- phenixbb - phenix-online.org

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

2 3

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

3 3

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 >>

4 4

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

2 1

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

1 0

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!

3 2

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

2 3

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

2 1

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.

4 5

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 > **************************************** >

4 4