- phenixbb - phenix-online.org

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 09 Sep '09

09 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 }

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