- phenixbb - phenix-online.org

Random seeds?
by Joseph Noel 10 Aug '10

10 Aug '10

Hi All, Okay, a fairly mundane question concerning random seeds in Phenix. Obviously they are random but any restrictions on how many digits phenix will accept? Any other restrictions? Are they (it) only used for coordinate refinement or do the random seeds get used for other things as well? I know about hydrogen building but wandering about other refinement protocols and the use of "new" random seeds. I realize some use different random seeds to create slightly different models after refinement. Is it useful to change the number from time to time when going through iterative rounds of re-building and coordinate refinement? What about ADP refinement? Sorry for the mundane questions! Joe ___________________________________________________________ Joseph P. Noel, Ph.D. Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________

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Restraint creation for ligand
by Hermella Woldemdihin 10 Aug '10

10 Aug '10

Hi! I was trying to fit my ligands into my model and density. And I have successfully fitted 2 ligands (same molecule) but my 3rd ligand is different molecule. After fitting my 3rd ligand (with COOT) and merged it with my protein, II created a restraint file with: phenix.elbow my_model_coot-0..pdb --do-all --output=all_ligands It created all_ligand.cif, which I used for in my next refinement with Phenix (GUI). I supplied my density, model and the restraint file and run phenix.refine. Unfortunatate I'm getting this error message when it starts to run phenix.refine and opening COOT window: Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown nonbonded energy type symbols: 1 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. I have use the same procedure for fitting my first 2 ligands. and it worked. But this time it failed! What do you think I should do? Thanks Hermi

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monomer-dimer
by intekhab alam 09 Aug '10

09 Aug '10

Hi everyone Sorry for some non specific query!!!!! i am working with a protein that shows a dimer in the crystal structure but when i tried to figure out that with standard molecular markers in gel filteration (superdex-200, 24ml column) it turned out to be a monnomer. Native gel analysis after incubating the protein at 20 degree, 37 degree showed more dimer at 20 degree celcius as compared to 37. I tried similar strategy in gel filteration by incubating my protein at various temperature,where a lot of precipitation was observed at 37 degree celcius and after removing the precipitates i run the gel filteration that has 0.5 ml higher elution volume as compared to samples incubated at 20 degree celcius and 4 degree celcius.( Is this significant) Furthermore i have done some experiments in cold room (4 degree) where the elution volume is stuck at a point irrespective of the conditions (as Flow rate, concentration of protein etc) and that is higher than that of the room temperature by 1 ml. Standard moleculr weight markers also show higher elution volume in cold room in comparison to the room temperature by 1 ml. I will be highly obliged if someone suggest some literature or any otherway to do gel filtrtaion so that i can clearly resolve this issue. Also let me know if there is some literature available on effect of temperature on the elution volume of proteins. Thanks in advance -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL

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Phenix reflection statistics
by Lepore, Bryan 07 Aug '10

07 Aug '10

in this table : Overall correlation: 0.901 unused: - 16.7088 [ 0/9 ] bin 1: 16.7088 - 2.0456 [5236/5928] 0.858 bin 2: 2.0456 - 1.6241 [5610/5946] 0.744 bin 3: 1.6241 - 1.4189 [5539/5925] 0.641 bin 4: 1.4189 - 1.2892 [5357/5873] 0.516 bin 5: 1.2892 - 1.1969 [5405/5972] 0.497 bin 6: 1.1969 - 1.1263 [5241/5939] 0.464 bin 7: 1.1263 - 1.0699 [5067/5903] 0.408 bin 8: 1.0699 - 1.0234 [4960/5934] 0.416 bin 9: 1.0234 - 0.9840 [4808/5941] 0.376 bin 10: 0.9840 - 0.9500 [4700/5931] 0.348 unused: 0.9500 - [3339/6874] 0.330 the average CC is 0.508 +/- 0.17 if y is the correlation, and x is bin number, and 0.330 is excluded, that line fits with a CC=-0.941 (therefore R^2=0.885) is the median resolution per bin used for the overall CC? how is "unused" treated? -bryan

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syntax for Averaged Kicked maps and maps.param
by amadrona＠uci.edu 06 Aug '10

06 Aug '10

Hello, Disclaimer: I am a newbie to both crystallagraphy and Phenix. I am running phenix.refine (v1.6-289) in the command line 1. I want to make averaged "kicked-maps" but I keep getting a syntax error. I tried renaming "maps.param" but this file was not recognized. 2. When I enter Phenix.maps into the command line I get a message that syas "not implemented" I am trying to get the latest versiou of phenix installed. The following is the syntax I put in my custom_params file Thanks -Yarrow refinement.main.number_of_macro_cycles = 2 #refinement.main.fix_rotamers = True refinement.refine.strategy = individual_sites+individual_adp refinement.output.prefix = CIN4_refine_omit refinement.output.serial = 12 refinement.output.write_def_file = True refinement.target_weights_wxc.scale = 0.2 refinement.main.max_number_of_interations=15 refinement.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 = True } map { mtz_label_amplitudes = "FOFCWT_kicked" mtz_label_phases = "PHFOFCWT_kicked" likelihood_weighted = True obs_factor = 1 calc_factor = 1 kicked = True fill_missing_f_obs_with_weighted_f_model = false }

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high average b-factor vs. Wilson B
by Geoffrey Feld 06 Aug '10

06 Aug '10

Dear PhenixBBers, I'm working on a 1.45 A structure I solved using MR (phaser) and I'm pretty close to finishing, just plopping in waters and fixing rotamers. Rw = 19.8 Rfree= 22.8. I am a little concerned because my Wilson B is 27.00 while my average B for macromolecule is more like 43, and for solvent is 48. I have enough data to use anisotropic ADP refinement, which was a big help in bringing down the Rfree, but the average B hasn't really moved much. Should I be concerned about this? Should I try adjusting the wxu, or some other parameter? Thanks! -- Geoffrey K. Feld Department of Chemistry 492 Stanley Hall University of California, Berkeley "Vigilia pretium libertatis"

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Phenix reflection statistics
by James Fraser 06 Aug '10

06 Aug '10

What does the correlation coefficient that is reported at the end of phenix.reflection_statistics represent? (I would assume the CC of F1 vs F2 for all reflections with an observation in datasets 1 and 2). The documentation "...the output will also show the correlations between the datasets and, if applicable, between the anomalous differences, both as overall values and in bins." is a bit ambiguous. Also in the below comparison, how would the overall correlation be 0.901 when all the bins have correlations between 0.330-0.858? CC Obs 2 3 0.901 h,k,l Correlation of: 2: 1.mtz:F-obs,SIGF-obs 3: 2.mtz:F-obs,SIGF-obs Overall correlation: 0.901 unused: - 16.7088 [ 0/9 ] bin 1: 16.7088 - 2.0456 [5236/5928] 0.858 bin 2: 2.0456 - 1.6241 [5610/5946] 0.744 bin 3: 1.6241 - 1.4189 [5539/5925] 0.641 bin 4: 1.4189 - 1.2892 [5357/5873] 0.516 bin 5: 1.2892 - 1.1969 [5405/5972] 0.497 bin 6: 1.1969 - 1.1263 [5241/5939] 0.464 bin 7: 1.1263 - 1.0699 [5067/5903] 0.408 bin 8: 1.0699 - 1.0234 [4960/5934] 0.416 bin 9: 1.0234 - 0.9840 [4808/5941] 0.376 bin 10: 0.9840 - 0.9500 [4700/5931] 0.348 unused: 0.9500 - [3339/6874] 0.330 Thanks, James -- James Fraser jaimefraser(a)gmail.com Alber Lab 356 Stanley Hall, QB3 UC Berkeley Berkeley, CA 94720 http://ucxray.berkeley.edu/~jfraser/

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indicating proper SUBJECT
by Alexandre Urzhumtsev 06 Aug '10

06 Aug '10

Hello, Sorry to interfere, in no case I want to play a police. However, I would like to ask all phenixbb-participants to respect other and when sending their mails : - to USE the "subject" in all sending mesages (no mails with empty "subject") and - to use it PROPERLY (just recently we had several examples of irrelevant subject; I do not want to point them out explicitly) Indicating a proper subject is a matter of saving time of others, making proper archives and facilitating searches in them later. This problem is also relevant to the CCP4bb even when a similar request of putting proper "subject" was posted there many times. (Personally, I think this should be done in ANY correspondence, even to your friends, not only to phenixbb or ccp4bb.) In addition, I think that a presence of your name at the end of your mail is also a rule of a politeness (that is also not respected in a number of letters to our bb-s). With best regards, Sacha

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unknown parameters file format?
by Kyle Dolan 05 Aug '10

05 Aug '10

Hi all, I tried to create my own set of refinement parameters by copying sections of a .def file to a new file I called myrefine1.params. When I tried to use this for phenix.refine from the command line I received this error message: Sorry: Unknown file format: myrefine1.params What should I do? Thanks, Kyle Kyle T. Dolan Department of Biochemistry and Molecular Biology The University of Chicago ktd(a)uchicago.edu

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Re: [phenixbb] follow up on message 2: phenix.maps --Message: not implemented
by amadrona＠uci.edu 05 Aug '10

05 Aug '10

Hello Pavel, The averaged kicked map looks great! I am able to see loop density that I could not see before. However, I still have one question: The kicked map were created when I put the map parameters in my custom_par file however, I was unable to run Phenix.maps in the command line. When I do this I get a message "Not implemented". I would like to create a ccp4 map for viewing in pymol without running refinement again. Do you know what could be causing this message? If I create "maps.params" by inserting the commands from the .def file Phenix does not recognize this file format. Any help would be appreciated. Thank you. -Yarrow > Send phenixbb mailing list submissions to > phenixbb(a)phenix-online.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://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. syntax for Averaged Kicked maps and maps.param (amadrona(a)uci.edu) > 2. Re: syntax for Averaged Kicked maps and maps.param (Pavel Afonine) > 3. Re: Phenix Autobuild (Thomas C. Terwilliger) > 4. New version complaint (Simon Kolstoe) > 5. Re: New version complaint (Nathaniel Echols) > 6. Re: New version complaint (Douglas Jacobsen) > 7. Re: New version complaint (Nathaniel Echols) > 8. Adequate size for Free R test set? (Joseph Noel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 2 Aug 2010 17:38:05 -0700 > From: amadrona(a)uci.edu > To: phenixbb(a)phenix-online.org > Subject: [phenixbb] syntax for Averaged Kicked maps and maps.param > Message-ID: > <c56fb1561f816b0462d50ccdeb996317.squirrel(a)webmail.uci.edu> > Content-Type: text/plain;charset=iso-8859-1 > > Hello, > > Disclaimer: I am a newbie to both crystallagraphy and Phenix. > > I am running phenix.refine (v1.6-289) in the command line > > 1. I want to make averaged "kicked-maps" but I keep getting a syntax > error. I tried renaming "maps.param" but this file was not recognized. > > 2. When I enter Phenix.maps into the command line I get a message that > syas "not implemented" > I am trying to get the latest versiou of phenix installed. > > The following is the syntax I put in my custom_params file > Thanks > > -Yarrow > > refinement.main.number_of_macro_cycles = 2 > #refinement.main.fix_rotamers = True > refinement.refine.strategy = individual_sites+individual_adp > refinement.output.prefix = CIN4_refine_omit > refinement.output.serial = 12 > refinement.output.write_def_file = True > refinement.target_weights_wxc.scale = 0.2 > refinement.main.max_number_of_interations=15 > > > refinement.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 = True > } > map { > mtz_label_amplitudes = "FOFCWT_kicked" > mtz_label_phases = "PHFOFCWT_kicked" > likelihood_weighted = True > obs_factor = 1 > calc_factor = 1 > kicked = True > fill_missing_f_obs_with_weighted_f_model = false > } > > > > ------------------------------ > > Message: 2 > Date: Mon, 02 Aug 2010 17:48:45 -0700 > From: Pavel Afonine <pafonine(a)lbl.gov> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] syntax for Averaged Kicked maps and maps.param > Message-ID: <4C57676D.9000901(a)lbl.gov> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Yarrow, > > you can use GUI or the command line for doing this. > > 0) It would be best if you update to the latest version, although I > believe it might work with the one you have too: > > http://www.phenix-online.org/download/ > > 1) GUI: launch PHENIX GUI and go to Maps -> Create Maps. then just add > as many maps you want (or use pre-defined ones) and check a box for kick > map. > > 2) From the command line type: > > phenix.maps > > and hit Enter (Return). That will create a file called something > maps.params. Edit that file to add/remove the maps you need/ don't need > and set > > kicked = True > > for the one you want to be "kicked", and then run > > phenix.maps maps.params > > Let me know if you have any questions or problems. > > Good luck! > Pavel. > > > On 8/2/10 5:38 PM, amadrona(a)uci.edu wrote: >> Hello, >> >> Disclaimer: I am a newbie to both crystallagraphy and Phenix. >> >> I am running phenix.refine (v1.6-289) in the command line >> >> 1. I want to make averaged "kicked-maps" but I keep getting a syntax >> error. I tried renaming "maps.param" but this file was not recognized. >> >> 2. When I enter Phenix.maps into the command line I get a message that >> syas "not implemented" >> I am trying to get the latest versiou of phenix installed. >> >> The following is the syntax I put in my custom_params file >> Thanks >> >> -Yarrow >> >> refinement.main.number_of_macro_cycles = 2 >> #refinement.main.fix_rotamers = True >> refinement.refine.strategy = individual_sites+individual_adp >> refinement.output.prefix = CIN4_refine_omit >> refinement.output.serial = 12 >> refinement.output.write_def_file = True >> refinement.target_weights_wxc.scale = 0.2 >> refinement.main.max_number_of_interations=15 >> >> >> refinement.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 = True >> } >> map { >> mtz_label_amplitudes = "FOFCWT_kicked" >> mtz_label_phases = "PHFOFCWT_kicked" >> likelihood_weighted = True >> obs_factor = 1 >> calc_factor = 1 >> kicked = True >> fill_missing_f_obs_with_weighted_f_model = false >> } >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb > > > > ------------------------------ > > Message: 3 > Date: Tue, 3 Aug 2010 07:26:46 -0600 (MDT) > From: "Thomas C. Terwilliger" <terwilliger(a)lanl.gov> > To: "Md. Munan Shaik" <munanbt2004(a)YAHOO.COM> > Cc: phenixbb(a)phenix-online.org > Subject: Re: [phenixbb] Phenix Autobuild > Message-ID: <24375.128.165.0.81.1280842006.squirrel(a)webmail.lanl.gov> > Content-Type: text/plain;charset=iso-8859-1 > > Hi Munan Shaik, > > Phenix autobuild can read several types of sequence files, but the basic > format is very simple: enter one copy of the sequence of each chain, > separated by a blank line or a line starting with ">" between chains. > You can optionally add any lines starting with ">" which will be ignored. > So here is an example: > >>>> alpha subunit (type 1) > MTMPYYASAEQIMRDRSELARKGIARGRSVVVLTFRDGVLFVAENPSTALHKVSELYDRL > GFAAVGKYNEFENLRRAGIVHADMRGYSYDRRDVTGRSLANAYAQTLGTIFTEQPKPYEV > EICVAEVGRVGSPKAPQLYRITYDGSIVDEQHFVVMGGTTEPIATAMRESYRADLDLEAA > VGIAVNALRQGGAGEGEKRNVDVASLEVAVLDQSRPRRAFRRIAGTALEQLVPAEPAAAS > ESAPEPKPDTETKPADTQD >>>> beta subunit (type 1) > MTADRPALRTGDRDTRLSFGSNLSSFTDYLRGHAPELLPENRIGHRSHSTRGGDGMESGD > LAPHGTTIVALTYKGGVLLAGDRRATQGNLIASRDVEKVYVTDEYSAAGIAGTAGIAIEL > VRLFAVELEHYEKIEGVPLTFDGKANRLASMVRGNLGAAMQGLAVVPLLVGYDLDADDES > RAGRIVSYDVVGGRYEERAGYHAVGSGSLFAKSALKKIYSPDSDEETALRAAIESLYDAA > DDDSATGGPDLTRGIYPTAVTITQAGAVHVSEETTSELARRIVAERTEQGGSAR > > Please let me know if that doesn't do it! > > All the best, > Tom T > > > > > > >>> Hi everybody, >>> I have a problem with Phenix autobuild. I want to input sequence file >>> together >>> with the pdb and mtz that I got from molecular replacement. But I have >>> no >>> idea >>> which types of sequence files its required. if anybody please help me >>> out. >>> >>> >>> thanks >>> =================================================== >>> Md. Munan Shaik >>> Department of Chemical Biology >>> University of Padova >>> via G. Colombo 03 >>> Padova 35131, Italy >>> >>> >>> > > > > ------------------------------ > > Message: 4 > Date: Tue, 3 Aug 2010 15:31:46 +0100 > From: Simon Kolstoe <s.kolstoe(a)ucl.ac.uk> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: [phenixbb] New version complaint > Message-ID: <8976EDFE-4E7E-42FD-96FE-319B56DE5413(a)ucl.ac.uk> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > Hi there, > > I've been using version 1.6.2-432 on a Macbook and was particularly > enjoying the "Show Histograms" button on the POLYGON results page. > However today I updated to version 1.6.4-486 using the dmg installer, > and that useful option has disappeared! Is there a good reason for the > absence of this function, and if not can we get it back? > > Thanks, > > Simon > > --------------------------------------------------------------- > Dr Simon Kolstoe > Laboratory for Protein Crystallography > Centre for Amyloidosis & Acute Phase Proteins > UCL Medical School > Rowland Hill Street, London NW3 2PF > > Tel: 020 7433 2765 > http://www.ucl.ac.uk/~rmhasek > -------------------------------------------------------------- > > > > ------------------------------ > > Message: 5 > Date: Tue, 3 Aug 2010 07:39:11 -0700 > From: Nathaniel Echols <nechols(a)lbl.gov> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] New version complaint > Message-ID: > <AANLkTikU_SS2Z2VU0aZuqRNgrYUiiXLCTfztYy7NZjOF(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > On Tue, Aug 3, 2010 at 7:31 AM, Simon Kolstoe <s.kolstoe(a)ucl.ac.uk> wrote: > >> I've been using version 1.6.2-432 on a Macbook and was particularly >> enjoying the "Show Histograms" button on the POLYGON results page. >> However >> today I updated to version 1.6.4-486 using the dmg installer, and that >> useful option has disappeared! Is there a good reason for the absence of >> this function, and if not can we get it back? >> > > There is a reason, but not a good one. I'll fix it later today. FYI, the > "PDB Statistics" tool offers another way to view histograms, although it > requires that you manually specify the resolution range. > > -Nat >

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