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wxu for anisotropic ADP refinement
by Joseph Noel 12 Aug '10

12 Aug '10

Dear Phenix User Community, If one would like to try different weights for anisotropic ADP refinement (ie fixing wxu) should one be focusing on numbers like - wxu = 199.878301 - instead of the usual low numbers such as - wxu = 0.25 - found during isotropic ADP refinement? While optimize X-ray/ADP weight is useful in phenix, I am still getting anistropic ADP values that are a bit outside what one might expect at 1.5 A compared to the PDB. For the latter, I check things using Parvati (http://skuld.bmsc.washington.edu/parvati/). Thanks! 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 ___________________________________________________________

2 1

difference in estimated error between phenix and refmac
by Ling Qin 12 Aug '10

12 Aug '10

Dear Colleagues, I am refining a 2.15 A structure that was previously refined with refmac by someone else. Without changing anything in the refmac-refined model and using all the default phenix.refine settings, I am getting pretty much the same R and Rfree (from 19.3%/21.7% to 18.9%/21.8%), with an ML estimated error of 0.22 A. In the refmac-refined pdb file, the estimated error is much lower: 0.16 (based on R), 0.144 (based on Rfree), and 0.096 (based on ML). I am using phenix.refine version 1.6_289, but also tried 1.5_2 with the same result. Is there an underlying reason for this difference? Thank you very much for your insightful opinions in advance. Cheers, Ling

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autosol
by Abd Ghani Abd Aziz 12 Aug '10

12 Aug '10

Dear All, Just been trying to run autosol for SAD data with the new phenix (1.6.4-486) on ubuntu, but I get an error message: *********************************************************** Failed to carry out AutoSol_scale_and_analyze_mad: None of the solve versions worked ********************************************************************** xtriage appears to run OK, and I get the same error with unmerged or merged scalepack data. The same files in 1.6-289 (admittedly on OSX) work fine. I wonder if there is a known problem with this version of phenix? Thanks for any suggestions, Ghani

3 4

Disappearing density?
by Kyle Dolan 12 Aug '10

12 Aug '10

Hi all, I attempted to improve the density around a helix and short linker region using an average kick map but it didn't make things look much better. I then tried creating a composite iterative-build omit map from phenix.autobuild, but in this case the electron density around the helix/linker in question largely disappeared! Is there another approach I can use that might improve my maps, or should I start questioning my data? The dataset has >95% completeness to 2.7 A so I am very curious as to why I am missing the backbone now, where before I was only missing the side chain densities. One thing I am wondering is if the problem could have something to do with symmetry; the part of the map I am looking at may be close to a two-fold crystallographic symmetry axis and I have been told that these regions tend to be very noisy and hard to model--comments? Kyle Kyle T. Dolan Department of Biochemistry and Molecular Biology The University of Chicago ktd(a)uchicago.edu

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Statistics for pdb deposition
by Elwood A. Mullins 11 Aug '10

11 Aug '10

I apologize if this has already been addressed. I'm trying to deposit a model to the pdb database, but there are a few required values in the Refinement Statistics section that I'm not sure where to find. 1,2) Cut-off sigma (F), Number unique reflections (observed) Looking at the log file, it appears that the cut-off is 0, which results in 330 reflections being rejected. The pdb header, however, lists the number of reflections at a value corresponding to 352 reflections being rejected. Why are these numbers different and which should I report? 3) R-factor (all) R-factor (all) includes both the working and test sets in addition to reflections rejected by the sigma cut-off. Does PHENIX calculate this value? I know R-factor (observed), which includes the working and test sets but not rejected reflections, is calculated. Thanks, Elwood

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elbow: more detailed website : 404
by Lepore, Bryan 11 Aug '10

11 Aug '10

this link : http://www.phenix-online.org/elbow/docs/index_image.html is 404 the link is found on this page : http://www.phenix-online.org/documentation/elbow.htm ... IS there a "more detailed website"? i saw the reel site. -bryan

2 1

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 ___________________________________________________________

3 2

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

3 2

monomer-dimer
by intekhab alam 10 Aug '10

10 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

2 2

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

2 1

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 }

3 3

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

2 1

unknown parameters file format?
by Kyle Dolan 06 Aug '10

06 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 06 Aug '10

06 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 >

6 14

B-factors
by Hermella Woldemdihin 05 Aug '10

05 Aug '10

Hi All! Where can I set B-factor for water in phenix.refine on the GUI version of phenix? Thanks!

3 2

r-work and r-free for specific resolution range(s)
by Kay Diederichs 04 Aug '10

04 Aug '10

Hi, is there a way to get the R-factor statistics from phenix.refine, for a specific resolution range, e.g. 2.5-2.6A ? The reason I ask is that I would like to specify the same resolution range as the data reduction program does. I tried with phenix.reflection_statistics x_map_coeffs.mtz x_data.mtz --low-resolution=2.6 --resolution=2.5 but with the default settings, phenix.refine writes 2FOFCWT and FOFCWT, but not FC . So it looks like I have to re-run phenix.refine and make it write out FC? Or is it easier to run phenix.xmanip for that purpose? thanks, Kay

3 2

MR with 1000+ aa chain
by Meghan Miller 04 Aug '10

04 Aug '10

Hello, I am trying to run AutoMR using a chain that is 1014 amino acids. The output pdb starts back at 0 once it reaches 1000. Is this a bug, or user error? Thanks, Meghan

2 1

Re: [phenixbb] r-work and r-free for specific resolution range(s)
by Kay Diederichs 04 Aug '10

04 Aug '10

> Date: Wed, 4 Aug 2010 10:37:45 -0700 > From: Nathaniel Echols<nechols(a)lbl.gov> > To: PHENIX user mailing list<phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] r-work and r-free for specific resolution > range(s) > Message-ID: > <AANLkTindW12Anq8iJVq-rh5LWiUyj4rZ52M3iyoy=7j8(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > On Wed, Aug 4, 2010 at 10:22 AM, Kay Diederichs< > kay.diederichs(a)uni-konstanz.de> wrote: > >> is there a way to get the R-factor statistics from phenix.refine, for a >> specific resolution range, e.g. 2.5-2.6A ? The reason I ask is that I would >> like to specify the same resolution range as the data reduction program >> does. >> > > phenix.refine will print R-factors by resolution shell, but the number of > shells it decides to use varies with the number of reflections - for a > really small structure (e.g. amyloid peptide) you will have only one > resolution shell (the argument being that R-free statistics aren't reliable > if you have very few reflections in the test set). You can set an upper > limit on this (refinement.main.max_number_of_resolution_bins), but it won't > give you ten shells if phenix.refine wants to use, say, five. There may be > another way to get this information that I'm not aware of, but I've always > done it directly in Python. > > I've been working on a project that potentially requires changing > phenix.model_vs_data to report these statistics; my plan was to use the last > of ten shells, since both HKL2000 and SCALA report everything that way > (don't know about XDS since I haven't used it). Is this sensible, or does > it need to be more flexible and accept explicit resolution ranges? (I'm not > actually sure whether this is possible right now, but 10 shells is easy.) > > -Nat Hi Nat, in fact this is a small protein, and phenix.refine only outputs a single resolution shell. phenix.model_vs_data currently does not give R-factors; it would be worthwhile to enhance this, and to have it accept shell limits. XDS has 9 shells whose limits are calculated internally, and one overall. For XSCALE, one can specify up to 20 RESOLUTION_SHELLS . In the meantime, I resort to sftools <<EOF read x_f_model.mtz Y select col R_FREE_FLAGS=0 correl col FOBS FMODEL resolution 2.6 2.5 shells 1 select all select col R_FREE_FLAGS=1 correl col FOBS FMODEL resolution 2.6 2.5 shells 1 stop y where x_f_model was written by phenix.refine . thanks, Kay

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Re: [phenixbb] DTT mediated disulfide crosslink across a crystallographic two-fold! (Pavel Afonine)
by Joseph Noel 04 Aug '10

04 Aug '10

Thanks Pavel! I will wait and see what Ralf says regarding defining the symmetry operator. If I am using the GUI for phenix.refine should I create a new file with the bond definition you mention and include it as one of the starting files or should I edit the Refine_*.eff file that gets created and insert it somewhere there? ___________________________________________________________ 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 ___________________________________________________________ On Aug 4, 2010, at 10:22 AM, 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://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. Re: DTT mediated disulfide crosslink across a > crystallographic two-fold! (Joseph Noel) > 2. Re: high average b-factor vs. Wilson B (Gino Cingolani) > 3. Re: high average b-factor vs. Wilson B (Frank von Delft) > 4. Re: DTT mediated disulfide crosslink across a > crystallographic two-fold! (Pavel Afonine) > 5. Re: high average b-factor vs. Wilson B (Pavel Afonine) > 6. r-work and r-free for specific resolution range(s) > (Kay Diederichs) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 4 Aug 2010 04:53:25 -0700 > From: Joseph Noel <noel(a)salk.edu> > To: phenixbb(a)phenix-online.org > Subject: Re: [phenixbb] DTT mediated disulfide crosslink across a > crystallographic two-fold! > Message-ID: <91F9FC5E-00E4-454C-AB99-2DD353BDC4A5(a)salk.edu> > Content-Type: text/plain; charset="us-ascii" > > Hi Ralf and Pavel, > > Unfortunately, Phenix didn't recognize a disulfide bond should exist between the sulfur atoms of DTT and the side chain sulfur atom of the cysteine residue in question. I position everything well in the Fo-Fc and 2Fo-Fc maps and ensured the two sulfurs were approximately 2.1 A apart. However, after refinement the DTT molecule moved so the two sulfurs in question where nearly 3 A away. Maybe this is because it is a mixed disulfide between a DTT molecule and a side-chain Cys rather then what most programs expect which is a disulfide between two Cys residues. Is it possible I need to define the complete chemical entity as a hetatm (the disulfide linked Cys residue? Is there a way to specify that a covalent bond should exist between the SG atom of the Cys in question and the S atoms of DTT with DTT lying across the crystallographic two-fold given its internal 2-fold symmetry? > > 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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by qun 04 Aug '10

04 Aug '10

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Re: [phenixbb] DTT mediated disulfide crosslink across a crystallographic two-fold!
by Joseph Noel 04 Aug '10

04 Aug '10

Hi Ralf and Pavel, Unfortunately, Phenix didn't recognize a disulfide bond should exist between the sulfur atoms of DTT and the side chain sulfur atom of the cysteine residue in question. I position everything well in the Fo-Fc and 2Fo-Fc maps and ensured the two sulfurs were approximately 2.1 A apart. However, after refinement the DTT molecule moved so the two sulfurs in question where nearly 3 A away. Maybe this is because it is a mixed disulfide between a DTT molecule and a side-chain Cys rather then what most programs expect which is a disulfide between two Cys residues. Is it possible I need to define the complete chemical entity as a hetatm (the disulfide linked Cys residue? Is there a way to specify that a covalent bond should exist between the SG atom of the Cys in question and the S atoms of DTT with DTT lying across the crystallographic two-fold given its internal 2-fold symmetry? 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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DTT mediated disulfide crosslink across a crystallographic two-fold!
by Joseph Noel 04 Aug '10

04 Aug '10

Hi Phenix Users, I have found a beautifully ordered DTT molecule stretching across a crystallographic two-fold and linking two symmetry related cysteine side chains. Since part of this molecule sits on across the two-fold (special position) I will specify the occupancy as 0.5. I am hoping to get some information on how easy (or how difficult) it is to specify this arrangement in Phenix for refinement since it is covalent and sitting across a crystallographic two-fold (and presumably stabilizing the lattice). Will ReadySet build the appropriate CIF file if I build the DTT into the density and give it a 0.5 occupancy? 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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Re: [phenixbb] Adequate size for Free R test set?
by Joseph Noel 03 Aug '10

03 Aug '10

Pavel, Thanks so much for the suggestions. They are really helpful! A few questions relative to Phenix. Is there a way to check with Phenix the thin resolution shells? I created Free Rs in Phenix using the thin resolution shells options but removed the 2000 limit and instead used 5%. Maybe I over-did it relative to your reply. Just wondering how to check each of these thin shells. Alternatively, does Phenix ensure one has an adequate number of test reflections in each "thin shell" if this option is set? If so, what should I used for the maximum number of reflections and/or %? Thanks again! 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 ___________________________________________________________ On Aug 3, 2010, at 11:02 AM, 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://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. Re: Adequate size for Free R test set? (Pavel Afonine) > 2. Re: follow up on message 2: phenix.maps --Message: not > implemented (amadrona(a)uci.edu) > 3. Re: follow up on message 2: phenix.maps --Message: not > implemented (Pavel Afonine) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 03 Aug 2010 10:38:57 -0700 > From: Pavel Afonine <pafonine(a)lbl.gov> > To: phenixbb(a)phenix-online.org > Cc: Joseph Noel <noel(a)salk.edu> > Subject: Re: [phenixbb] Adequate size for Free R test set? > Message-ID: <4C585431.7000107(a)lbl.gov> > Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" > > Hi Joe, > > I think almost every one has his/her own opinion on this... Here is what > I think: > > 1) The test set should be such that each "relatively thin resolution > shell" receives at least 50 reflections, and we empirically found that > 150 is "good enough" withing phenix.refine framework. > For "relatively thin resolution shell" definition see: > Lunin & Skovoroda. Acta Cryst. (1995). A51, 880-887. "R-free > likelihood-based estimates of errors for phases calculated from atomic > models". > > This basically defines how many test reflections you need. > > 2) It is customary to set aside either 5 or 10% for test set, with the > total maximum 2000. These are all "magic numbers", that I presume more > or less satisfy "1)" so they became widely used. > > 3) Presence of high-order NCS and selecting free-flags using "thin > shells" algorithm is a different story (Acta Cryst. (2006). D62, > 227--238). It is good to do that because it removes the cross-talk > between test and work reflections due to NCS, but at the same time it > invalidates the requirement "1)". So, this is a gray area (for me at least). > > 4) Some people believe that the final refinement run should be done > using all reflections, arguing that taking away 5-10% of test > reflections worsens the maps. There is some truth in this, yes, removing > the data worsens the maps, but: > a) it is noticeable (in a sense that it can reduce the interpretability > of some parts of the map) only in extreme cases of somewhat low > resolution or low completeness data, b) in most of all other cases it is > simply negligible, c) removing reflections randomly has much smaller > effect than removing them systematically (see page #40 here: > http://www.phenix-online.org/presentations/latest/pavel_maps.pdf and > some relevant references in 2010 PHENIX paper in Acta D). However, if > you do that "final run", you will invalidate the final refinement > statistics, Rfree and Rwork, and thus obtained final structure cannot > have the Rfree associated with it anymore. > > Pavel. > > > On 8/3/10 10:04 AM, Joseph Noel wrote: >> Hi Folks, >> >> Its been a while since I personally refined many structures. In the >> past, I used as a default, 5% of my unique reflections for the Free R >> test set. I have a high resolution structure with 150,000 unique >> reflections and noticed that Phenix defaults are 5% or 2000 >> reflections which ever is smaller. What is the current consensus on an >> adequate number of unique reflections to use for cross-validation? >> >> Thanks! >> Joe >> >> P.S. I really, really love Phenix. >> ___________________________________________________________ >> 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 <mailto:[email protected]> >> >> Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 >> Web Site (HHMI): http://hhmi.org/research/investigators/noel.html >> ___________________________________________________________ >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb > >

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