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Judging AutoSol Output
by agb838＠mail.usask.ca 30 Apr '06

30 Apr '06

I have some basic questions about the output from Phenix. Basically I have a data set that gave a solution, but I am not exactly sure how to tell about the quality of the solution from the outputs. The overall score is 110. I am not sure exactly what that refers to or how good/bad it is. I have attached the AutoSol.output file. Any basic suggestions at what I should be looking at, or if this is even the right file, would be helpful. The resolve.mtz and resolve.pdb look alright. They are a good start, but much improvement is needed. If anyone has some suggestions as to how to improve the output, that would also be helpful. I have also run the data through solve/resolve through the command prompt and it repeatedly locates four heavy atom sites (the data set is SAD). Yet, when Phenix is used, 16 sites are found. Why the difference and how do I tell what is working better and why. Thank you, Angela Hoffort

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Re: [phenixbb] Judging AutoSol Output
by Petrus H Zwart 30 Apr '06

30 Apr '06

----- Original Message ----- From: agb838(a)mail.usask.ca Date: Monday, April 24, 2006 3:18 pm Subject: [phenixbb] Judging AutoSol Output > I have some basic questions about the output from Phenix. > Basically I > have a data set that gave a solution, but I am not exactly sure > how to > tell about the quality of the solution from the outputs. The overall > score is 110. I am not sure exactly what that refers to or how > good/badit is. I have attached the AutoSol.output file. Any basic > suggestions at > what I should be looking at, or if this is even the right file, > would be > helpful. The resolve.mtz and resolve.pdb look alright. They are a good > start, but much improvement is needed. If anyone has some > suggestions as > to how to improve the output, that would also be helpful. > > I have also run the data through solve/resolve through the command > prompt and it repeatedly locates four heavy atom sites (the data > set is > SAD). Yet, when Phenix is used, 16 sites are found. Why the difference > and how do I tell what is working better and why. > Autosol is finding sites using HySS and subsequently iterates phasing, solvent flattening with the use of difference maps to find more sites. Juding from your output, it find most sites in 1 go. If you want to compare sites you find by Solve, Hyss, or famous programs from Buffalo or Goettingen, use iotbx.emma ha_from_autosol.pdb other.pdb To get an idea how many sites are matching. As far as I understand it, the overall score is a score relative to the other hand and other solutions and its absolute value is not so important, as long as it is (much) larger that any other solution. In your case, solution 1 has a score of 110, solution has a solution of 63. It is also finding NCS, which seems to be good (NCS correlation of 0.66 early no allready). Improvement of the pdb file is obtained by runnnig the modelbuild wizard I think. The Autosol wizard only carries out a limit number of model building cycles and the modelbuild wizard does a more thorough job. HTH Peter _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://www.phenix-online.org/mailman/listinfo/phenixbb

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phenix.refine Crashes with "ZeroDivisionError: float division"
by Dale Tronrud 14 Apr '06

14 Apr '06

Hi, I'm new to phenix and phenix.refine. I am trying to refine a protein with phenix.refine but the program crashes quite quickly. I have appended all of the output below, but the critical part is (I believe): File "/usr/local/phenix-1.1a/cctbx/cctbx/miller.py", line 432, in auto_anomalous anomalous_flag = (2*self.n_bijvoet_pairs()/self.indices().size() ZeroDivisionError: float division Apparently, self.indices().size() is zero, but I don't know why or really what that is. My mtz file does not contain any anomalous data. It just has F, SigF, and a free R flag for the positive octant of data. (Well, since this is P6122 the positive duodecant.) Any advise would be appreciated. Dale Tronrud # Date 2006-04-14 Time 15:14:52 PDT -0700 #phil __OFF__ ------------------------------------------------------------------------------ PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography Version: 1.1a Platform: intel-linux linux User: dale ------------------------------------------------------------------------------ phenix.refine: Macromolecular Structure Refinement ------------------------------------------------------------------------------ Phenix developers include: P.D. Adams, P. Afonine, K. Gopal, R.W. Grosse-Kunstleve, L.-W. Hung, T.R. Ioerger, A.J. McCoy, N.W. Moriarty, R.K. Pai, R.J. Read, T.D. Romo, J.C. Sacchettini, N.K. Sauter, L.C. Storoni, T.C. Terwilliger Phenix home page: http://www.phenix-online.org/ ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ Phenix components are copyrighted by: - Lawrence Berkeley National Laboratory - Los Alamos National Laboratory - University of Cambridge - Texas Agricultural Experiment Station & Texas Engineering Experiment Station ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ Major third-party components of Phenix include: Python, wxPython, Boost, SCons, Clipper, CCP4 I/O libraries, PyCifRW, FFTPACK, L-BFGS Enter phenix.acknowledgments for details. ------------------------------------------------------------------------------ Processing inputs. This may take a minute or two. Crystal symmetry: Unit cell: (93.016, 93.016, 130.096, 90, 90, 120) Space group: P 61 2 2 (No. 178) phs1rb-coot-1-no-peak.pdb Total number of atoms: 2733 Number of models: 1 Model: 0 Number of conformers: 3 Conformer: "A" Number of atoms: 2723 Number of chains: 5 Number of residues, atoms: 1, 12 Unusual residues: {'GLC': 1} Classifications: {'unknown': 1} Number of residues, atoms: 1, 12 Unusual residues: {'GLC': 1} Classifications: {'unknown': 1} Number of residues, atoms: 315, 2389 Classifications: {'peptide': 315} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 306, 'PCIS': 1} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan2': 1, 'GLN:plan1': 3, 'GLN:plan2': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Number of residues, atoms: 6, 11 Unusual residues: {' ZN': 1, ' CA': 4} Inner-chain residues flagged as termini: ['ALA, ,316, , '] Classifications: {'unknown': 5, 'peptide': 1} Modifications used: {'COO': 1} Link IDs: {None: 5} Number of residues, atoms: 299, 299 Classifications: {'water': 299} Link IDs: {None: 298} Conformer: "B" Number of atoms: 2723 Common with "A": 2718 Number of chains: 5 Number of residues, atoms: 1, 12 Unusual residues: {'GLC': 1} Classifications: {'unknown': 1} bond proxies already assigned to first conformer: 12 Number of residues, atoms: 1, 12 Unusual residues: {'GLC': 1} Classifications: {'unknown': 1} bond proxies already assigned to first conformer: 12 Number of residues, atoms: 315, 2389 Classifications: {'peptide': 315} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 306, 'PCIS': 1} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan2': 1, 'GLN:plan1': 3, 'GLN:plan2': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 2442 Number of residues, atoms: 6, 11 Unusual residues: {' ZN': 1, ' CA': 4} Inner-chain residues flagged as termini: ['ALA, ,316, , '] Classifications: {'unknown': 5, 'peptide': 1} Modifications used: {'COO': 1} Link IDs: {None: 5} bond proxies already assigned to first conformer: 5 Number of residues, atoms: 299, 299 Classifications: {'water': 299} Link IDs: {None: 298} Conformer: "C" Number of atoms: 2723 Common with "A": 2718 Common with "B": 2718 Number of chains: 5 Number of residues, atoms: 1, 12 Unusual residues: {'GLC': 1} Classifications: {'unknown': 1} bond proxies already assigned to first conformer: 12 Number of residues, atoms: 1, 12 Unusual residues: {'GLC': 1} Classifications: {'unknown': 1} bond proxies already assigned to first conformer: 12 Number of residues, atoms: 315, 2389 Classifications: {'peptide': 315} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 306, 'PCIS': 1} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan2': 1, 'GLN:plan1': 3, 'GLN:plan2': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 2442 Number of residues, atoms: 6, 11 Unusual residues: {' ZN': 1, ' CA': 4} Inner-chain residues flagged as termini: ['ALA, ,316, , '] Classifications: {'unknown': 5, 'peptide': 1} Modifications used: {'COO': 1} Link IDs: {None: 5} bond proxies already assigned to first conformer: 5 Number of residues, atoms: 299, 299 Classifications: {'water': 299} Link IDs: {None: 298} Time building chain proxies: 12.22, per 1000 atoms: 4.47 Traceback (most recent call last): File "/usr/local/phenix-1.1a/phenix/phenix/command_line/refine.py", line 5, in ? command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.1a/phenix/phenix/refinement/command_line.py", line 35, in run log=log) File "/usr/local/phenix-1.1a/phenix/phenix/refinement/command_line.py", line 128, in __init__ reflection_file_server = self.reflection_file_server() File "/usr/local/phenix-1.1a/phenix/phenix/refinement/command_line.py", line 337, in reflection_file_server err=self.log) File "/usr/local/phenix-1.1a/iotbx/iotbx/reflection_file_utils.py", line 303, in __init__ force_symmetry=self.force_symmetry)) File "/usr/local/phenix-1.1a/iotbx/iotbx/reflection_file_reader.py", line 160, in as_miller_arrays base_array_info=base_array_info) File "/usr/local/phenix-1.1a/iotbx/iotbx/mtz/__init__.py", line 363, in as_miller_arrays dataset=dataset) File "/usr/local/phenix-1.1a/iotbx/iotbx/mtz/__init__.py", line 495, in group_columns observation_type=observation_type)) File "/usr/local/phenix-1.1a/iotbx/iotbx/mtz/__init__.py", line 516, in column_group indices=group.indices).auto_anomalous(min_fraction_bijvoet_pairs=2/3.) File "/usr/local/phenix-1.1a/cctbx/cctbx/miller.py", line 432, in auto_anomalous anomalous_flag = (2*self.n_bijvoet_pairs()/self.indices().size() ZeroDivisionError: float division

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Passing keyword to a Wizard
by Andrzej LYSKOWSKI 24 Mar '06

24 Mar '06

Hi, I'm getting a feedback from AutoBuild Wizard that I should set it with coarse_grid keyword (info from LAST.LOG). However, this keyword isn't present in Set Variable menu. How can set it? Regards, Andrzej -- < Andrzej Lyskowski (andrzej[dot]lyskowski[at]uni-graz[dot]at) < Chemistry Institute - Phys. Chem./Structural Biology < Heinrichstrasse 28 < A-8010 Graz, Austria < Tel.: 43 316 380 54 69 < Fax.: 34 316 380 98 50 > A designer knows he has achieved perfection > not when there is nothing left to add, > but when there is nothing left to take away. > Antoine de Saint-Exupery

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Re: [phenixbb] PHENIX installation issues
by Ralf W. Grosse-Kunstleve 14 Mar '06

14 Mar '06

> > Another thing is i installed in a user so whenever i do project it > gives permission denied . I suspect you have the following situation: drwx------ 2 rwgk cci 4096 Mar 14 10:47 phenix-1.1a I.e. when you installed phenix the "umask" was set such that "group" and/or "others" don't have read permission. Please verify my suspicion with ls -d $PHENIX If you see the "drwx------" or maybe "drwxr-x---" it is easy to fix. Use the su command to become root, then: find phenix-1.1a -exec chmod go+r {} \; find phenix-1.1a -type d -exec chmod go+x {} \; Cheers, Ralf

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PHENIX installation issues
by Peter Zwart 14 Mar '06

14 Mar '06

I see. Unfortunately, the switching between bash and csh is needed until the next release. I am not quite sure what this > Another thing is i installed in a user so whenever i do project it gives permission denied . error/problem exactly is or how it can be solved, but maybe some of my collegues have an idea. Peter Ethayathulla Abdulsamath wrote: > hi Petrus: > > yes, it got installed I replied in phenixbb. > > But problem is everytime i have to do csh then source phenix_env file. > Then again change back to bash. > > Another thing is i installed in a user so whenever i do project it > gives permission denied . > > Everytime i logged in root then do thinz IS there any sol for it >

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Re: [phenixbb] phenixbb Digest, Vol 4, Issue 5
by Ralf W. Grosse-Kunstleve 13 Mar '06

13 Mar '06

> > how to change bash setup ot csh. > > I guess you can change shell (type csh or so) in a single window for > installing, sourcing Exactly. > and running phenix. Not necessarily. This trick should work: bash prompt $ csh csh prompt % source phenix_env csh prompt % bash bash prompt $ Providing a phenix_env.sh is on our todo list. Cheers, Ralf

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Re: [phenixbb] phenixbb Digest, Vol 4, Issue 5
by Petrus H Zwart 12 Mar '06

12 Mar '06

> how to change bash setup ot csh. I guess you can change shell (type csh or so) in a single window for installing, sourcing and running phenix. > In ccp4 there is a file for everything but how to i do for Phenix ! Yes. It is a bit clumsy, I agree. However note that the release you have is still an alpha release (http://en.wikipedia.org/wiki/Development_stage), indicating that not everything is as much in place as one might like it to be. Let us know if you have any (additional) problems. HTH Peter _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://www.phenix-online.org/mailman/listinfo/phenixbb

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Re: [phenixbb] phenixbb Digest, Vol 4, Issue 5
by Ethayathulla A.S 11 Mar '06

11 Mar '06

Dear peter: how to change bash setup ot csh. I understood that the program is written for csh and tcsh how do change to bash format so that it gets installed In ccp4 there is a file for everything but how to i do for Phenix ! Thanking you Ethayathulla

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Re: [phenixbb] Regarding installation
by Petrus H Zwart 09 Mar '06

09 Mar '06

Hai Ethayathulla, Have a look at the following posting: http://www.phenix-online.org/pipermail/phenixbb/2006- February/000004.html i.e., things do not work in bash, but do in csh/tcsh. HTH Peter Hi I tried to install Phenix in RED HAT 9.0 LINUX It got installed succesfully But when tried to source it gives error message bash :/ command not found :/usr/local/phenix1.1a/phenix_env line 38 unexpected end of line plz suggest Thanking you -- A.S.Ethayathulla Department of BIophysics All India Institute of Medical Sciences Ansai Nagar New Delhi-110029 India _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://www.phenix-online.org/mailman/listinfo/phenixbb

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