MR_ROSETTA
by Wei Shi 19 Nov '11

19 Nov '11

Hi all, I am trying to run phenix.mr_rosetta using the following script for rebuilding the model with Rosetta before MR from phenix website except omitting specifying ncs_copies number. Following is the script I am using: phenix.mr_rosetta \ seq_file = seq.dat \ data=coords1.mtz \ search_models=coords1.pdb \ run_prerefine=True \ number_of_prerefine_models=1000 \ fragment_files = test3.gz \ fragment_files = test9.gz \ rescore_mr.relax=False \ rosetta_models=20 \ space_group=p222 \ use_all_plausible_sg=False \ nproc=4 \ group_run_command=qsub\ When I run the above script, it gives the following error message: child process stderr output: command: 'qsub /home/wei/MR_ROSETTA_14/GROUP_OF_PLACE_MODEL_1/RUN_FILE_1' /bin/sh: qsub: not found Then, I omit the last line in the command “group_run_command=qsub\”. MR_ROSETTA seems to be running. But, it takes forever to run. My questions is: 1. Does anyone happen to know why it tells me “qsub: not found” when I include “group_run_command=qsub” in my script? 2. When I omit “group_run_command=qsub” in the script, mr_rosetta seems to be running. But it just gives me the following message and it takes forever to run. Almost 10h later, no job is finished. I don’t know whether this is normal. If not, any idea about why it’s so slow and any suggestions about how to speed up the run? Thank you so much! Splitting work into 1 jobs and running with 4 processors using sh background=True in /home/wei/MR_ROSETTA_15/GROUP_OF_PLACE_MODEL_1 Starting job 1...Log will be: /home/wei/MR_ROSETTA_15/GROUP_OF_PLACE_MODEL_1/RUN_FILE_1.log

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error: Duplicate selections
by Sebastiano Pasqualato 17 Nov '11

17 Nov '11

Hi all, sorry guys, this might be a silly one, but I can't see where I'm making the mistake. Whenever I turn on TLS refinement, I get this error message. And, as you can see, the Log file doesn't tell me much more. I have generated the TLS groups wit the 'TLS groups selection' tool in phenix. Any hint? Thanks in advance, ciao s -- Sebastiano Pasqualato, PhD Crystallography Unit IFOM-IEO Campus Cogentech - Consortium for Genomic Technologies via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5172 fax +39 02 9437 5990

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Scattering from riding hydrogens?
by Damian Ekiert 16 Nov '11

16 Nov '11

Hello, I have a question regarding two parameters and how they affect riding hydrogens. contribute_to_f_calc = True high_resolution_limit_to_include_scattering_from_h = 1.6 At lower resolution, setting contribute_to_f_calc = false is frequently helpful when using riding hydrogens and has been discussed before. But what is high_resolution_limit_to_include_scattering_from_h = 1.6 doing? If scattering from hydrogens is only included at higher than 1.6A resolution, it would seem like contribute_to_f_calc = True/False would not have any effect at say, 3.5A, but comparing identical refinement runs with contribute_to_f_calc = True or contribute_to_f_calc = False clearly gives different results. Can hydrogens contribute to Fcalc in a way aside from their scattering, or is their contribution accounted for independent of the position of the riding hydrogen (e.g., additional scattering term added to the associated heavy atom)? I think I am misunderstanding what these two parameters are doing and would appreciate some clarification. Thanks, Damian Ekiert

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Multiple TLS groups per molecule
by Yarrow Madrona 15 Nov '11

15 Nov '11

Hi, I would like run TLS and individual isotropic refinement. I want to separate one molecule into four TLS groups. I havn't found documentation for this. Is the number of TLS groups automatically done by phenix refine when you tell it to run TLS refinement on the whole molecule? Thanks for your help -Yarrow -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

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Small issue with residue PTR
by Terry Lang 15 Nov '11

15 Nov '11

Hey Everyone, I have found a small issue with atom naming for residue PTR. When phenix.ready_set adds hydrogens to the residue, it names the hydrogens connected to the CB atom to be HB3 and HB2. However, the hydrogens in the cif file located in chem_data/mon_lib are labeled HB1 and HB2. Manually changing either the cif file or the atom name in the pdb file solves the problem. Terry -- P. Therese Lang Post Doc Alber Lab, UC Berkeley

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How can I add another chain to my PDB by Coot
by Dialing Pretty 15 Nov '11

15 Nov '11

Dear All, By Phenix refine I got a PDB (Only one chain) and mtz output files. After analysis by Coot I find I need to add a protein fragment so that a large blob will disappear. I know I use Baton to construct the protein fragment. Will you please tell me how can I input the sequence file of the protein fragment so that I can refine the protein fragment by Coot? I am looking forward to getting your reply. Regards. Dialing

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twin/pseudo-symmetry question
by Green, Todd 12 Nov '11

12 Nov '11

Hello all- I have a question regarding the possibility of twinning and or psuedo-symmetry. I have a crystal that processes well in R32, ie. less than 6% r-merge at 2.2 angstrom. We collected multiple potential derivatives and were able to get some phasing from one that was good enough to model in the helices. The strange thing is that when looking at the harker sections there were a lot of unexplained strong peaks. And there is a very narrow range of parameters that we could get the sites with Shelx and end up with interpretable maps(i know that this part might not be unusual). My first thought was that there could be twinning. Since there is no twin law for this space group, I thought that it might suggest that there was twinning in a lower symmetry space group and/or that we have a pseudo-R32 crystal. Processing works well in C2 and R3, as expected. In those cases Xtriage suggests that the real symmetry is likely to be R32. In the case of C-2, xtriage suggetss if it is twinned then it is about 45% twinned. That's the background. Fast forward with the help of phenix Autobuild and some manual correction, we have been able to refine the structure with the R32 processed data(with tls) to r_work = 0.1894, r_free = 0.2287, bonds = 0.007, angles = 0.908 at 2.2 angstrom with almost everything accounted for. I think I should be quite comfortable with this. BUT, I'm still wondering about those Harker sections. I've been reading the manuscripts of Dauter regarding twinning and I think I am at this point more curious than anything. But not leaving well enough alone, I went back to the data processed in C2. I can easily do molecular replacement, following refinement at 2.3 angstrom(I need a lot more frames for this sg so the cutoffs are a bit lower but r-merge is ~ the same as R32) with TLS I get r_work = 0.1850, r_free = 0.2249, bonds = 0.007, angles = 0.946. this doesn't seem significant to me. However if I refine with the two possible twin operations, the values drop with one being better than the other. both have the same starting model: r_work = 0.1639 r_free = 0.1880 bonds = 0.006 angles = 0.902 r_work = 0.1582 r_free = 0.1866 bonds = 0.006 angles = 0.891 The twin fraction from the refined pdb header is 0.544 for the better statistical model and the r-values seem too low for 2.3 angstrom data. Is the high twin fraction suggestive of the higher symmetry space group or inconclusive towards that. of interest is that the maps look better to me than the r32 maps. by that i mean that the maps don't have what i would call minor dots of negative density for some(not a lot) of the side chains as we see for some side chains in the R32 case. also some side chains look better in the C2 twin refined case. Lastly for some of the monomers(there are now 6 copies versus 2 in the R32 case), I can add an additional residue or two on the termini which are not seen before. I wonder if this also suggests that the true space group is C2. Are these r-values too low? does the difference in values according to each twin law mean something? In the end, the models are essentially the same in either space group (with the exception of a couple of residues at the termini). So, I don't think I learn much one way or the other. But the curiocity keeps coming back. So is it likely to be R32 or C2 or C2 with a hefty twin fraction? Anyone have an explanation? Thanks in advance- Todd

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peptide link problem solved LINKR in pdb is not recognized but LINK is
by Christian Roth 11 Nov '11

11 Nov '11

Hi, In my pdb from Refmac the keyword LINKR is used but only LINK is interpreted by phenix. I changed this and now it works as it should. Sorry, a careful analysis sometimes help. Regards Christian

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peptide link
by Christian Roth 11 Nov '11

11 Nov '11

Hi, I have an modified aminoacid in my peptide chain (backbone modified). I have a cif file and I refined it previously in Refmac. I put the Link definition in the pdb and Refmac has interpreted the peptide link as I wanted. Now I did a run in phenix to compare the results and the chain is broken I created the SNN cif file with ReadySet Reel and I tried to incorporate the link definition via GUI in the following way apply_cif_link: data_link: TRANS residue_selection_1: chain A and resseq 366 residue_selection_2: chain A and resseq 367 apply_cif_link: data_link: TRANS residue_selection_1: chain A and resseq 367 residue_selection_2: chain A and resseq 368 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7983 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 496, 7926 Unusual residues: {'SNN': 1} Classifications: {'undetermined': 1, 'peptide': 495} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 37, 'TRANS': 456, None: 2} Not linked: pdbres="ASP A 366 " pdbres="SNN A 367 " Not linked: pdbres="SNN A 367 " pdbres="GLY A 368 " Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 This fails with an error message that it cannot interpret the links. In my previous pdbs I have also defined the atoms which I wanted to link. Maybe I have to do this also somhow in Phenix. I have tried to extract the Link definition using phenix.link_edits but the resulting .edits file is empty. How can I resolve issue? Thanks Christian

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Rebetta fragment library
by Wei Shi 11 Nov '11

11 Nov '11

Hi everyone, I am trying to generate a fragment library in Rebetta server for my sequence of interest to use with mr_rosetta. I can open the 9-mer and 3-mer fragment results: aat000_09_05.200_v1_3 and aat000_03_05.200_v1_3, but didn't see link to download these two files. Does anyone know how to download these two files? If I do copy and paste, what file type or format is compatible with mr_rosetta? Thank you so much! Best, Wei

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define angle between groups of atom 'planes' for refinement restraint?
by Francis E Reyes 11 Nov '11

11 Nov '11

Hi all I was wondering if there was language in the monomer restraint libraries (.cif) or a custom phenix.refine geometry restraint a that defines an angle between two planes, where each plane is a group of coplanar atoms. Thanks! F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

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nproc for autobuild
by Michael Thompson 09 Nov '11

09 Nov '11

Hello, I apologize if this question seems very basic, but I am new to phenix.autobuild. I would like to set up a series of phenix.autobuild runs on our cluster, and would like to maximize the speed. I am trying to make single rebuilt models using the command below: phenix.autobuild data=data.mtz model=coords.pdb map_file=map_coeffs.mtz multiple_models_number=1 n_cycle_rebuild_max=5 ncycle_refine=5 s_annealing=true refine_with_ncs=True place_waters=True nproc=?? run_command=/home/qsub.sh The AutoBuild documentation says "if you are using rebuild_in_place=False, then use nproc=4" and "if you are using rebuild_in_place=True, then use nproc=5. (Any more will not make any difference)." My interpretation of the documentation is that for the above AutoBuild run with multiple_models_number=1, I should set nproc=5 (or 4?). Is this correct? Also, if I were to change the command so that multiple_models_number=10, should I then use nproc=50 (i.e. 5 processors per model), or is it still the case that setting nproc>5 doesn't make a difference? Thanks in advance for your help! Mike -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles miket(a)chem.ucla.edu

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phenix.phaser output .param file
by G Y 09 Nov '11

09 Nov '11

Dear Experts, I run my script for phenix.phaser in bash shell and one of the output file is filename.param (please note there is no "s" at the end of param) There are only two lines inside this file: # [no title set] TNCS IGNORE ON I do not really know what this file doing for. And, if I run the phaser from GUI, I will not find any .param file. What is this file doing for? Is it some kind of redundant information which is not useful at all? What should I edit in input params.eff file to avoid this output file? I would appreciate to any help from you. Thanks. Best, G

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Constrained group refinement
by Christian Roth 09 Nov '11

09 Nov '11

Dear all, I defined the following contrained groups which should a ligand in two alternative forms and an ion at the same position refine to an summed occupancy of 1. constrained_group { selection = chain Z and resname 2CL and altloc A selection = chain Z and resname 2CL and altloc B selection = chain r and resname Cl } constrained_group { selection = chain c and resname 2CL and altloc A selection = chain c and resname 2CL and altloc B selection = chain m and resname Cl } constrained_group { selection = chain N and resseq 69 and altloc A selection = chain N and resseq 69 and altloc B selection = chain o and resname 2Cl } } At the end I get an error because of the very small nonbonded interactions. it seems that my definition are not correct, but I am at the moment unsure why. Could someone point me to the mistake. Thanks in advace for your help Best Regards Christian

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Constrained group refinement Addendum
by Christian Roth 08 Nov '11

08 Nov '11

Do the ions have to be altlocC for the group definition? Best Regards Christian

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Cross Validation Reflection Set question
by Yuri 08 Nov '11

08 Nov '11

Thanks for the replies. >I just tried doing this, and it looks like the R-free flags will cover >the full resolution range, at least with the current code. By current code, you mean 1.7.2-869 and newer, right? >Is this really necessary in this case (refine against lower res data, >then continue with the whole data set I think I have a backbone shift in this structure (relative to native protein used for MR) so I wanted to do it this way befor trying to go all the way down to 2A. One last question does phnix do NCS averaging to improve maps? -- Yuri Pompeu

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Re: [phenixbb] AutoBuild runtime
by Nathaniel Echols 08 Nov '11

08 Nov '11

On Mon, Nov 7, 2011 at 9:14 AM, Shya Biswas <shyabiswas(a)gmail.com> wrote: > Thanks for the suggestions. Unfortunately my MR solution is not good enough > to get a good map. Autobuild does give me a solution when i put in my > sequence but the map does not look good. I was wondering if the final model > that Autobuild gives has undergone density modification. Strictly speaking, it's the map that undergoes density modification - but yes, this will be done unless you explicitly disable it. -Nat

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Cross Validation Reflection Set question
by Yuri 07 Nov '11

07 Nov '11

Dear All, Here is the situation, I have data to 2 A. I refined the model to 3 A first with S.A. Now I want to use higher res data for the rest of refinement. My Rfree created in the first round when I only used data to 3A. Was Rfree set created using all the data or just up to 3A shell? or do I have to extend into higher res shells? one caviot is I had twin law h,-k,-h-l enabled when they were created. Thanks, -- Yuri Pompeu

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Re: [phenixbb] AutoBuild runtime
by Nathaniel Echols 06 Nov '11

06 Nov '11

On Sat, Nov 5, 2011 at 12:02 PM, Shya Biswas <shyabiswas(a)gmail.com> wrote: > I was running autobuild using my protein sequence and the best MR model that > I got out of phaser, however it is taking really long to finish the job. Is > there a way to reduce the time period? Several options: - turn on quick mode (quick=True, or equivalent button in GUI) - use multiple processors if you have them (nproc=X, or equivalent control in GUI) - cut back resolution: if you have really good and/or high-resolution data*, you may be able to get nearly as good a model with fewer reflections, and it will be much faster (mostly due to refinement time, I think). However, this can also significantly degrade your model if the data aren't that great. - instead of AutoBuild, use phenix.phase_and_build (also in the GUI), which is basically the building procedure from AutoSol. It will usually not produce as complete a model (or R-factors as low) as AutoBuild, but it's much faster. -Nat (* the p9-sad tutorial is a good example of this - when we run workshops, we usually tell attendees to set the resolution limit for AutoSol to 3.0 instead of using all data to 1.7. The resulting model is nearly complete, and it finishes in less than half the time. Of course these data are unusually good...)

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Call for submissions to Computational Crystallography Newsletter (corrected)
by Nigel Moriarty 06 Nov '11

06 Nov '11

Calling for articles and short communications of interest tostructural biologists. The deadline for publication in the January2012 issue is 1st Dec, 2011. The Computational Crystallography Newsletter (CCN) is an electronicnewsletter for structural biologists, and is published online every 6months. Feature articles, meeting announcements and reports can besubmitted to me at any time for consideration. Submission of text byemail or word-processing files using the CCN templates is requested.Past newsletters and the template are available atwww.phenix-online.org/newsletter. Cheers Nigel -- Nigel W. Moriarty Building 64R0246B, 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

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Call for subscriptions to Computational Crystallography Newsletter
by Nigel Moriarty 05 Nov '11

05 Nov '11

Calling for articles and short communications of interest to structural biologists. The deadline for publication in the January 2012 issue is 1st Dec, 2011. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and the template are available at www.phenix-online.org/newsletter. Cheers Nigel -- Nigel W. Moriarty Building 64R0246B, 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

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metal coordination restraints
by Laurie Betts 05 Nov '11

05 Nov '11

How does PHENIX know where to look for proper bond lengths and angles for a metal ion I add to a protein structure - do I just add the metal into difference density and any waters, and then run ready set and it knows where to look for that particular metal and the atoms to which is is coordinated? And shouldn't there be a 'cif file that it outputs, or is that something that I need to get myself? Sorry it's still not obvious to me from the documentation. Thanks Laurie Betts

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Postdoctoral Position at King's College London, UK
by Steiner, Roberto 05 Nov '11

05 Nov '11

A three-year postdoctoral position in the field of mechanistic enzymology is immediately available in the Steiner Laboratory of King’s College London. The salary is £33,193 per annum inclusive of London allowance. The project aims at studying the intriguing biological process of cofactor-independent oxygenation catalysis (1). To understand how dioxygen chemistry takes place in a cofactor-less manner we will use enzymes for which we have recently obtained structural information in various catalytically relevant states (2). The ideal candidate has a strong biochemistry/chemistry background, extensive experience in structural biology focused on enzyme mechanisms and an interest in molecular dynamics (MD). The MD work will be carried out in collaboration with Prof. Ceccarelli of the University of Cagliari, Italy, where the postdoc will be able to spend some time to improve his/her skills in MD techniques. The postdoc will also be in close contact with the Manchester group of Prof. Scrutton where complementary spectroscopic and kinetic studies will be carried out. This project will equip the post-holder with a rare and sought-after skill-set as well as a comprehensive overview of an inter-disciplinary study. To apply for this position go to http://www.kcl.ac.uk/depsta/pertra/vacancy/external/pers_detail.php?jobinde…. Please make sure you quote the reference number G6/JKA/772/11-JT. Informal enquiries are welcome at roberto.steiner(a)kcl.ac.uk<mailto:[email protected]>. The closing date for this application is 24 Nov. 2011. (1) Fetzner S. and Steiner RA (2010). Cofactor-independent oxidases and oxygenases. Appl. Microbiol. Biotechnol. 86, 791-804. (2) Steiner RA, Janssen HJ, Roversi P, Oakley OJ, Fetzner S (2010). Structural basis for cofactor independent dioxygenation of N-heteroaromatic compounds at the •/•-hydrolase fold. Proc. Natl. Acad. Sci. USA, 107, 657-662. Roberto Steiner, PhD Randall Division of Cell and Molecular Biophysics Group Leader King's College London Room 3.10A New Hunt's House Guy's Campus SE1 1UL, London, UK Tel 0044-20-78488216 Fax 0044-20-78486435 roberto.steiner(a)kcl.ac.uk<mailto:[email protected]>

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Re: [phenixbb] Molecule and maps will not load into coot from Phenix 1.7.1-743
by Jobichen Chacko 03 Nov '11

03 Nov '11

Dear Nat, Any progress in this matter. To add, do you have any version of Phenix which is working perfectly (the communication of Phenix with pymol and coot) in ubuntu system in you lab? Jobi On Tue, Nov 1, 2011 at 5:08 PM, Jobichen Chacko <jobichenc(a)gmail.com> wrote: > Dear Nat, > Just to add when I try open the files in pymol, it doesnot open up and > show this output. > > /usr/local/phenix-1.7.1-743/build/intel-linux-2.6-x86_64/base/bin/python2.7: > No module named pymol > > Jobi > > > On Tue, Nov 1, 2011 at 10:58 AM, Jobichen Chacko <jobichenc(a)gmail.com> wrote: >> Dear Nat, >> I installed the the coot version you sent to me. Still not working. >> jobi >> >> On Tue, Nov 1, 2011 at 10:43 AM, Nathaniel Echols <nechols(a)lbl.gov> wrote: >>> On Mon, Oct 31, 2011 at 7:34 PM, Jobichen Chacko <jobichenc(a)gmail.com> wrote: >>>> Dear Nat, >>>> Thank you for your help. >>>> Please see the attached output after running coot_test.py >>>> I will also try to install the coot version you send to me. >>>> Jobi >>>> ... >>>> 'import site' failed; use -v for traceback >>> >>> Wow, that's way more broken than I was expecting. I think this means >>> a library conflict, but I've only come across this error on Mac. Can >>> you try one more thing? >>> >>> export PYTHONVERBOSE=1 >>> coot --script coot_test.py >>> >>> (If you're using csh or tcsh as your shell, the first line should be >>> "setenv PYTHONVERBOSE 1" instead.) >>> >>> -Nat >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://phenix-online.org/mailman/listinfo/phenixbb >>> >> >

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Ligands at special positions
by Subhani Bandara 03 Nov '11

03 Nov '11

Hi everyone, There are some ligands in my protein structure, that are very close to a special position. But they are not exactly at a special position, so when I apply symmetry in coot it generates another ligand away from the original one. How can I move them exactly on to a special position. Is there any script I can use for this? Thanks Subhani

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NMR vs Xtal structures
by Yuri 03 Nov '11

03 Nov '11

Could someone point me to a good paper on comparing of structures of the same protein determined by X-ray vs. NMR Best, -- Yuri Pompeu

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Autosol
by Kiran Kulkarni 02 Nov '11

02 Nov '11

Hi, I am getting following error message while running Autosol. *************ERROR ENDING ******************* ******************************************************************************** Failed to carry out AutoSol_guess_setup_for_scaling: 'nat_der_list' ******************************************************************************** *************ERROR ENDING ******************* Please help me to fix this. Details: PHENIX VERSION: 1.7.2 of 23-09-2011 PHENIX RELEASE_TAG : 869 PHENIX MTYPE : mac-intel-osx-x86_64 PHENIX MVERSION : osx-10.6.8 Space group: P41 EXPT_TYPE = SIR Native data Resolution= 3.8A Derivative data Resolution= 6.5A Program runs smoothly for derivative data alone (i.e. for SAD mode). Many thanks, -Kiran

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Molecule and maps will not load into coot from Phenix 1.7.1-743
by Jobichen Chacko 01 Nov '11

01 Nov '11

The same old problem, I tried to add the coot path using preferences. Coot version result: COOT_PREFIX is /usr/local /usr/local/bin/coot-real --version 0.6.1 (revision 2740) [with guile 1.8.7 embedded] [with python 2.6.0 embedded] The coot opens just after phenix-refine job starts and after the job finishes. But no maps and models are loaded. Thanks. Jobi

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"ATP" monomer in phenix_refine
by Zhang yu 29 Oct '11

29 Oct '11

Hi, I had a trouble of refining "ATP" in Phenix. I appreciate any help. ATP with tri-phosphate is in the 5' end of RNA chain. It is added to the RNA chain in coot as a monomer "ATP", and it could be connected to the downstream base after I changed the "_chem_comp.group" option to "RNA" in the cif file. But when I refine the model in Phenix, Phenix treated the "ATP' as a monomer and didn't connect it to the downstream base. I tried two ways to solve it 1. Add the the modified (chang the "_chem_comp.group" option to "RNA") cif file in phenix_refine, but Phenix doesn't recognize it. 2. In REEL, I found phenix has its own cif file for ATP, but the its header couldn't be edited. Any suggestions? Thanks. Yu

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Problem avoiding real space refinement
by Jerome Nwachukwu 28 Oct '11

28 Oct '11

Hi: We noticed that in some of our refinements, real space refinement was performed even though we chose not to do this. I tried to opt out of real space refinement as follows: " refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp *tls *occupancies group_anomalous ..." however, the R-free is identical whether we select real space refinement or not, and the logfile shows " Validate: |--------START--------| |--------FINAL--------| residue map_cc 2mFo-DFc mFo-DFc map_cc 2mFo-DFc mFo-DFc "LYS A 18 " 0.9359 16.78 0.00 0.9107 17.60 0.00 "ARG A 19 " 0.9513 21.82 0.00 0.9470 20.97 -6.52 <<< "ARG A 26 " 0.9440 26.72 0.00 0.9474 27.33 -2.43 "ARG A 69 " 0.9685 31.36 0.00 0.9659 32.58 0.00 "GLN A 86 " 0.9681 23.57 -5.81 0.8850 19.29 -18.27 <<< "GLU A 89 " 0.9689 26.30 -4.43 0.8977 23.67 -11.59 <<< "LYS A 93 " 0.9746 25.19 0.00 0.9682 26.47 2.90 ... " and suggesting that real space refinement was performed. Is there a way to correct this, or to ensure that real space refinement is not performed during refinement? Thank you, -Jerome Jerome C. Nwachukwu, PhD Dept. of Cancer Biology The Scripps Research Institute-Florida

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problem to add D atom on carbonyl group (enol) as alternate conformation
by Maxime Cuypers 27 Oct '11

27 Oct '11

Dear all, i have a problem that i block on for quite a while. i need to add a D atom on carbonyl group (enol) as alternate conformation to a main chain protein amide group to refine with phenix.refine. It is not something that the program phenix.reduce can perdeuterate as it is an unusual position. it actually perdeuterates all the rest of the protein successfully. Does anyone have an idea how to proceed? i tried so far to rename the residue and give .cif restraints generated with readyset for the new tautomer. phenix seemed to recognised it but it failed due to the fact it does not recognise the residue as being a residue to link to the other residues and bounds bounce off. A friend told me a cif_link was the problem. Then i tried to apply cif_modification in a parameter file with the corresponding .cif file as explained briefly on: http://www.phenix-online.org/documentation/refinement.htm#anch88 it does not solve the problem. the link between the new tautomer residue and the rest of the residues does not occur in refinement. Thanks for your help in advance. i am getting deseperate. Maxime

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exploring the conformational space of sidechains
by Francois Berenger 27 Oct '11

27 Oct '11

Hello, Is there a way to do this with Phenix? I.e., from a given model, obtain models with different but also reasonable sidechains conformations. N.b.: I don't have X-ray data so I am looking for a geometric thing, and I'm OK if the model's backbone undergoes some small movement because of the sidechains having moved. Thanks a lot, F.

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Molecule and maps will not load into coot from Phenix 1.7.1-743
by Yuri 27 Oct '11

27 Oct '11

Read the thread I waas just a part of maybe it is related -- Yuri Pompeu

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Re: [phenixbb] COOT not "connected" to PHENIX
by Yuri 26 Oct '11

26 Oct '11

I installed the version with python embedded in coot And it works!! Thanks a lot!! On Tue, 25 Oct 2011 11:41:38 -0700, Nathaniel Echols wrote: > On Tue, Oct 25, 2011 at 11:40 AM, Yuri <yuri.pompeu(a)ufl.edu> wrote: >> Now here comes the stupid question... >> How do I fix it? >> Install a different coot version or is it something in my >> architecture? > > Install a different Coot. If you're downloading from Paul Emsley's > page, you need a package with "python" in the file name. I have no > idea whether the Linux binaries distributed by CCP4 have Python or > not > (the Mac version definitely does). > > -Nat -- Yuri Pompeu

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COOT not "connected" to PHENIX
by Yuri 25 Oct '11

25 Oct '11

Hello everyone, I am running 1.7.2-869 and coot 0.6.2 By telling phenix where hte path is, I can get it to launch from any phenix job tab. However in one of my machines, even though COOT launches through phenix it is not connected to it which does not allow me to look at clashes when building in coot- a very useful feature may I add!!! In one of my RHEL5 machines it is working nicely, and I dont see any obvious differences between the working and the non-working one. Any ideas? Thank you much -- Yuri Pompeu

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phenix.phaser generate .sol file
by G Y 25 Oct '11

25 Oct '11

Dear Experts, I run phaser in phenix with GUI and script using params.eff. For both case, I can not find .sol file in the outputs. What option or command I should used in GUI and params.eff to generate the .sol file in the outputs? Thanks for your kind help! GY

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phenix.pdbtools --show-adp-statistics
by Krzysztof Bzymek 25 Oct '11

25 Oct '11

Hi, I noticed that this option is longer supported in phenix 1.7.2-869. Is there an equivalent command that would print out the statistics? Thanks, Chris

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coot from phenix
by Andreas Förster 24 Oct '11

24 Oct '11

Dear all, I'm running phenix 1.7.2-869 on RHEL 6.1 64-bit. When I click on "Open in Coot" after refinement, coot doesn't open and I get the following error in the shell from which I started phenix: /csb/soft/Linux64/share/phenix-1.7.2-869/phenix-1.7.2-869/phenix/phenix/command_line/start_coot.sh: line 33: /csb/soft/Linux/src/coot-0.6/bin/coot: No such file or directory In the script that launches coot, $PHENIX_COOT is defined as /csb/soft/Linux/src/coot-0.6/bin/coot, which doesn't exist (and is a path that we used in the old days of 32-bit). Typing phenix.find_coot_command in the shell from which phenix was started returns /csb/soft/Linux64/src/coot-0.7-rev3689/bin/coot, which is the right coot. To me it seems the phenix script to launch coot is falling back on an internally defined $PHENIX_COOT variable (that's not defined from the shell). That's shouldn't be, should it? How do I fix this short of hardwiring $PHENIX_COOT as /csb/soft/Linux64/src/coot-0.7-rev3689/bin/coot? Thanks. Andreas -- Andreas Förster, Research Associate Paul Freemont & Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk

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Unusual CCP4 to Phenix data conversion result
by R.M. Garavito 24 Oct '11

24 Oct '11

In upgrading to CCP4 6.2.0 and Phenix-1.7.2-869 (from CCP4 6.1.13 and Phenix-1.7.1-743, respectively) a bug has crept into reading of the MTZ files. We tend to scale and merge XDS processed data with Scala in CCP4, then use the resulting data in CCP4 and Phenix (with great success I might add). However, I just noticed that in testing the upgraded CCP4 and Phenix on OSX 7.2 (Lion) that the MTZ file is no longer read correctly. An example is below where after the output from scaling and merging of nonanomalous data from the CCP4i GUI gives, at the end of FREERFLAG, some 47,000 reflections. Putting this into xtriage or the reflection file editor in the Phenix GUI, one finds that the data for the F and the DANO columns are used; just selecting Fs alone is impossible. The end result is a doubling of the reflection number and the switching of the anomalous flag on. Processing with earlier versions did not do this except when actually using anomalous data. Why this has happened is not clear to me, but the column order in the MTZ file changed slightly between CCP4 6.1.13 and CCP4 6.2.0. Any ideas, am I missing something, or is this a push to only refine with intensities? Regards, Michael ***************** From Scala (3.3.20) Total number unique : 46813 From FREERFLAG Number of Reflections = 47044 (including non-observed NaN reflections) MTZ column labels H K L FreeR_flag F_S13E_X2 SIGF_S13E_X2 DANO_S13E_X2 SIGDANO_S13E_X2 F_S13E_X2(+) SIGF_S13E_X2(+) F_S13E_X2(-) SIGF_S13E_X2(-) ISYM_S13E_X2 IMEAN_S13E_X2 SIGIMEAN_S13E_X2 I_S13E_X2(+) SIGI_S13E_X2(+) I_S13E_X2(-) SIGI_S13E_X2(-) ****************** In Phenix: Xtriage output choosing "Imean" Miller array info: /Users/garavito/ccp4_projects/sus1_S13/reflections_tmp.mtz:IMEAN_S13E_X2,SIGIMEAN_S13E_X2 Observation type: xray.amplitude Type of data: double, size=46772 Type of sigmas: double, size=46772 Number of Miller indices: 46772 Anomalous flag: False Xtriage output choosing "Fs" Miller array info: /Users/garavito/ccp4_projects/sus1_S13/reflections_tmp.mtz:F_S13E_X2,SIGF_S13E_X2,DANO_S13E_X2,SIGDANO_S13E_X2 Observation type: xray.amplitude Type of data: double, size=88486 Type of sigmas: double, size=88486 Number of Miller indices: 88486 Anomalous flag: True **************************************************************** R. Michael Garavito, Ph.D. Professor of Biochemistry & Molecular Biology 513 Biochemistry Bldg. Michigan State University East Lansing, MI 48824-1319 Office: (517) 355-9724 Lab: (517) 353-9125 FAX: (517) 353-9334 Email: garavito(a)msu.edu ****************************************************************

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phenix.pdbtools
by Abhinav Kumar 22 Oct '11

22 Oct '11

Hi, I had been using the pdbtools to obtain the rmsd on various geometry parameters using the command: phenix.pdbtools my.pdb --show-geometry-statistics Now pdbtools does not recognize the option "--show-geometry-statistics" What is the option now? I am using phenix-1.7.2-869. -- Thanks, Abhinav JCSG@SSRL, SLAC Phone: (650) 926-2992 Fax: (650) 926-3292

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