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Sequence file for DNA
by jens j birktoft 12 Sep '09

12 Sep '09

Hi: What is the proper format for a sequence file for double stranded DNA duplex/helix ? Do both strands have to be entered, separated by >'s or just one of the complimentary strands Cheers Jay

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Phaser-Gui question
by Jonathan Grimes 11 Sep '09

11 Sep '09

Dear Developers, As a late developer I have recently started to use the new GUI. Its very impressive but what I would like to do is to fire off a number of jobs to vary parameters say in refinement or auto-rebuilding. I havent been able to work out how to submit multiple jobs via the same configuration tab window. Is this possible ? Am I missing a trick. Thanks Jon -- Dr. Jonathan M. Grimes, University Research Lecturer Division of Structural Biology Wellcome Trust Centre for Human Genetics University of Oxford Roosevelt Drive, Oxford OX3 7BN, UK Email: Jonathan(a)strubi.ox.ac.uk, Web: www.strubi.ox.ac.uk Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547

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SA omit map
by Pascal Egea 11 Sep '09

11 Sep '09

Dear All,I have a theoretical/practical question about omit maps and refinement. I am completing the refinement (in Phenix) of a protein-ligand complex at 1.3A resolution. I solved it by MR and automatic rebuilding of the protein alone first then built in the ligand. Rfree and Rfac are 19.4%/18.2% after TLS and water-picking in Phenix. The model includes everything protein, water, ligand and some ions. However I have some slight doubts one region in my ligand. What would be the best map, less biased, to look at this "very late" stage of the refinement. Are composite or systematic SA omit map useful options at this stage ? Thanks a lot in advance Pascal F. Egea, PhD Assistant Professor UCLA, David Geffen School of Medicine Department of Biological Chemistry 314 Biomedical Sciences Research Building office (310)-825-1013 lab (310)-825-8722 email pegea(a)mednet.ucla.edu

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Re: [phenixbb] SA omit map
by Thomas C. Terwilliger 11 Sep '09

11 Sep '09

Hi Pascal, I think that if you are only concerned about one ligand then there are four overall options. The first, going back before you added the ligand, is likely to be the least biased, then the iterative-build omit, then the SA-omit and kicked maps. The iterative-build omit map is probably the best way to get rid of bias once it has been introduced, but it is also very computationally intensive. As you are only interested in the ligand, you probably do not need to do a composite map, saving you a lot of time. So the options are: 1. You can go back to the structure you had just prior to adding that ligand, and simply refine that structure and look carefully at the maps. As the structure has never seen the ligand, you have no worries about bias at all in that map. Of course that map may be from a much earlier stage, so it may not be so clear either...leading to the other options of.. 2. Take your current structure and run an SA-omit map or an iterative-build omit map, omitting around a PDB file that you create that contains only the ligand. 3. Or, pretty much equivalent to #2, you can remove your ligand from the structure and just do a run of SA or rebuild-in-place and calculate a map, 4. Or you can calculate a kicked map. For the kicked map, quoting Pavel Afonine: in your parameter file just add another map scope to the electron_density_maps scope, like this: electron_density_maps { map { mtz_label_amplitudes = "2FOFCWT_kick" mtz_label_phases = "PH2FOFCWT_kick" likelihood_weighted = True obs_factor = 2 calc_factor = 1 kicked = True fill_missing_f_obs_with_weighted_f_model = False } map { mtz_label_amplitudes = "FOFCWT_kick" mtz_label_phases = "PHFOFCWT_kick" likelihood_weighted = True obs_factor = 1 calc_factor = 1 kicked = True fill_missing_f_obs_with_weighted_f_model = False } } This will create two additional kick maps in addition to the default maps. All the best, Tom T , >> Dear All,I have a theoretical/practical question about omit maps and >> refinement. >> I am completing the refinement (in Phenix) of a protein-ligand complex at >> 1.3A resolution. I solved it by MR and automatic rebuilding of the protein >> alone first then built in the ligand. Rfree and Rfac are 19.4%/18.2% after >> TLS and water-picking in Phenix. The model includes everything protein, >> water, ligand and some ions. >> However I have some slight doubts one region in my ligand. >> What would be the best map, less biased, to look at this "very late" stage >> of the refinement. Are composite or systematic SA omit map useful options >> at this stage ? >> >> Thanks a lot in advance >> >> >> Pascal F. Egea, PhD >> Assistant Professor >> UCLA, David Geffen School of Medicine >> Department of Biological Chemistry >> 314 Biomedical Sciences Research Building >> office (310)-825-1013 >> lab (310)-825-8722 >> email pegea(a)mednet.ucla.edu >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >>

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Auto builiding
by Jonathan Grimes 11 Sep '09

11 Sep '09

Dear Developers, I have a molecular replacement solution with a model that has 58 seq identity to my protein. There is 1 insertion in my protein of 1 residue and 1 deletion of 4 residues compared to the model. There are 2 mols in the asym unit. When I run autobuild with standard settings (but either Auto or Yes for the rebuild in place) it falls over with this error. **************************************** AutoBuild Input failed Sorry, the PDB file and sequence file could not be aligned (with no gaps and >50.0% identity) Please restart the wizard... You have several possibilities to try .... You can set rebuild_in_place=No You can set input_sequence_file=None You can edit your model to make sure it has no residues extending N-terminal of the beginning of the corresponding sequences in your sequence file You can set min_seq_identity_percent to a lower value You can set highest_resno to a higher value You can specify start_chains_list if your PDB file sequence starts with a residue number greater than the number of residues in the sequence. **************************************** It runs with rebuild_in_place=No but given the low resolution of the data (3.5A) I thought it would be best to keep as much of the model as possible. What am I doing wrong. Thanks Jon -- Dr. Jonathan M. Grimes, University Research Lecturer Division of Structural Biology Wellcome Trust Centre for Human Genetics University of Oxford Roosevelt Drive, Oxford OX3 7BN, UK Email: Jonathan(a)strubi.ox.ac.uk, Web: www.strubi.ox.ac.uk Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547

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Re: [phenixbb] SA omit map
by Gino Cingolani 11 Sep '09

11 Sep '09

Dear Pascal, my suggestion to convince yourself that your ligand is there ..... 1. omit the atoms corresponding to your ligand from your pdb 2. compute electron density difference maps using data between 15-2.5A. High res maps (1.3-2.5A) will look worst than medium res maps if your ligand is partially occupied/mobile (typically bound on the surface of your proteins as opposed to a cavity). 3. Also, make sure you aren't wiping off the ligand by using an improper solvent masks during solvent flattening. If your ligand is really there, but not quite there.... you may try to pressure freeze your crystals instead of using conventional cryo-protectants. Good luck. Gino

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how to generate anomalous difference map in phenix
by crystallogrphy 10 Sep '09

10 Sep '09

Hi, Does anyone know how to generate anomalous difference map by phenix? I have the data file with the scalepack format and the refined model against this data. Thanks!

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Changing the resolution cutoff for water picking
by Sam Stampfer 10 Sep '09

10 Sep '09

Hi, I'm refining a 2.88 resolution structure and would like to pick waters. I assume the default low_resolution is set to 2.8 Angstroms and so my lower resolution map is not yielding any waters. How do I change the resolution cutoff for water picking to be 3.0 Angstroms? I tried adding "refinement.ordered_solvent.low_resolution=3.0" to my command line arguments and phenix is reading this, but the refinement crashes about 15 seconds in with the message: ================== Extract refinement strategy and selections ================= Sorry: Selection string 'water' results in empty selection (selects no atoms). Thanks for your help! -Sam

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Ligandfit problems with ligand geometry
by Kendall Nettles 10 Sep '09

10 Sep '09

I just tried ligandfit for the first time and it did not maintain proper geometry of the ligand. There were problems with both bond lengths and planarity. Is there a way to specify a .cif file? The ligand pdb was generated with PROGRD2, and I have had good success refining a structure that contains a very close analog with phenix.refine. Kendall Nettles

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Phaser and anisotropy question
by Peter Grey 10 Sep '09

10 Sep '09

Dear Phenix users, I have a very anisotropic data as phaser reports anisotropic deltaB = 60.2. I would be grateful for advice of several issues. 1.Could you please tell me if phaser map coefficients FWT,PHWT take into account the anisotropic scaling ? 2.This means that these coefficients will be different from those calculated from a partial model in sigmaa because sigmaa has no anisotropic scaling (and no bulk solvent correction) ? 3.In the case of such severe anisotropy can the scaling diminish too strongly the well measured high resolution reflections ? If so should I calculate the coefficients my self by sigmaa and not use pahser mtz output or is there a better solution ? Many thanks in advance for sharing your thoughts and experience, Peter.

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Re: [phenixbb] Phenix crashes
by Katya Heldwein 10 Sep '09

10 Sep '09

Nat, 1.4-160 works just fine. Thank you. Katya Ekaterina Heldwein, Ph.D. Assistant Professor Department of Molecular Biology and Microbiology Tufts University School of Medicine 136 Harrison Ave Boston, MA 02111 phone: 617-636-0858 fax: 617-636-0337 e-mail: katya.heldwein(a)tufts.edu phenixbb-request(a)phenix-online.org wrote: > Send phenixbb mailing list submissions to > phenixbb(a)phenix-online.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.phenix-online.org/mailman/listinfo/phenixbb > or, via email, send a message with subject or body 'help' to > phenixbb-request(a)phenix-online.org > > You can reach the person managing the list at > phenixbb-owner(a)phenix-online.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of phenixbb digest..." > > > Today's Topics: > > 1. Phenix crashes (Katya Heldwein) > 2. Re: Phenix crashes (sbiswas2(a)ncsu.edu) > 3. Re: Phenix crashes (Nathaniel Echols) > 4. Re: Phenix crashes (Nathaniel Echols) > 5. specifying column labels for input MTZ file > (Tirumala Kumar Chowdary) > 6. Re: specifying column labels for input MTZ file > (Schubert, Carsten [PRDUS]) > 7. Re: specifying column labels for input MTZ file (Pavel Afonine) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 09 Sep 2009 12:02:36 -0400 > From: Katya Heldwein <Katya.Heldwein(a)tufts.edu> > Subject: [phenixbb] Phenix crashes > To: phenixbb(a)phenix-online.org > Message-ID: <20090909120236.c2mlsf9lww00kwsk(a)webmail.tufts.edu> > Content-Type: text/plain; charset=ISO-8859-1; format="flowed" > > Hi, > > I am running phenix-1.4-159 on an Intel Mac. I get the following error: > > Bus error (Python call stack above) > This crash may be due to a problem in any imported > Python module, including modules which are not part > of the cctbx project. To disable the traps leading > to this message, define these environment variables > (e.g. assign the value 1): > BOOST_ADAPTBX_FPE_DEFAULT > BOOST_ADAPTBX_SIGNALS_DEFAULT > This will NOT solve the problem, just mask it, but > may allow you to proceed in case it is not critical. > > If I fix it by > > setenv BOOST_ADAPTBX_FPE_DEFAULT 1 > > I still get the same error. > > If I also do > > setenv BOOST_ADAPTBX_SIGNALS_DEFAULT 1 > > I don't get the error but phenix crashes nonetheless. > > How do I get around this problem? > > Thanks, > > Katya > > > > > ------------------------------ > > Message: 2 > Date: Wed, 9 Sep 2009 12:17:36 -0400 (EDT) > From: sbiswas2(a)ncsu.edu > Subject: Re: [phenixbb] Phenix crashes > To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> > Message-ID: <1476.152.1.132.71.1252513056.squirrel(a)webmail.ncsu.edu> > Content-Type: text/plain;charset=iso-8859-1 > > Hi, > This looks like a version problem, try installing the latest nightly builds. > Shya > > > >> Hi, >> >> I am running phenix-1.4-159 on an Intel Mac. I get the following error: >> >> Bus error (Python call stack above) >> This crash may be due to a problem in any imported >> Python module, including modules which are not part >> of the cctbx project. To disable the traps leading >> to this message, define these environment variables >> (e.g. assign the value 1): >> BOOST_ADAPTBX_FPE_DEFAULT >> BOOST_ADAPTBX_SIGNALS_DEFAULT >> This will NOT solve the problem, just mask it, but >> may allow you to proceed in case it is not critical. >> >> If I fix it by >> >> setenv BOOST_ADAPTBX_FPE_DEFAULT 1 >> >> I still get the same error. >> >> If I also do >> >> setenv BOOST_ADAPTBX_SIGNALS_DEFAULT 1 >> >> I don't get the error but phenix crashes nonetheless. >> >> How do I get around this problem? >> >> Thanks, >> >> Katya >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >> >> > > > > ------------------------------ > > Message: 3 > Date: Wed, 9 Sep 2009 09:37:50 -0700 > From: Nathaniel Echols <NEchols(a)lbl.gov> > Subject: Re: [phenixbb] Phenix crashes > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Message-ID: <2C512891-F9F0-40FB-AC0A-FA8C810F65AF(a)lbl.gov> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > On Sep 9, 2009, at 9:02 AM, Katya Heldwein wrote: > >> I am running phenix-1.4-159 on an Intel Mac. I get the following >> error: >> Bus error (Python call stack above) >> >> If I fix it by >> setenv BOOST_ADAPTBX_FPE_DEFAULT 1 >> I still get the same error. >> If I also do >> >> setenv BOOST_ADAPTBX_SIGNALS_DEFAULT 1 >> >> I don't get the error but phenix crashes nonetheless. >> >> How do I get around this problem? >> > > > Which programs are you running, and did you see a stack trace before > the error message? I just noticed the same thing running > phenix.refine from the same installer on my Mac, so it is probably an > undiagnosed bug. > > ------------------- > Nathaniel Echols > Lawrence Berkeley Lab > 510-486-5136 > NEchols(a)lbl.gov > > > > > > ------------------------------ > > Message: 4 > Date: Wed, 9 Sep 2009 09:46:24 -0700 > From: Nathaniel Echols <NEchols(a)lbl.gov> > Subject: Re: [phenixbb] Phenix crashes > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Message-ID: <6207C287-B0BB-4A7B-AD8E-2290222334FE(a)lbl.gov> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > On Sep 9, 2009, at 9:17 AM, sbiswas2(a)ncsu.edu wrote: > >> Hi, >> This looks like a version problem, try installing the latest nightly >> builds. >> Shya >> > > > Actually, 1.4-159 was the latest build until ten minutes ago, but I > just checked 1.4-160 and it does not appear to have this problem, so > it's now ready to download. Sorry for the trouble. > > -Nat > > ------------------- > Nathaniel Echols > Lawrence Berkeley Lab > 510-486-5136 > NEchols(a)lbl.gov > > > > > > ------------------------------ > > Message: 5 > Date: Wed, 09 Sep 2009 14:10:27 -0400 > From: Tirumala Kumar Chowdary <Tirumala.Chowdary(a)tufts.edu> > Subject: [phenixbb] specifying column labels for input MTZ file > To: phenixbb(a)phenix-online.org > Message-ID: <20090909141027.belblmob7s4s440w(a)webmail.tufts.edu> > Content-Type: text/plain; charset=ISO-8859-1; format="flowed" > > Hi, > > I am trying to run phenix.refine with a sharp output MTZ file (column > labels H K L NUMORB FB PHIB FOM HX HY FH PHIH FP SIGFP HLA HLB HLC HLD > HL0 Fcent PHIcent FOMcent Fmap PHImap FHref PHIHref Fav SIGFav). > > Phenix.refine stopped at > > 'Multiple equally suitable arrays of observed xray data found. > > Possible choices: > sharp_sad_se_eden.mtz:FP,SIGFP > sharp_sad_se_eden.mtz:Fav,SIGFav > > Please use refinement.input.xray_data.labels' > > Can someone tell me on how to use this > 'refinement.input.xray_data.labels' and how to specify which column > labels to use. There is nothing written in the documentation about it. > > Thanks > Tirumal > > > > > > > ------------------------------ > > Message: 6 > Date: Wed, 9 Sep 2009 14:22:40 -0400 > From: "Schubert, Carsten [PRDUS]" <CSCHUBER(a)its.jnj.com> > Subject: Re: [phenixbb] specifying column labels for input MTZ file > To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> > Message-ID: > <204D6E1BD9ACEA40B3F76FE9C125528F035DE9FF(a)JNJUSSHGMS01.na.jnj.com> > Content-Type: text/plain; charset="us-ascii" > > Tirumal: > > refinement.input.xray_data.labels="FP,SIGFP" > > should do the trick. > > Cheers, > > Carsten > > > >> -----Original Message----- >> From: phenixbb-bounces(a)phenix-online.org [mailto:phenixbb- >> bounces(a)phenix-online.org] On Behalf Of Tirumala Kumar Chowdary >> Sent: Wednesday, September 09, 2009 2:10 PM >> To: phenixbb(a)phenix-online.org >> Subject: [phenixbb] specifying column labels for input MTZ file >> >> Hi, >> >> I am trying to run phenix.refine with a sharp output MTZ file (column >> labels H K L NUMORB FB PHIB FOM HX HY FH PHIH FP SIGFP HLA HLB HLC >> > HLD > >> HL0 Fcent PHIcent FOMcent Fmap PHImap FHref PHIHref Fav SIGFav). >> >> Phenix.refine stopped at >> >> 'Multiple equally suitable arrays of observed xray data found. >> >> Possible choices: >> sharp_sad_se_eden.mtz:FP,SIGFP >> sharp_sad_se_eden.mtz:Fav,SIGFav >> >> Please use refinement.input.xray_data.labels' >> >> Can someone tell me on how to use this >> 'refinement.input.xray_data.labels' and how to specify which column >> labels to use. There is nothing written in the documentation about it. >> >> Thanks >> Tirumal >> >> >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >> > > > > > ------------------------------ > > Message: 7 > Date: Wed, 09 Sep 2009 11:24:46 -0700 > From: Pavel Afonine <PAfonine(a)lbl.gov> > Subject: Re: [phenixbb] specifying column labels for input MTZ file > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Cc: Tirumala.Chowdary(a)tufts.edu > Message-ID: <4AA7F2EE.6080106(a)lbl.gov> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Tirumala, > > I agree, you are not the first who confused by this and an example right > in the message would help. > > First, your MTZ file contains the following data: (FP,SIGFP) and > (Fav,SIGFav) and it is your choice to select the one that you want to > use in refinement. > > Second, once decided on the data - for example it is FP, then just add > to your command line this: > > refinement.input.xray_data.labels=FP > > or, which is the same > > xray_data.labels="FP,SIGFP" > > Pavel. > > > > On 9/9/09 11:10 AM, Tirumala Kumar Chowdary wrote: > >> Hi, >> >> I am trying to run phenix.refine with a sharp output MTZ file (column >> labels H K L NUMORB FB PHIB FOM HX HY FH PHIH FP SIGFP HLA HLB HLC HLD >> HL0 Fcent PHIcent FOMcent Fmap PHImap FHref PHIHref Fav SIGFav). >> >> Phenix.refine stopped at >> >> 'Multiple equally suitable arrays of observed xray data found. >> >> Possible choices: >> sharp_sad_se_eden.mtz:FP,SIGFP >> sharp_sad_se_eden.mtz:Fav,SIGFav >> >> Please use refinement.input.xray_data.labels' >> >> Can someone tell me on how to use this >> 'refinement.input.xray_data.labels' and how to specify which column >> labels to use. There is nothing written in the documentation about it. >> >> Thanks >> Tirumal >> >> >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >> >> > > > ------------------------------ > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb > > > End of phenixbb Digest, Vol 46, Issue 14 > **************************************** >

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run autosol with rough phases from shelx?
by Francis E Reyes 09 Sep '09

09 Sep '09

Hi all Is it possible to input the phs file from a shelx run into an autosol run for some phase improvement with solve/resolve?? I tried putting in the HA sites but then the resultant map is worse. Also what are acceptable skews for low resolution phasing (worse than 4A) ? I understand the docs say 0.1 but does that also apply for low res? Thanks FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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Phenix crashes
by Katya Heldwein 09 Sep '09

09 Sep '09

Hi, I am running phenix-1.4-159 on an Intel Mac. I get the following error: Bus error (Python call stack above) This crash may be due to a problem in any imported Python module, including modules which are not part of the cctbx project. To disable the traps leading to this message, define these environment variables (e.g. assign the value 1): BOOST_ADAPTBX_FPE_DEFAULT BOOST_ADAPTBX_SIGNALS_DEFAULT This will NOT solve the problem, just mask it, but may allow you to proceed in case it is not critical. If I fix it by setenv BOOST_ADAPTBX_FPE_DEFAULT 1 I still get the same error. If I also do setenv BOOST_ADAPTBX_SIGNALS_DEFAULT 1 I don't get the error but phenix crashes nonetheless. How do I get around this problem? Thanks, Katya

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question about pick water in autobuild
by crystallogrphy 08 Sep '09

08 Sep '09

Hi, I am building a model against a 2.1A data set using phenix.autobuild. Right now Rfree is about 35%. I do not want to pick water in this stage because I see denisty at N-terminal of my model which need to build more residues. However, the program still picks water even after I say 'place_waters=False'. Does anyone know why? phenix.autobuild data=exptl_fobs_phases_freeR_flags.mtz model=AutoBuild_run_4_/overall_best-090905a.pdb seq_file=../ztb-sd.seq refinement.place_waters=False refinement.refine_with_ncs=True nproc=2

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RuntimeError
by Young-Jin Cho 08 Sep '09

08 Sep '09

Hi everyone, while I was running phenix, I got the following error message. Could some one give me any tips to deal with such this problem? Thanks in advace, YoungJin Traceback (most recent call last): File "/home/yjcho2/Phenix/phenix-1.4-95/phenix/phenix/command_line/refine.py", line 19, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/home/yjcho2/Phenix/phenix-1.4-95/phenix/phenix/refinement/command_line.py", line 68, in run log=log) File "/home/yjcho2/Phenix/phenix-1.4-95/phenix/phenix/refinement/command_line.py", line 227, in __init__ self.pdb_file_names) File "/home/yjcho2/Phenix/phenix-1.4-95/cctbx_project/mmtbx/utils.py", line 876, in process_pdb_files raw_records = raw_records) File "/home/yjcho2/Phenix/phenix-1.4-95/cctbx_project/mmtbx/utils.py", line 907, in _process_pdb_file log = self.log) File "/home/yjcho2/Phenix/phenix-1.4-95/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 2912, in __init__ log=log) File "/home/yjcho2/Phenix/phenix-1.4-95/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 1962, in __init__ self.site_symmetry_table().special_position_indices() File "/home/yjcho2/Phenix/phenix-1.4-95/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 2217, in site_symmetry_table sites_cart=self.sites_cart) File "/home/yjcho2/Phenix/phenix-1.4-95/cctbx_project/cctbx/crystal/__init__.py", line 394, in site_symmetry_table assert_min_distance_sym_equiv=self.assert_min_distance_sym_equiv()) RuntimeError: cctbx Error: site_symmetry: min_distance_sym_equiv too large. --

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Re: [phenixbb] question about pick water in autobuild
by Thomas C. Terwilliger 08 Sep '09

08 Sep '09

Hi Qun, With your command you need to add one more keyword to get rid of all the waters: place_waters_in_combine=False I'm sorry that doesn't happen automatically if you say place_waters=False ...I will make that happen in the future. Note however that these waters should not interfere with building...as waters are always deleted prior to building model. I note also that your command does not add new residues; it only adjusts the ones that are there. To build new model add: rebuild_in_place=False All the best, -Tom T >> Hi, >> >> from what you explain, the main issue I see here is that the model building program does not treat water simply as density peaks, and so removes them (waters) if necessary to build a protein chain instead. >> >> Otherwise, it's probably a good idea in general to fill in all unmodeled >> places with some placeholders like water, or probably isolated N atoms would work even better (if I recall correctly). >> >> Pavel. >> >> >> On 9/7/09 6:18 AM, crystallogrphy wrote: >>> Hi, Pavel: >>> The problem here is that autobuild placed waters into the densities where they are the N-terminal residues. Without the waters here, autobuild will build residues, not waters, to decrease R and Rfree with less model bias. Now with water picking, autobuild does not build more residues, just water. >>> I still do not know why 'place_waters=False' cannot work. Tom has not given me the answer yet. >>> On Mon, Sep 7, 2009 at 1:45 AM, Pavel Afonine <PAfonine(a)lbl.gov <mailto:[email protected]>> wrote: >>> Hi, >>> I hope Tom gives you the answer about how to stop water picking in autobuild. >>> From my side, I'm wondering why it bothers you (I'm not saying that not working option is good)? Why don't you consider those waters as a tool for improving your map? You are free to remove any of them them later on. This can be viewed as a prototype of what ARP/wARP does, or other "density growing" techniques... In your case you just temporarily place waters where the model is still absent, and when you build those missing places just consider waters as density peaks (I hope model building programs assume waters as just density peaks and remove waters if they are on the macromolecule's way). On the other hand, model >>> incompleteness may make the map ugly even for relatively well defined places. >>> Pavel. >>> On 9/6/09 7:38 AM, crystallogrphy wrote: >>>> Hi, >>>> I am building a model against a 2.1A data set using >>>> phenix.autobuild. Right now Rfree is about 35%. I do not want to pick water in this stage because I see denisty at N-terminal of my model which need to build more residues. However, the program still picks water even after I say 'place_waters=False'. Does anyone know why? >>>> phenix.autobuild data=exptl_fobs_phases_freeR_flags.mtz >>>> model=AutoBuild_run_4_/overall_best-090905a.pdb >>>> seq_file=../ztb-sd.seq refinement.place_waters=False >>>> refinement.refine_with_ncs=True nproc=2 >>>> ------------------------------------------------------------------------ _______________________________________________ >>>> phenixbb mailing list >>>> phenixbb(a)phenix-online.org <mailto:[email protected]> http://www.phenix-online.org/mailman/listinfo/phenixbb >>

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about kick map generation
by crystallogrphy 04 Sep '09

04 Sep '09

Hi, I am generating a averaged kick maps with the following script. According to the script, there should be both kick map and normal 2fofc maps. However, there is only one map files created. I am not sure it is kick map or routine 2fofc map. Does anyone knows? electron_density_maps { map_format = *xplor map_coefficients_format = *mtz phs suppress = None map { mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" likelihood_weighted = True obs_factor = 2 calc_factor = 1 kicked = False fill_missing_f_obs_with_weighted_f_model = True } map { mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" likelihood_weighted = True obs_factor = 1 calc_factor = 1 kicked = False fill_missing_f_obs_with_weighted_f_model = True } map { mtz_label_amplitudes = "2FOFCWT_kick" mtz_label_phases = "PH2FOFCWT_kick" likelihood_weighted = True obs_factor = 2 calc_factor = 1 kicked = True fill_missing_f_obs_with_weighted_f_model = False } map { mtz_label_amplitudes = "FOFCWT_kick" mtz_label_phases = "PHFOFCWT_kick" likelihood_weighted = True obs_factor = 1 calc_factor = 1 kicked = True fill_missing_f_obs_with_weighted_f_model = False } map { mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" likelihood_weighted = True obs_factor = 2 calc_factor = 1 kicked = False fill_missing_f_obs_with_weighted_f_model = False } map { mtz_label_amplitudes = "FOFCWT_no_fill" mtz_label_phases = "PHFOFCWT_no_fill" likelihood_weighted = True obs_factor = 1 calc_factor = 1 kicked = False fill_missing_f_obs_with_weighted_f_model = False } anomalous_difference_map { mtz_label_amplitudes = "ANOM" mtz_label_phases = "PHANOM" } grid_resolution_factor = 0.25 region = *selection cell atom_selection = None atom_selection_buffer = 3 apply_sigma_scaling = True apply_volume_scaling = False }

2 1

assertion error with autobuild (phenix 1.4.3)
by Jan Stout 04 Sep '09

04 Sep '09

Dear, I am trying to run the Autobuild Wizard to make a iterative-build omit map. I get the following errors after running Autobuild using the input file autobuild.eff generated by the wizard itself. I am working with phenix 1.4.3. Any input will be greatly appreciated. Many thanks, Jan Stout Traceback (most recent call last): File "/usr/local/PHENIX/phenix-1.4.3/phenix-1.4-3/phenix/phenix/command_line/autobuild.py", line 339, in <module> run_autobuild=run_autobuild(args=sys.argv[1:]) File "/usr/local/PHENIX/phenix-1.4.3/phenix-1.4-3/phenix/phenix/autosol/wizard_command_line.py", line 598, in __init__ self.RunWizard() File "/usr/local/PHENIX/phenix-1.4.3/phenix-1.4-3/phenix/phenix/autosol/wizard_command_line.py", line 973, in RunWizard self.runWizard.run() File "/usr/local/PHENIX/phenix-1.4.3/phenix-1.4-3/phenix/phenix/autosol/wizard_command_line.py", line 230, in run self.Wizard.Run(info='script') File "/usr/local/PHENIX/phenix-1.4.3/phenix-1.4-3/phenix/phenix/autosol/AutoBaseExtend.py", line 726, in Run ok=self.CollectInputs()# raises AssertionError on failure File "/usr/local/PHENIX/phenix-1.4.3/phenix-1.4-3/phenix/phenix/autosol/AutoBaseExtend.py", line 1790, in CollectInputs getattr(self,"finish_"+str(self.application_method))() File "/usr/local/PHENIX/phenix-1.4.3/phenix-1.4-3/phenix/phenix/wizards/AutoBuild.py", line 1074, in finish_AutoBuild_start all_files_ok=self.finish_Build_start() File "/usr/local/PHENIX/phenix-1.4.3/phenix-1.4-3/phenix/phenix/autosol/BuildBase.py", line 382, in finish_Build_start all_files_ok=self.Build_finish_up_start() File "/usr/local/PHENIX/phenix-1.4.3/phenix-1.4-3/phenix/phenix/autosol/BuildBase.py", line 508, in Build_finish_up_start str(self.Facts['input_data_file'])+"'") File "/usr/local/PHENIX/phenix-1.4.3/phenix-1.4-3/phenix/phenix/autosol/UserMethods.py", line 84, in Error raise AssertionError,self.ErrorLine AssertionError: Sorry, cannot find the input_data_file ''

2 1

question about phenix.refine
by crystallogrphy 03 Sep '09

03 Sep '09

Hi, I want to use phenix to refine a model right after autobuild with the following script: phenix.refine xray_data.file_name=exptl_fobs_phases_freeR_flags.mtz overall_best-090903a.pdb strategy=rigid_body+individual_sites simulated_annealing=true simulated_annealing.start_temperature=8000 sites.rigid_body="chain A" sites.rigid_body="chain B" However, the program says " F-obs: exptl_fobs_phases_freeR_flags.mtz:FP,SIGFP If previously used R-free flags are available run this command again with the name of the file containing the original flags as an additional input. If the structure was never refined before, or if the original R-free flags are unrecoverable, run this command again with the additional definition: refinement.input.xray_data.r_free_flags.generate=True when I use phenix.mtz.dump exptl_fobs_phases_freeR_flags.mtz, it indicates that it has FreeR_flag=1. Can anyone tell me why there is FreeR_flag in my data, while the refinement program does not recognize it? label #valid %valid min max type H 35619 100.00% 0.00 22.00 H: index h,k,l K 35619 100.00% 0.00 45.00 H: index h,k,l L 35619 100.00% -33.00 33.00 H: index h,k,l FP 35619 100.00% 0.00 114.22 F: amplitude SIGFP 35619 100.00% 0.15 6.13 Q: standard deviation PHIM 35619 100.00% 0.00 0.00 P: phase angle in degrees FOMM 35619 100.00% 0.00 0.00 W: weight (of some sort) FreeR_flag 35619 100.00% 0.00 1.00 I: integer FC 35619 100.00% 0.00 0.00 F: amplitude

2 1

target omit map
by Susan Tsutakawa 03 Sep '09

03 Sep '09

I am trying to generate a simulated annealing omit map of a Mg-water cluster in the active site of my protein but when I run the SA omit map, I can only see the Mg when I use the Mgwater cluster as the target pdb. When I was building the model which did not have the metal present (phases solved by MR), I observed this Mg-water cluster in the Fo-Fc maps. Geometry and distance were ideal, etc. Now that I'm at the final stages of refinement, I would like to do a SA omit map as a figure for the paper. However, if I goto the lowest sigma, I only see the Mg. I'm using coot with the weights included to view the SA omit maps. I noticed that there is very little noise at the lowest sigma and so I'm wondering if the 0 sigma is truly 0 sigma and any suggestions on what to do. Thank you in advance. Sincerely, Susan

2 1

reflection file utils : .cif?
by Bryan W. Lepore 03 Sep '09

03 Sep '09

[ phenix 1.4r3 cctbx tag: 2008_12_07_1353 intel-linux-2.6 redhat-e4.7 ] i obtained a recent .cif from the PDB, then run : phenix.reflection_file_converter --mtz=output.mtz test.cif file_name: test.cif file_type: None No reflection data found in input file. .... not sure where to go from here (a clip of the file is below, hope not too much) - i know i can run ccp4:cif2mtz, but are .cif part of phenix.reflection_file_converter? -bryan (sample of test.cif): data_testsf # _diffrn_radiation.id 1 _diffrn_radiation.pdbx_wavelength 1.00600 # _audit.revision_id 1_0 _audit.creation_date 2009-07-07 _audit.update_record 'Initial release' # _symmetry.Int_Tables_number 1 _symmetry.space_group_name_H-M 'P 1' # _cell.length_a 79.6610 _cell.length_b 104.1490 _cell.length_c 154.0250 _cell.angle_alpha 81.9570 _cell.angle_beta 75.9250 _cell.angle_gamma 73.7280 # _reflns.d_resolution_high 2.967 _reflns.d_resolution_low 46.392 _reflns.limit_h_max 26 _reflns.limit_h_min -25 _reflns.limit_k_max 34 _reflns.limit_k_min -34 _reflns.limit_l_max 51 _reflns.limit_l_min 0 _reflns.number_all 93210 _reflns.number_obs 85990 # loop_ _symmetry_equiv.id _symmetry_equiv.pos_as_xyz 1 'X, Y, Z' # loop_ _refln.crystal_id _refln.wavelength_id _refln.scale_group_code _refln.status _refln.index_h _refln.index_k _refln.index_l _refln.F_meas_au _refln.F_meas_sigma_au 1 1 1 o -25 -16 1 218.4 77.9 1 1 1 o -25 -15 1 250.7 87.9 1 1 1 o -25 -15 2 217.9 78.8 (... etc... here is a free set hkl :) 1 1 1 f -25 -7 3 315.6 89.7 (... etc... until the end :) #END OF REFLECTIONS

2 1

Custom Planar Restraints
by cheung＠lmb.uni-muenchen.de 03 Sep '09

03 Sep '09

Hi all - is it possible to specify custom planar restraints in phenix.refine? I'm refining a 3.8A protein-dna complex and although i've set hydrogen bonding restraints between base pairs, they still become very twisted and buckled after refinement. Alan

2 1

question about autobuild
by crystallogrphy 03 Sep '09

03 Sep '09

Hi, I have used phenix.automr followed by phenix.autobuild to build a 264 residue model against my 2.1A resolution data set. The first run of autobuild gives me about 180 residues built. I have adjusted the model according to the denity. The N-terminal of the model has OK density to add more residues to the model. Can phenix.autobuild has some command to just put more residues to the N-terminal of my current model according to the density, so that the cost of CPU time will be much less than rerun the job completely? Thanks!

2 1

Chain id of water is not reading by coot
by Raja Dey 02 Sep '09

02 Sep '09

Dear Friends, I have 7 chains in my pdb file. When I am reading the pdb file in COOT, for some reason the chain id(W) of water is not coming in the list. I clicked on 'draw' and then 'go to atom'. I can see all other chains but not W. I created water in PHENIX Is there any wrong in my pdb? HETATM 7562 O HOH W 542 -9.043 -2.133 -12.633 1.00 34.55 W O HETATM 7563 O HOH W 543 -22.004 8.228 -21.695 1.00 34.55 W O HETATM 7564 O HOH W 544 5.926 38.977 -11.538 1.00 34.55 W O HETATM 7565 O HOH W 545 -31.162 5.813 -31.403 1.00 34.55 W O Raja

2 1

Improving picture quality of ED map in PYMOL
by Raja Dey 02 Sep '09

02 Sep '09

Dear Friends, Sorry, for the of topic question. Does anyone can tell how to improve the quality of a picture showing the electron density map of dna in a complex using PYMOL. I created the figure, but not happy with the quality as it is now. Might be there is a way to improve which I don't know. I want the lines in the mesh to be more sharp and fine. Any suggested program to prepare a publication quality figure to show the ED map would be of great help. Thanking you in advance... Raja

6 5

Source for Nightlys Location?
by Andrew Ring 02 Sep '09

02 Sep '09

Is it possible to get a source distribution for the nightlys? If so, where is it located? I can only finding the builds on the nightlys downloads page. For my systems and uses, the --openmp switch on version 1.4-3 has given encouraging results and I would like to investigate with something newer. -- =================================== Andrew Ring System Administrator Kuriyan Laboratory http://jkweb.qb3.berkeley.edu/ Doudna Laboratory http://rna.berkeley.edu/ University of California, Berkeley Office: 542 Stanley Hall Shipping: 176 Stanley Hall, QB3 Berkeley, CA 94720-3220 tel: (510) 643 0166 fax: (510) 643 2352 ====================================

2 2

R-work is too low
by Sam Stampfer 01 Sep '09

01 Sep '09

Hi, I'm refining a 2.88 Angstrom structure and am getting a difference of greater than 6% between the R-work and R-free. The best result (I think) is what I have from minimization alone: Start R-work = 0.3219, R-free = 0.3505 (no bulk solvent and anisotropic scale) Final R-work = 0.2424, R-free = 0.3174 (no bulk solvent and anisotropic scale) Start R-work = 0.3220, R-free = 0.3500 Final R-work = 0.2411, R-free = 0.3176 The results from simulated annealing are the following: Start R-work = 0.3219, R-free = 0.3505 (no bulk solvent and anisotropic scale) Final R-work = 0.2454, R-free = 0.3322 (no bulk solvent and anisotropic scale) Start R-work = 0.3220, R-free = 0.3500 Final R-work = 0.2403, R-free = 0.3333 I have also done the refinement with ncs but ncs is probably not appropriate for my structure. The final R-free ends up being higher (though the difference between R-free and R-work ends up being 6-7%) My PI (who is on vacation until next week) said that it was a problem if R-work was more than 0.06 lower than R-free. Any recommendations for me? Is it possible to reduce this difference? Is it worth it to rebuild the refined pdb if the R-work is this different from the R-free? My refinement script is: phenix.refine ss46_p3_cv.mtz ss46_rebuilt.pdb \ output.prefix=results/ss46_rebuilt_sa \ strategy=individual_sites+group_adp cif_link.params nag-nag.cif \ twin_law="h,-h-k,-l" \ simulated_annealing=true (the cif_link.params and nag-nag.cif files are made to handle the N-glycosylation sites, I think). Thanks for your help! -Sam

3 2

error TLS refinement
by Marjolein Thunnissen 01 Sep '09

01 Sep '09

I'm trying to finish refining a structure that has been almost refined completely about a year ago with an older version of Phenix.refine. When I start TLS refinement I get the following error message: RuntimeError : mean_weighted() argument is an empty array Traceback: Traceback (most recent call last): File "/usr/local/phenix-1.4-3/phenix/wxGUI2/Refine.py", line 259, in OnExcept raise event.data RuntimeError: mean_weighted() argument is an empty array I do not get this error when refining without TLS, only when I switch it on. The program advises me to post the error here so... Thanks Marjolein ________________________________________________________________________ Marjolein Thunnissen Phone +46-(0)46-22 24584 Associate Professor Fax +46-(0)46-22 24692 Dept of Molecular Biophysics, Lund University http://www.mbfys.lu.se PO-Box 124 S-221 00 Lund, Sweden Scientific coordinator I911 (Max-lab): MAD and fixed-wavelength stations for macromolecular crystallography ________________________________________________________________________

2 1

Specifying the number of processors to run phenix with
by Sam Stampfer 31 Aug '09

31 Aug '09

Hi- anyone know how to specify the number of processors to run phenix under in linux? Or how to tell what the default is? I'm running linux (fedora) with 4 processors and can't tell whether phenix is using all of them or not. I do the refinement with .csh files and tried doing "myfile.csh --nproc=4". The file ran but no faster- I can't tell if it is using 4 by default or if that's the incorrect command to specify the use of 4 processors. Thanks for your help! -Sam

3 3

Best first map for RESOLVE after MR
by Peter Grey 31 Aug '09

31 Aug '09

Hello all, I try to solve the structure of a big complex at rather low resolution. I have a molecular replacement solution with a partial model from Phaser. I would like to use RESOLVE for density modification. I ask for your advice regarding the first map that should be the input into RESOLVE. Should it be the 2mFo-DFc map directly from Phaser or would it be better to do rigid body refinement in phenix.refine and use the bulk solvent corrected 2mFo-DFc map ? Many thanks in advance for your suggestions, Peter.

3 5

high resolution bin statistics
by Sebastiano Pasqualato 31 Aug '09

31 Aug '09

Hi there, i just wanted to know how is determined the number of bins for which the statistics of refinement are given in the header of the pdb refined with phenix.refine, and if there's a way to have more than the number of bins that is default output. For example, what if I'd like to have statistics for the 2.6-2.5 bin, here: REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 32.4159 - 3.9625 0.99 2545 131 0.1921 0.2232 REMARK 3 2 3.9625 - 3.1460 1.00 2447 116 0.1650 0.2289 REMARK 3 3 3.1460 - 2.7486 1.00 2433 121 0.1917 0.2682 REMARK 3 4 2.7486 - 2.4974 1.00 2405 130 0.2244 0.2890 thanks a lot in advance, ciao s -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sperimentale Istituto Europeo di Oncologia via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5094

2 2

question about kick map
by crystallogrphy 29 Aug '09

29 Aug '09

Hi, I am trying to use kick map to remove model bias with the following script phenix.refine MR.1_refine_data.mtz MR.1_refine_001_refine_001.pdb output.prefix=refine-090828a simulated_annealing=True simulated_annealing.start_temperature=8000 strategy=individual_sites refine.params However, the program says: Sorry: Unknown file format: refine.params I do not understand why the format of refine.params cannot be read, which has the following contents. Does anyone know why? refinement { electron_density_maps { map { mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT likelihood_weighted = True obs_factor = 2 calc_factor = 1 kicked= True fill_missing_f_obs_with_weighted_f_model=True } map { mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT likelihood_weighted = True obs_factor = 1 calc_factor = 1 kicked= True fill_missing_f_obs_with_weighted_f_model=True } }

3 2

reflection file utility and use of modified phases in refinement
by Engin Ozkan 28 Aug '09

28 Aug '09

Hi everybody, I had some trouble with the reflection file utility today. I've been trying to import Rfree-flag column from one of the mtz's to my combined mtz, and it never does. The R-free flag is always left out of the output even when I have it selected. Have you guys seen this (I'm using 147)? Another question I have is about the output of phenix.autobuild. Phenix.autobuild tells me to use modified phase probabilities (HLAM, etc.) in refinement. I am assuming this is density-modified phases. But I've always thought that this would be bad practice (possibly because of unrealistically high FOMs and possible flattening of loops, etc, but maybe resolve does a better job than, say DM). Any ideas on that one? Thanks, Engin -- Engin Özkan Post-doctoral Scholar Dept of Molecular and Cellular Physiology Howard Hughes Medical Institute Stanford University School of Medicine ph: (650)-498-7111

3 5

Tracing and refining b-strands at 3.3A resolution
by Gino Cingolani 28 Aug '09

28 Aug '09

Hi Phenix community, I'm tracing a 3.3A averaged electron density map of a large macromolecular complex (~18,500 residues in the asymmetric unit). The map has great continuity and appears quite 'tubular'. While it is easy to interpret in a-helical regions, b-strands are more challenging, as I can't see the 'bump' corresponding to the carbonyl. If I built b-strands into the tubular density, refinement usually 'undoes' them and turns them into pseudo-loops/turns. On the positive side, a related molecule (~70% identical to mine) was solved to 1.9A resolution. So my question is, is there a way in Phenix to use a 'reference model' during refinement to force a given stretch of polypeptide chain to 'stay' b-stranded during refinement? Thanks in advance for the feedback, Gino ****************************************************************************** Gino Cingolani, Ph.D. Associate Professor Thomas Jefferson University Dept. of Biochemistry & Molecular Biology 233 South 10th Street - Room 826 Philadelphia PA 19107 Office (215) 503 4573 Lab (215) 503 4595 Fax (215) 923 2117 E-mail: gino.cingolani(a)jefferson.edu ****************************************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e conoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120)

6 7

Re: [phenixbb] Tracing and refining b-strands at 3.3A resolution
by Gino Cingolani 28 Aug '09

28 Aug '09

Sean, thanks to you and to whoever else responded to my email. Yes, I'd like to get your script. Thanks in advance! Gino ****************************************************************************** Gino Cingolani, Ph.D. Associate Professor Thomas Jefferson University Dept. of Biochemistry & Molecular Biology 233 South 10th Street - Room 826 Philadelphia PA 19107 Office (215) 503 4573 Lab (215) 503 4595 Fax (215) 923 2117 E-mail: gino.cingolani(a)jefferson.edu ****************************************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e conoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120) ---- Original message ---- >Date: Fri, 28 Aug 2009 08:35:08 +0100 >From: Wai-Ching Hon <hon(a)mrc-lmb.cam.ac.uk> >Subject: Re: [phenixbb] Tracing and refining b-strands at 3.3A resolution >To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > >Dear Sean, > >That sounds wonderful. Can I have your scripts too? > >many thanks > >waiching. > >Sean Johnson wrote: >> Gino, >> >> My lab recently refined a 3.4 A structure and dealt with similar >> problems. We found that using secondary structure restraints was the >> only effective way to maintain reasonable geometry during refinement. It >> is kind of a daunting task to input all of the definitions by hand, so >> we wrote a couple python scripts that are integrated with PyMol to write >> the appropriate restraint definition files. All you have to do is click >> on the atoms that you want restrained. You are welcome to the scripts if >> you like. Feel free to contact me if you are interested. >> >> Sean Johnson >> >> >> Gino Cingolani wrote: >> >>> Hi Phenix community, >>> >>> I'm tracing a 3.3A averaged electron density map of >>> a large macromolecular complex (~18,500 residues in the asymmetric unit). The map has great continuity and appears quite 'tubular'. While it is easy to interpret in a-helical regions, b-strands are more challenging, as I can't see the 'bump' corresponding to the carbonyl. If I built b-strands into the tubular density, refinement usually 'undoes' them and turns them into pseudo-loops/turns. On the positive side, a related molecule (~70% identical to mine) was solved to 1.9A resolution. So my question is, is there a way in Phenix to use a 'reference model' during refinement to force a given stretch of polypeptide chain to 'stay' b-stranded during refinement? >>> >>> Thanks in advance for the feedback, >>> >>> Gino >>> >>> >>> >>> >>> ****************************************************************************** >>> Gino Cingolani, Ph.D. >>> Associate Professor >>> Thomas Jefferson University >>> Dept. of Biochemistry & Molecular Biology >>> 233 South 10th Street - Room 826 >>> Philadelphia PA 19107 >>> Office (215) 503 4573 >>> Lab (215) 503 4595 >>> Fax (215) 923 2117 >>> E-mail: gino.cingolani(a)jefferson.edu >>> ****************************************************************************** >>> "Nati non foste per viver come bruti, ma per seguir virtute e conoscenza" >>> ("You were not born to live like brutes, but to follow virtue and knowledge") >>> Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120) >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://www.phenix-online.org/mailman/listinfo/phenixbb >>> >>> >> >> >________________ >hon.vcf (1k bytes) >________________ >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://www.phenix-online.org/mailman/listinfo/phenixbb

1 0

P43212 spacegroup change to C2221?
by Leigh Allen 28 Aug '09

28 Aug '09

Hello Phenix users. I recently solved the structure of my enzyme using SAD to a resolution of 1.9A. The R values were 0.19/0.25 and the space group was P43212 with a unit cell ~80, 80, 220. I then starting collecting datasets cocrystallized with ATP analogs and noticed that a lot of my datasets have a different unit cell when scaled in P43212. It comes out to be ~60, 60, 220 and I can NOT get a solution in Phaser with this data. If I scale it in C2221, then the unit cell is the same (80, 80, 220), but upon refinement, the R factors don't go much below 0.26/0.32. Has anyone ever seen something like this happen? I'm unsure if I should feel like the solution is C2221 since there are space groups of higher symmetry with similar residuals that seem plausible in indexing just the smaller unit cell. Should I keep trying to get a solution out of the data that leads to different unit cell parameters, but has higher symmetry? Xtriage seems to find twinning, but I think it's from NCS since my ASU contains a homodimer. I could also be wrong about this... Thanks in advance for any advice! ******* Leigh Allen Ph.D Candidate McCafferty Lab Duke University Department of Chemistry

9 13

Questions about molecular replacement.
by Yuan Cheng 27 Aug '09

27 Aug '09

Hi, I am working on solving a protein structure using phenix.automr. There is likely four monomers in a ASU based on phenix.xtriage.I am using a search model with 30% identity with my protein. After finding three monomers in a ASU, the LLG is 1740 and R factor is 56%. After finding the fourth monomer, the LLG increased to 2080,but the R factor also increased to 58%. I have several question here: 1) how much should LLG and R factor be if the model from molecular replacement is correct? I guess the answer might not be a exact number. But I am still wondering what should be the correct range. 2) Whether R factor and LLG should always be positively correlated? I used phenix.refine to refine the model with 3 monomers and the model with 4 monomers in a ASU. The Rwork and Rfree are similar for these two models,47% and 53% respectively. I think that one more monomer should either improve or ruin the model.I don't quite understand why one extra monomer doesn't matter too much here. In addition, do you think it is worthy to keep doing model building and refinement in consideration such high R factors. All you suggestions and opinions will be greatly appreciated! Yuan

2 1

Finding correct Se sites with autosol
by YS. Chung 27 Aug '09

27 Aug '09

Dear all, I have a 3 angstrom structure which I am trying to solve with MAD or SAD. The structure was previously solved with molecular replacement but refinement could not continue due to poor phasing at the N-terminal domain of the protein. I have run solve and autosol which are able to find the Se sites. However, Se sites are not anywhere near the methionines when I superimpose the ha.pdb and the pdb file that I obtain from a new run of molecular replacement. The exptl_fobs_phases_freeR_flags.mtz and the overall_best.pdb do not show any connected densities. I have also tried autobuild with the solutions from AutoSol, but the model that it builds in is incorrect. Any suggestions would be appreciated. Thank you, Yu Seon Chung

2 1

Re: [phenixbb] another difficult space group
by Maia Cherney 26 Aug '09

26 Aug '09

Hi Randy, thank you for your help. Today we collected at the CLS two newer crystals of this form. I will process them and see, if they give me better results. For the dataset that I have done mor. rep, here is information from the headers of solutions P6222: LLG 2194 in p32: LLG 6840 C222: LLG=5252 C2: LLG 7942 P62: LLG 4058 Z-scores are very high, too, between 40 and 60. Refinement of any of these solutions gives Rfree around 50-55%, actually, it goes up at every cycle of refinement. Randy, what is the best file to send to you: which space group for the sca or mtz file , which solution? Maia Randy J. Read wrote: > Hi Maia, > > If it's a molecular replacement issue, we might be able to help. I'd > be happy to look at your data. > > All the best, > > Randy > > On Aug 25 2009, Maia Cherney wrote: > >> Thank you Peter for your reply. >> >> I will try the p1 expansion. Thank you for the suggestion. And really >> data look very good, the Rmerge is very low, chi squares are around >> one, looked like a perfect data set to me; >> >> one molecule in AU (in p6222). The model is exactly the same protein >> solved in two other space groups. >> >> And it's not one crystal, all these bipyramids are like this. I can >> send you my p1.sca if you are curious to look at it. >> >> Maia >> >> >> Peter Zwart wrote: >>> Hi Maia, >>> >>> Two points: >>> >>> 1) : >>> >>> Given that fact that you can process the data in p622, you can expand >>> the data to p1: >>> >>> phenix.reflection_file_converter mydata.sca --sca=p1.sca --expand_to_p1 >>> >>> Eventhough this is not the same as having 'real' p1 data, you know >>> that the data merges well in p622, so no harm is done (or at least not >>> a lot). >>> >>> Do you have pseudo translational symmetry by any chance? I wasn't able >>> to find any relation between the two provided unit cells. It is very >>> curious that their volume are equal though. >>> >>> >>> >>> 2): >>> >>> The fact that you cannot solve it might also be due to the fact that >>> your MR model is incorrect for some obscure reason. >>> >>> >>> HTH >>> >>> Peter >>> >>> >>> >>> >>> >>> >>> >>> >>> 2009/8/25 Maia Cherney <chern(a)ualberta.ca>: >>> >>>> Hi everybody, >>>> >>>> I have two types of hexagonal crystals: rods and bipyramids with >>>> dimensions 150x150x83 (rods) and 142x142x93 (bipyramids). Both >>>> types of >>>> crystals give the same spacegroup P6222. However, the rods gave a good >>>> solution and refined to low R factors, whereas the bipyramids give a >>>> solution with high LLG and Z-score, but don't refine at all (R factors >>>> around 50%). The xtriage does not indicate any twinning. Lower >>>> symmetry >>>> spacegroups (trigonal and monoclinic) have the same problem: give >>>> solutions with high scores that would not refine. The resolution is >>>> 2.3A. Unfortunately, the dataset processed in p1 has only 60% >>>> completeness (as it was collected according to p3 strategy). Should I >>>> try to solve in p1 with this low completeness? What can be a problem? >>>> >>>> Maia >>>> >>>> >>>> >>>> Peter Zwart wrote: >>>> >>>>> Good point. >>>>> >>>>> For now the best thing to do is to read the RvsR paper cited in >>>>> the text. I'll add a section to the manual as well. >>>>> >>>>> Ideally of course, xtriage should make its own judgement. Some >>>>> code is >>>>> there, but I took it out as it is not well-tested (and didn't do the >>>>> job) >>>>> >>>>> P >>>>> >>>>> >>>>> 2009/8/25 Pavel Afonine <PAfonine(a)lbl.gov>: >>>>> >>>>> >>>>>> Hi Peter, >>>>>> >>>>>> do you have any guidance to how interpret this table summarized >>>>>> somewhere in the documentation? Otherwise it looks a bit cryptic >>>>>> to me (I tried it while ago, may be it is improved now). >>>>>> Alternatively, it would be nice if Xtriage prints out its own >>>>>> verdict based on that table. >>>>>> >>>>>> Thanks! >>>>>> Pavel. >>>>>> >>>>>> >>>>>> On 8/25/09 10:47 AM, Peter Zwart wrote: >>>>>> >>>>>> >>>>>>> Subsequently, run >>>>>>> >>>>>>> phenix.xtriage p1data.mtz reference.structure.file=MR.1.pdb >>>>>>> >>>>>>> and start interpreting the RvsR tables. >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>> _______________________________________________ >>>>>> phenixbb mailing list >>>>>> phenixbb(a)phenix-online.org >>>>>> http://www.phenix-online.org/mailman/listinfo/phenixbb >>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>>> >>>> _______________________________________________ >>>> phenixbb mailing list >>>> phenixbb(a)phenix-online.org >>>> http://www.phenix-online.org/mailman/listinfo/phenixbb >>>> >>>> >>> >>> >>> >>> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >> > >

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Re: [phenixbb] Problem with BOOST_ADAPTBX_FPE_DEFAULT and BOOST_ADAPTBX_SIGNALS_DEFAULT
by Sam Stampfer 25 Aug '09

25 Aug '09

Thanks for everyone's help! I got the refinement working in version 1.4-125 and am all set. -Sam On Tue, Aug 25, 2009 at 4:19 PM, Ben Eisenbraun <bene(a)crystal.harvard.edu>wrote: > There's version 1.4-125 in the SBGrid software tree. Did you try it? Is > that version too old? > > You should ask Katya to update her user list. You're not in our database. > > -ben > > On Tue, Aug 25, 2009 at 04:13:44PM -0400, Sam Stampfer wrote: > > I couldn't get the source code to compile- the final message was: "error: > > configuration step incomplete, exiting". Any ideas? > > Thanks, > > -Sam > > > > [A copy of my problem is pasted here]: > > > > I'm running the latest complete version of phenix (version 1.4-147, on > Linux > > 2.6-x86 64). When I run my .csh file I get the following error (with the > 4 > > previous lines included): > > > > > > > /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/bin/python(PyDict_SetItem+0x1fd) > > [0x446bdd] > > > > > /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/bin/python > > [0x4396e4] > > > > > /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/bin/python > > [0x4470a9] > > /lib64/libc.so.6 [0x30fca322a0] > > Segmentation fault (Python and libc call stacks above) > > This crash may be due to a problem in any imported > > Python module, including modules which are not part > > of the cctbx project. To disable the traps leading > > to this message, define these environment variables > > (e.g. assign the value 1): > > BOOST_ADAPTBX_FPE_DEFAULT > > BOOST_ADAPTBX_SIGNALS_DEFAULT > > This will NOT solve the problem, just mask it, but > > may allow you to proceed in case it is not critical. > > > > When I type the command "setenv BOOST_ADAPTBX_FPE_DEFAULT 1" and then run > my > > .csh file, it runs for a slightly longer period of time before ending > with a > > different error: > > > > 311240e000-3112410000 rw-p 0000e000 fd:00 14237822 > > /lib64/libbz2.so.1.0.4 > > 2ad973412000-2ad973414000 rw-p 2ad973412000 00:00 0 > > 2ad973429000-2ad97346d000 rw-p 2ad973429000 00:00 0 > > 2ad97346e000-2ad9734af000 rw-p 2ad97346e000 00:00 0 > > 2ad9734e1000-2ad973563000 rw-p 2ad9734e1000 00:00 0 > > 2ad973563000-2ad973567000 r-xp 00000000 fd:00 5727920 > > > /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lib/python2.6/lib-dynload/time.so > > 2ad973567000-2ad973666000 ---p 00004000 fd:00 5727920 > > > /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lib/python2.6/lib-dynload/time.so > > 2ad973666000-2ad973668000 rw-p 00003000 fd:00 5727920 > > > /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lib/python2.6/lib-dynload/time.so > > 2ad973668000-2ad97366d000 r-xp 00000000 fd:00 5727941 > > > /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lib/python2.6/lib-dynload/select.so > > 2ad97366d000-2ad97376c000 ---p 00005000 fd:00 5727941 > > /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lAbort > > > > However, the file ran fine and successfully output an improved .pdb file > > without any BOOST-related problems on my PI's Mac- she is running version > 95 > > of Phenix (which I was unable to obtain for linux- is it available > > somewhere?) > > > > Can you help me with this? > > > > Thanks! > > > > -Sam > > > > > > On Tue, Aug 25, 2009 at 3:28 PM, Ralf W. Grosse-Kunstleve > > <rwgk(a)cci.lbl.gov>wrote: > > > > > Could you try with a source installation? > > > > > > > > > > https://www.phenix-online.org/download/phenix/nightly/?version=1.4-147&show… > > > > > > I recommend you rm -rf the binary installation before ./install from > > > sources. > > > Add > > > --nproc=N > > > to the ./install command to use all N cpus in your machine for the > > > installation. > > > > > > Let me know if the problem persists. > > > > > > Ralf > > > _______________________________________________ > > > phenixbb mailing list > > > phenixbb(a)phenix-online.org > > > http://www.phenix-online.org/mailman/listinfo/phenixbb > > > > > > _______________________________________________ > > phenixbb mailing list > > phenixbb(a)phenix-online.org > > http://www.phenix-online.org/mailman/listinfo/phenixbb > > > > -- > | Ben Eisenbraun | Tools Sysadmin | > | Structural Biology Grid | http://sbgrid.org | > | Harvard Medical School | http://hms.harvard.edu | > >

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Problem with BOOST_ADAPTBX_FPE_DEFAULT and BOOST_ADAPTBX_SIGNALS_DEFAULT
by Sam Stampfer 25 Aug '09

25 Aug '09

Hi, I'm running the latest complete version of phenix (version 1.4-147, on Linux 2.6-x86 64). When I run my .csh file I get the following error (with the 4 previous lines included): /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/bin/python(PyDict_SetItem+0x1fd) [0x446bdd] /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/bin/python [0x4396e4] /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/bin/python [0x4470a9] /lib64/libc.so.6 [0x30fca322a0] Segmentation fault (Python and libc call stacks above) This crash may be due to a problem in any imported Python module, including modules which are not part of the cctbx project. To disable the traps leading to this message, define these environment variables (e.g. assign the value 1): BOOST_ADAPTBX_FPE_DEFAULT BOOST_ADAPTBX_SIGNALS_DEFAULT This will NOT solve the problem, just mask it, but may allow you to proceed in case it is not critical. When I type the command "setenv BOOST_ADAPTBX_FPE_DEFAULT 1" and then run my .csh file, it runs for a slightly longer period of time before ending with a different error: 311240e000-3112410000 rw-p 0000e000 fd:00 14237822 /lib64/libbz2.so.1.0.4 2ad973412000-2ad973414000 rw-p 2ad973412000 00:00 0 2ad973429000-2ad97346d000 rw-p 2ad973429000 00:00 0 2ad97346e000-2ad9734af000 rw-p 2ad97346e000 00:00 0 2ad9734e1000-2ad973563000 rw-p 2ad9734e1000 00:00 0 2ad973563000-2ad973567000 r-xp 00000000 fd:00 5727920 /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lib/python2.6/lib-dynload/time.so 2ad973567000-2ad973666000 ---p 00004000 fd:00 5727920 /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lib/python2.6/lib-dynload/time.so 2ad973666000-2ad973668000 rw-p 00003000 fd:00 5727920 /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lib/python2.6/lib-dynload/time.so 2ad973668000-2ad97366d000 r-xp 00000000 fd:00 5727941 /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lib/python2.6/lib-dynload/select.so 2ad97366d000-2ad97376c000 ---p 00005000 fd:00 5727941 /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lAbort However, the file ran fine and successfully output an improved .pdb file without any BOOST-related problems on my PI's Mac- she is running version 95 of Phenix (which I was unable to obtain for linux- is it available somewhere?) Can you help me with this? Thanks! -Sam

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ruthenium parameters
by Terry Lang 25 Aug '09

25 Aug '09

Hey Everyone, I am working on an xray structure that contains a ruthenium. I have been able to use elbow to create a cif file that phenix can read and refine without throwing error messages. However, there is a large amount of positive electron density after the refinement. I am looking into modeling coordinate waters, but I first wanted to check that the ruthenium is being read correctly by phenix. How do I figure out if it is properly recognized (eg correct scattering factors, bond and angle restraints, etc)? Thanks, Terry -- P. Therese Lang Postdoctoral Scholar Alber Lab, UC Berkeley

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phenix.refine 1.3 vs. 1.4 map quality ?
by William G. Scott 24 Aug '09

24 Aug '09

Hi folks: About a year ago I refined a 1.6 Å RNA structure with phenix.refine 1.3b-rc6 and then got distracted. I picked it up today and essentially repeated the last round of refinement with 1.4-57 (and also 1.4-159). The maps are subtly different, but consistently slightly worse with 1.4. Here are two examples: http://sage.ucsc.edu/~wgscott/mystuff/old_vs_new.pdf In the second example, this would lead to deletion of one of the octahedrally coordinated waters on a known Mg++ ion. 2OEU is similar, except 2.0 Å resolution, and it has Mn2+ instead of Mg ++. A similar thing happens with the corresponding water in that structure. Has the weighting for the bulk solvent mask or something like that been increased? Thanks. Bill Scott

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difference in B factor for NCS groups
by James Whittle 21 Aug '09

21 Aug '09

Dear all, I'm working with a structure were one NCS copy has significantly high B-factors than the other. That one copy makes few crystal contacts to stabilize it. Is there a recommended way to adjust the refinement to reflect this ... using TLS? Decreasing b_factor_weight? Is there a way refine a group_b to be added to the b-factor of each atom in that chain? --James

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Error in running Autosol....
by S. Karthikeyan 20 Aug '09

20 Aug '09

Dear All, I am using phenix-1.4-138 in RHEL5 Xeon-64 bit workstation. I am trying to solve a structure of Se-Met through phenix.autosol_gui. Once the programs starts it goes to several stages including converting from mtz to sca, xtriage and so on. Finally it gives an error message as follows: ******************************************************************************** Failed to carry out AutoSol_scale_and_analyze_mad: None of the solve versions worked See overall log file and also solve log file (in AutoSol_run_2_/LAST.LOG) ******************************************************************************** I found the LAST.LOG file is empty. I am trying to find out what could be problem? Any suggestions or help is much appreciated! Thanking you S.Karthikeyan

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Problem with LLP ligand
by James Naismith 19 Aug '09

19 Aug '09

Dear All, I am trying to refine a structure which has a Lys linked to PLP. In the PDB this is called LLP. When I take it through refine it crashes complaining about the ligand. "Sorry : Fatal problems interpreting PDB file: Number of atoms with unknown nonbonded energy type symbols: 8 Please edit the PDB 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 (see phenix.refine documentation). Also note that phenix.elbow is available to create restraint definitions for unknown ligands. Traceback: None " I know I have to use REEL to fix this in some way. I have used REEL to make ligands not bound to protein before. It is how to do this when the ligand is covalently bound that I am stuck with. Any help (particularly a cif restraints file!) gratefully received. best Jim ------------------------------------------------------------------------------- Major third-party components of Phenix include: Python, wxwidgets, wxPython, Boost, SCons, Clipper, CCP4 Monomer Library, CCP4 I/O libraries, PyCifRW, FFTPACK, L-BFGS Enter phenix.acknowledgments for details. ------------------------------------------------------------------------------- Processing inputs. This may take a minute or two. Working crystal symmetry after inspecting all inputs: Unit cell: (50.677, 137.283, 62.258, 90, 109.637, 90) Space group: P 1 21 1 (No. 4) Monomer Library directory: "/usr/local/phenix-1.4-115/chem_data/mon_lib" Total number of atoms: 13558 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6752 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 420, 6747 Unexpected atoms: {'LLP,HD3': 1, 'LLP,HG3': 1, 'LLP,HB3': 1, 'LLP,HE3': 1} Classifications: {'peptide': 420} Link IDs: {'PTRANS': 14, 'TRANS': 401, 'PCIS': 4} Chain breaks: 3 Conformer: "A" Number of residues, atoms: 420, 6747 Unexpected atoms: {'LLP,HD3': 1, 'LLP,HG3': 1, 'LLP,HB3': 1, 'LLP,HE3': 1} Classifications: {'peptide': 420} Link IDs: {'PTRANS': 14, 'TRANS': 401, 'PCIS': 4} Chain breaks: 3 bond proxies already assigned to first conformer: 6820 Chain: "B" Number of atoms: 6800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 6800 Unexpected atoms: {'LLP,HD3': 1, 'LLP,HG3': 1, 'LLP,HB3': 1, 'LLP,HE3': 1} Classifications: {'peptide': 423} Link IDs: {'PTRANS': 14, 'TRANS': 404, 'PCIS': 4} Chain breaks: 3 Chain: "M" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' SM': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Number of atoms with unknown nonbonded energy type symbols: 8 "ATOM 3149 HG3 LLP A 211 .*. H " "ATOM 3151 HE3 LLP A 211 .*. H " "ATOM 3153 HD3 LLP A 211 .*. H " "ATOM 3155 HB3 LLP A 211 .*. H " "ATOM 9896 HG3 LLP B 211 .*. H " "ATOM 9898 HE3 LLP B 211 .*. H " "ATOM 9900 HD3 LLP B 211 .*. H " "ATOM 9902 HB3 LLP B 211 .*. H " Time building chain proxies: 9.24, per 1000 atoms: 0.68 The University of St Andrews is a charity registered in Scotland : No SC013532

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RESOLVE with RNA/protein structure at low resolution
by Peter Grey 19 Aug '09

19 Aug '09

Hello all, I try to solve the structure of RNA and RNA/protein complex at low resolution (5A). Phases come from partial model MR solution. I would really welcome advice about density modification in such cases with RESOLVE.. Does the RESOLVE database of density distributions contain RNA/protein examples ? Can RESOLVE work at low resolution given that histograms profiles are at resolutions from 1.2 A to 4 A ? Many thanks for you help, Peter.

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AutoBuild help
by Timothy C. Umland 18 Aug '09

18 Aug '09

I am new to running the AutoMR and AutoBuild Wizards, and I am having a problem getting AutoBuild to run. I have run AutoMR and it appeared to run fine, yielding a solution. However, when it did the default hand-off of the MR solution to AutoBuild, AutoBuild crashed. I then tried to run AutoBuild by itself, using the MR solution as the input model. Again, AutoBuild crashed. The error was the same in both cases. I was running AutoMR and AutoBuild from the command line. I am running Phenix version 1.4-3 on an Intel Mac (OS X 10.5.8). The AutoBuild error was **************************************************************************** **** Failed to carry out AutoBuild_build_cycle: child process stderr output: command: 'csh /AutoBuild_run_3_/TEMP0/RUN_FILE_1' sort: invalid option -- 4 Try `sort --help' for more information. **************************************************************************** **** I tried the suggested "sort --help", but at least to me it wasn't helpful. I am guessing that I have some incompatibility with my local installation of "sort" and Phenix? Any help is appreciated. Thanks, Tim

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1-2 October: What is a Macromolecular Complex ? meeting at the NKI, Amsterdam
by Anastassis Perrakis 18 Aug '09

18 Aug '09

Dear all, This is a reminder and some news for the meeting: "What is a macromolecular Complex? Shades of Meaning Across Cellular, Systems, and Structural Biology" http://xtal.nki.nl/Oct2009 - Registration closes on Monday 7th September at 12:00 noon. No exceptions after the deadline. - There will be eight (8) fellowships for attending the meeting, 500 Euro (max) each (*) Best regards on behalf of the organizers, Tassos (*) Only available if your lab is NOT part of the EU programs that support the meeting (SPINE-2-Complexes, TEACH-SG, 3D-Repertoire) and you really wanted to attend but could not for financial reasons, but 500 Euro will make it possible for you to join us, please email a.perrakis.AT.nki.nl with a short motivation and research interests, 10-15 lines max (no attachments please, simple text). Preference will be given to people not yet registered, since we might well assume that people that already registered had the money already sorted. The amount is the MAXimum available per person for ALL expenses, and it will be reimbursed after the meeting, *** based on receipts ***!

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Re: [phenixbb] Error in running Autosol....
by Thomas C. Terwilliger 15 Aug '09

15 Aug '09

Hi Karthikeyan, I'm sorry for the trouble! I see that you are running the very latest phenix from last night. This version passed our automated tests and it appears fine in general. Somehow the solve scaling step is not working in your run. I haven't seen this happen before, but my guesses are: 1. I have been making small changes in the autosol printout and it is possible that there is a place where solve is printing something out and the format does not match the variable type, and I didn't catch it in our tests. If this is the case you should be able to find it by running from the command-line and adding the keyword debug=true and it should print out a clearer error message for you that you can send me. You can run from the command line in the same place you ran from the GUI by saying phenix.autosol autosol.eff debug=True because the GUI writes out autosol.eff when it runs, saving your inputs. Then you can override those values by putting debug=True on the command line. Other less-likely possibilities: 2. your input datafiles are of a type that was unexpected (normally .sca, .mtz are fine, but perhaps the columns in an mtz are unusual). 3. Your structure is very large or high-resolution. 4. Something is unusual in your setup so that not much memory is available. If none of these helps, you are welcome to send me the files and I'll check it out. All the best, Tom T >> Dear All, >> >> I am using phenix-1.4-138 in RHEL5 Xeon-64 bit workstation. >> >> I am trying to solve a structure of Se-Met through phenix.autosol_gui. >> Once the >> programs starts it goes to several stages including converting from mtz to >> sca, >> xtriage and so on. >> Finally it gives an error message as follows: >> >> ******************************************************************************** >> Failed to carry out AutoSol_scale_and_analyze_mad: >> >> None of the solve versions worked >> See overall log file and also solve log file (in AutoSol_run_2_/LAST.LOG) >> ******************************************************************************** >> I found the LAST.LOG file is empty. >> >> I am trying to find out what could be problem? Any suggestions or help is >> much >> appreciated! >> >> Thanking you >> >> S.Karthikeyan >> >> >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >>

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