- phenixbb - phenix-online.org

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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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!

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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

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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

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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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访问我的Netlog个人主页
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 ___________________________________________________________

2 1

DTT mediated disulfide crosslink across a crystallographic two-fold!
by Joseph Noel 03 Aug '10

03 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 > >

2 1

Adequate size for Free R test set?
by Joseph Noel 03 Aug '10

03 Aug '10

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 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

New version complaint
by Simon Kolstoe 03 Aug '10

03 Aug '10

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 --------------------------------------------------------------

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Re: [phenixbb] Phenix Autobuild
by Thomas C. Terwilliger 03 Aug '10

03 Aug '10

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 >> >> >>

1 0

coot links on Mac
by Joseph Noel 02 Aug '10

02 Aug '10

Dear Phenix Team, I noticed that coot behaves unusually on the MacOS version of phenix. It will open when you hit the button in the GUI but it will not open any of the files you specify. Just the main coot window which you then have to load everything as you would normally if running coot stand alone. Also, I noticed that when you run coot from the gui link on MacOS that after manipulating the structure for rebuilding, etc it will freeze requiring a force quit of x-windows to recover. However, if I open coot directly from my xterm on MacOS it works fine and no freezes. Just a note. Love the program! 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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Phenix version 1.6.4 released
by Paul Adams 31 Jul '10

31 Jul '10

The Phenix developers are pleased to announce that version 1.6.4 of Phenix is now available. Binary installers for Linux, and Mac OSX platforms are available at the download site: http://phenix-online.org/download/ Just some of the new features in this version (1.6.4) are: - GUI: - new interfaces for eLBOW, CIF to MTZ conversion, phenix.find_ncs, phenix.superpose_maps - new structure comparison tool (evaluation of multiple related structures) - supports execution of jobs on the Sun Grid Engine queueing system - maps for PyMOL now output in (smaller, faster) CCP4 format - display of sequence and secondary structure in wizards and validation - new wide-format windows for wizards and phenix.refine - many bug fixes - Automated model building: - phenix.autosol now much faster and improved model-building after density modification - phenix.phase_and_build (carries out an iterative process of building a model as rapidly as possible and uses this model in density modification to improve the map. Up to 10x faster compared to AutoBuild, but model quality is nearly as good) - phenix.build_one_model (quickly build a single model from a map and sequence file, or extend an existing model) - phenix.assign_sequence (carry out an improved sequence assignment of a model that you have already built. Uses the new loop libraries available in phenix.fit_loops) - phenix.apply_ncs (apply NCS operators to a single copy of a protein to create all the NCS‐related copies) - phenix.find_ncs (now supports identification of NCS operators from a density map) - phenix.fit_loops (two main algorithms now available - fit short gaps using a loop library derived from high‐resolution structures in the PDB, or build loops directly by iterative extension with tripeptides - phenix.refine: - reference model restraints (restraint dihedral angles to a higher resolution reference model) - alternate ideal angles for torsion definitions (preserves side chain rotameric states) - automatic flipping of incorrect N/Q/H rotamers - custom planarity restraints - hydrogen-bond restraints for Watson-Crick base pairs - reflections with Fobs=0 used in refinement - automatic optimization of mask parameters - map parameters now consistent with phenix.maps - new custom_nonbonded_symmetry_exclusions atom selection parameter to fine tune non-bonded interactions across symmetry axes - Phasing: - Option for Phaser likelihood scoring of substructure solutions in HySS - SOLVE converted to C++; FORTRAN compiler no longer required for Phenix compilation - Other: - KiNG kinemage viewer incorporated into Phenix - Real space refinement option in ligand fitting - B-factor sharpening option for maps For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that there is a new publication that should be used to cite use of Phenix: PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010). Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Marian Harris [ MSHarris(a)lbl.gov ] [ 1-510-486-6886 ] --

1 0

what should I do after making an iterative-build omit map
by J J 30 Jul '10

30 Jul '10

Hello everyone, I used default setting in phenix and made an iterative-build omit map (it took 3 days!!!). Input: a pdb file (6 identical chains in AU); an mtz file output: a resolve_composite_map.mtz; an overall_best_edited.pdb questions: 1) There is only one chain in overall_best_edited.pdb, the resolve_composite_map.mtz clearly indicates there are 6 chains in AU. 2) What's the next step for me after obtaining resolve_composite_map.mtz? a) use phenix.refine to do refinement? if this is the case, what files should I use? b) use phenix.assign_sequence to assign sequence to resolve_composite_map.mtz? c) something else? Thanks in advance. Jason U Pitt

2 1

r_free_flags.generate
by wtempel 30 Jul '10

30 Jul '10

Dear colleagues, I would like to confirm which, if any, twin laws/symmetry operators were applied during a given run of "r_free_flags.generate", but I cannot find the information in the log file of phenix.refine. Am I missing something? If not, could the program be modified to write out that information? In my concrete example, I ran phenix refine with a scalepack file in P4, for which xtriage suggested a P422 point group. Thank you, Wolfram Tempel

3 2

Five sets of PDFs about Refinement, Maps, Validation and PHENIX
by Pavel Afonine 29 Jul '10

29 Jul '10

Hi Everyone, recently I had to update or do from scratch my talk "slides" on various subjects such as crystallographic structure refinement, maps, validation and some general PHENIX overview. Since I spent pretty significant amount of time making all these "slides" , ... I was thinking that may be this might be of use for some of you, so here it is... - 42 pages of general introduction to structure refinement: http://www.phenix-online.org/presentations/latest/pavel_refinement_general.… - 45 pages of phenix.refine overview (including extended details about its use from the command line): http://www.phenix-online.org/presentations/latest/pavel_phenix_refine.pdf - 42 pages of "Some Facts About Maps": http://www.phenix-online.org/presentations/latest/pavel_maps.pdf - 50 pages of "Crystallographic Structure Validation": http://www.phenix-online.org/presentations/latest/pavel_validation.pdf - 31 pages of introduction to PHENIX: http://www.phenix-online.org/presentations/latest/pavel_phenix_intro.pdf Most of the slides in "Introduction to PHENIX" came from Paul Adams, Tom Terwilliger and Nat Echols. Thanks Nat and Jeff Headd for providing with interesting examples of structures with unusual geometry. All the best! Pavel.

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Fwd: autobuild failure
by abhishek dey 29 Jul '10

29 Jul '10

---------- Forwarded message ---------- From: abhishek dey <41.abhishek(a)gmail.com> Date: 29 July 2010 21:27 Subject: autobuild failure To: phenixbb(a)phenix-online.org Dear all, I am facing some problem while running the Autobuild option for PHENIX-1.6-289 version. I uploaded the mtz file, sequence of my protein and the pdb file and started running AUTOBUILD. but the program stopped with the following error message SG: P 2 21 21 Cell: [49.539999999999999, 99.140000000000001, 144.41999999999999, 90.0, 90.0, 90.0] Inverse hand of space group: P 2 21 21 Creating sg entry from /data/dey/2779/rv2779p22121_sort2.mtz Unit cell: (49.54, 99.14, 144.42, 90, 90, 90) Space group: P 2 21 21 (No. 18) Space group name is: P 2 21 21 symbol is: p22121 **************************************** AutoBuild Input failed Need a symfile for solve .the working spacegroup is P 2 21 21 it will be helpful if someone give useful suggestion on this. thanks in advance -- Abhishek Dey

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Re: [phenixbb] phenixbb Digest, Vol 56, Issue 30
by Leonid Flaks 29 Jul '10

29 Jul '10

> Message: 4 > Date: Tue, 27 Jul 2010 08:39:17 -0700 > From: Nathaniel Echols<nechols(a)lbl.gov> > To: PHENIX user mailing list<phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] 32-bit binaries for version 1.6.3-473 > Message-ID: > <AANLkTinSzHiX4z9VPsrbMLFY7xFuwqwkghzCzj2WPjmd(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > On Tue, Jul 27, 2010 at 8:15 AM, Leonid Flaks<flaks(a)bnl.gov> wrote: > > >> I am running phenix 1.6.2-432 on a set of systems running 32-bit version of >> fedora-12. The latest version of phenix (1.6.3-473) has binaries mostly for >> 64-bit OS. The only 32-bit OS I see is fedora-3. I would be happy to switch >> to 64-bit OS one day, but HKL2000 that runs on the same computers has a big >> warning about instability of it on the 64-bit (it is dated back to 2005!) >> Coot is also crashing on the the 64-bit test system, so I have to stay with >> 32-bit for now. >> Does anybody know if fc-3 version would run on f-12? >> >> > I suspect it will be okay, but I haven't tested it. It partly depends on > which features will be used - the GUI is twitchier about system libraries on > Linux. Fortunately, we also distribute all of the source code for Phenix, > so if the binary installer doesn't work, I'd recommend switching to the > source installer. Are these the same machines (and OS) that were used for > RapiData? > > Yes, same 'cafe' systems. They all run f-12-32bit. > Would it be possible to have 32-bit version built for f-12 or f-13? > >> > Possibly - we are probably going to pull some machines from our queueing > system because they have only 8 cores, and some of these will become build > machines for additional platforms (64-bit Ubuntu and CentOS are candidates). > Also, we now build a CentOS 5 (similar to FC6) installer - it didn't work > properly for 1.6.3, but I think I've fixed it now, and we're going to push > out a 1.6.4 very soon because of some unrelated problems in 1.6.3. > > -Nat > > And on top of that, I don't see coot with python binary available for f-12 anymore. I will be testing fc-3 version then. Leon

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32-bit binaries for version 1.6.3-473
by Leonid Flaks 27 Jul '10

27 Jul '10

Hi! I am running phenix 1.6.2-432 on a set of systems running 32-bit version of fedora-12. The latest version of phenix (1.6.3-473) has binaries mostly for 64-bit OS. The only 32-bit OS I see is fedora-3. I would be happy to switch to 64-bit OS one day, but HKL2000 that runs on the same computers has a big warning about instability of it on the 64-bit (it is dated back to 2005!) Coot is also crashing on the the 64-bit test system, so I have to stay with 32-bit for now. Does anybody know if fc-3 version would run on f-12? Would it be possible to have 32-bit version built for f-12 or f-13? Thanks, Leon

2 1

LigandFit parameters?
by Hermella Woldemdihin 27 Jul '10

27 Jul '10

Hi, I am using LigandFit on the GUI version of Phenix. In my electron density map there is a good density for my ligand. And I have my ligand in pdb format. As an input to LigandFit I gave my ligand file(pdb), an MTZ file from my data processing and my protein at some stage of refinement (@ a good R-values). I used the default settings (Resolution=0, Minimum CC of ligand to map=0.75 and Ligand map shape=Fo-Fc) and I got a bad result. My overall CC=0.33 and Score=68.68). What shall I do to get the best solution??? Thanks all! Hermi

2 1

Planarity restraint for covalent linkage
by Elwood A. Mullins 24 Jul '10

24 Jul '10

I'm trying to refine a thioester linkage (CoA to glutamate). Is it possible to define planarity restraints in a refinement.geometry_restraints.edits file along with bonds and angles? If not, what would be the best way to restrain the linkage?

3 3

questions about ncs copy in autobuild
by J J 23 Jul '10

23 Jul '10

Dear All, I am using phenix.autobuild .eff file to build a structure (version 1.6.1). For the input I have a pdb model file with 6 chains; a sequence file which contains residues of a single chain (the sequence file has a few more residues at N-terminal than the pdb model file); an mtz amplitude file; I also specified ncs_copies=6 (I know there are 6 copies in the au). What confuses me is the output pdb file only has one chain (huge Rwork&Rfree, >0.5). Should there be 6 chains? The other issue is that the output chain has fewer residues than my sequence file (both N&C-terminal). It also has fewer residues compared with the pdb model file. Is this because I do not have enough resolution to resolve those missing residues? Thanks in advance. Jason U Pitt

5 5

Defining heavy atom sites for AutoSol
by Kyle Dolan 23 Jul '10

23 Jul '10

Hi all, I used AutoSol to generate SAD phases for a protein after completing a partial MR model. My strategy worked, but I noticed there were more heavy atom sites in the solution than I was expecting. Having continued to build and refine the structure, I am fairly certain that I know which sites are the real sites and which ones are noise. I would like to use the real sites to reproduce the experimental phases in AutoSol or another Phenix module to perhaps improve the map quality (essentially running just SOLVE or Phaser without HYSS or model-building). What is the right approach? I am guessing something like this: phenix.autosol data.sca sequence.dat sites_file=sites.pdb build=False Cheers, Kyle Kyle T. Dolan Department of Biochemistry and Molecular Biology The University of Chicago ktd(a)uchicago.edu

3 2

Re: [phenixbb] phenix.automr ensemble/component question
by Thomas C. Terwilliger 23 Jul '10

23 Jul '10

Hi Scott, Your first command looks good to me. It is saying that the composition of the crystal is 2 copies of each chain: component_1.component_copies=2 component_2.component_copies=2 and you want to search for 2 copies of each of your search models: ensemble_1.copies_to_find=2 ensemble_2.copies_to_find=2 All the best, Tom T > Hi Phenixers, > > I'm a bit confused about the proper syntax for my phenix.automr job. > This is probably a simple concept, but I'm running on 3 hours of sleep > as my kid was up all night, and my synapses aren't working so good. > > I expect 2 copies of my protein per AU > > My protein is composed of two domains > > I have a single PDB search model for each domain > > is either of these commands correct? > > phenix.automr data=mydata.sca \ > ensemble_1.coords=domain1.pdb \ > ensemble_1.identity=95 \ > ensemble_1.copies_to_find=2 \ > component_1.mass=40579 \ > component_1.component_copies=2 \ > ensemble_2.coords=domain2.pdb \ > ensemble_2.identity=95 \ > ensemble_2.copies_to_find=2 \ > component_2.mass=13410 \ > component_2.component_copies=2 > > > or > > > phenix.automr data=mydata.sca \ > ensemble_1.coords=domain1.pdb \ > ensemble_1.identity=95 \ > ensemble_1.copies_to_find=1 \ > component_1.mass=40579 \ > component_1.component_copies=2 \ > ensemble_2.coords=domain2.pdb \ > ensemble_2.identity=95 \ > ensemble_2.copies_to_find=1 \ > component_2.mass=13410 \ > component_2.component_copies=2 > > > essentially I'm not really using an ensemble of search models, I only > have a single PDB for each domain. So should ensemble_1.copies_to_find > and ensemble_2.copies_to_find be set to 1 or 2? > > > Thanks, > Scott > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Scott Classen, Ph.D. > SIBYLS Beamline 12.3.1 > http://bl1231.als.lbl.gov > Advanced Light Source > Lawrence Berkeley National Laboratory > 1 Cyclotron Rd > MS6R2100 > Berkeley, CA 94720 > C) 510.206.4418 > O) 510.495.2697 > Beamline) 510.495.2134 > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

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writing composite omit maps in .xplor
by Susan Tsutakawa 23 Jul '10

23 Jul '10

Hi all, Continuing the conversation on looking at Phenix maps in pymol, what is the best way to generate .xplor maps in Autobuild. I would like to generate a figure in pymol with an omit map. I wasn't able to find documentation explicitly stating how this can be done. Sincerely, Susan

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Questions about sequence file vs pdb model file in Autobuild
by J J 22 Jul '10

22 Jul '10

Dear All, Facts: -input: a sequence file, a pdb model file, an mtz file; the sequence file is the same as the pdb model except that the sequence file has 6 more residues at N-terminal; the pdb model is almost the same as my protein structure. (In a word, I just want to add a few more residues to the current pdb model. Of course I can do it in coot by manually placing residues at the N-terminal, but why not autobuild?) -problem: the output chain sequence is not the same as the sequence file (not the same as the input model file either). It misses some residues at the N-terminal and it adds some residues at the C-terminal (but disconnected from the C-terminal). Is it normal in autobuild? How to correct it? Thanks. Jason U Pitt

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Hydrogen bonds
by Owen Pornillos 21 Jul '10

21 Jul '10

Hi - Is it possible to explicitly declare a hydrogen bond restraint for non- backbone atoms, e.g., one between a helix capping Ser Ogamma atom and a backbone NH? Thanks, Owen

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Re: [phenixbb] Selecting ellipsoid of data
by Kay Diederichs 20 Jul '10

20 Jul '10

Hi Frank, "such a tool" is at http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Aniso_cutoff where it's meant to be applied to INTEGRATE.HKL which comes out of XDS. Doing it this way has the benefit that the statistics printed out by XDS' CORRECT (or SCALA/TRUNCATE; there are people who prefer that route) match the data you refine agains. HTH, Kay > Message: 1 > Date: Thu, 15 Jul 2010 06:32:40 +0100 > From: Frank von Delft<frank.vondelft(a)sgc.ox.ac.uk> > To: PHENIX user mailing list<phenixbb(a)phenix-online.org> > Subject: [phenixbb] Selecting ellipsoid of data > Message-ID:<4C3E9D78.5030203(a)sgc.ox.ac.uk> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi, is there a tool in phenix that allows me to select an ellipsoid of > data -- specified e.g. by the highest resolutions in three reciprocal > lattice directions. (Yes, I'm playing with anisotropy, "playing" being > the operative word.) > > phx > > > ------------------------------ > > Message: 2 > Date: Wed, 14 Jul 2010 22:47:30 -0700 > From: "Ralf W. Grosse-Kunstleve"<rwgk(a)cci.lbl.gov> > To: phenixbb(a)phenix-online.org > Subject: Re: [phenixbb] Selecting ellipsoid of data > Message-ID:<201007150547.o6F5lUoL018490(a)cci.lbl.gov> > Content-Type: text/plain; charset=us-ascii > > Hi Frank, > >> Hi, is there a tool in phenix that allows me to select an ellipsoid of >> data -- specified e.g. by the highest resolutions in three reciprocal >> lattice directions. (Yes, I'm playing with anisotropy, "playing" being >> the operative word.) > > I'm not aware of such a tool. > > Ralf > > > ------------------------------ > > Message: 3 > Date: Thu, 15 Jul 2010 07:15:58 +0100 > From: Frank von Delft<frank.vondelft(a)sgc.ox.ac.uk> > To: "Ralf W. Grosse-Kunstleve"<rwgk(a)cci.lbl.gov>, PHENIX user mailing > list<phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] Selecting ellipsoid of data > Message-ID:<4C3EA79E.2030503(a)sgc.ox.ac.uk> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Ralf > > Yeah, I figured. So if I want to use cctbx, where do I start? Just a > pointer to a) package and b) function where I'll see the syntax. > > So equation for ellipsoid is x^2/a^2 + y^2/b^2 + z^2/c^2 = 1; so I > imagine I take each reflection, convert each of h,k,l to 1/reso, and > with a = 1/res(a*), I just check whether the above is< 1. > > The main thing I still need is to convert h,k,l into orthogonal > coordinates.... or do I? I suppose I don't, as what I care for is not > whether it's "really" an ellipsoid, only whether it cuts through miller > index space anisotropically. > > Hmmmm... I may be able to do it in sftools; but if you can in<1minute > give me a link to where to look to get started in cctbx, that would be > awesome. > > (Thanks for listening :) > > > > >> Hi Frank, >> >> >>> Hi, is there a tool in phenix that allows me to select an ellipsoid of >>> data -- specified e.g. by the highest resolutions in three reciprocal >>> lattice directions. (Yes, I'm playing with anisotropy, "playing" being >>> the operative word.) >>> >> I'm not aware of such a tool. >> >> Ralf

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Iodide scattering factor
by Owen Pornillos 20 Jul '10

20 Jul '10

Hi BB, I am refining a structure that contains iodide ions. I remember some previous posts that PHENIX does not take into account the charge state and uses scattering factors for neutral atoms only. Is this still true? Thanks, Owen

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error on the latest phenix
by Jian Wu 20 Jul '10

20 Jul '10

Hi all, Today, I download the latest version phenix-1.6.3-473 and everything is ok during the installation. However, when I open the graphical phenix, something wrong has happened showed as below: Traceback (most recent call last): File "/local/prog/phenix-1.6.3-473/phenix/wxGUI2/command_line/main.py", line 13, in <module> run(sys.argv[1:]) File "/local/prog/phenix-1.6.3-473/phenix/wxGUI2/command_line/main.py", line 7, in run from wxGUI2 import App File "/local/prog/phenix-1.6.3-473/phenix/wxGUI2/App.py", line 6, in <module> import wx.lib.dialogs ImportError: No module named wx.lib.dialogs Any suggestions and comments will be appreciated. Best, Jian -- Jian Wu Ph.D. Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences (CAS) Tel: 0086-21-54921217 Email: protease(a)gmail.com

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Whic mtz file to use and parameters for phenix.refine (GUI) to set?
by Hermella Woldemdihin 19 Jul '10

19 Jul '10

Hi, I am new to phenix.refine. I'm using the graphical interface. I hav processed my dfiffraction data and used Phaser MR for molecular replacement. And I goyt a result: a solution pdb file and the associated mtz file. 1. So I use the mtz file from this Phaser MR solution or the original file from my data processing in phenix.refine? 2. I have set parameters for phenix.refine like this: Is there other settings for the parameter which I should do for a better result? PDB data: my solution from Phaser MR XRAY DATA= ???? Simulated Annealing=1000 Update waters Refine Target weights: Wxc=0.8 Wxu=1.6 Cycles=5 Fix rotamers Fix bad side chains

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modify the helices
by xinghua qin 19 Jul '10

19 Jul '10

hi everyone: Thanks for all the response! what I said last time may be chinglish and lead to some misunderstanding, the word I said fix a helix means that the model quality of the helix is not very good, I want to modify it manually.It is so hard to do this in low resolution.I modified the helix according to the electron density map, after refinement, large red areas appear in the difference map. That made me crazy! Are there any suggestions or any reviews about this point? I am new beginner to structural biology, any suggestions are welcomed ! Best regards Xinghua Qin Xinghua Qin College of Biological Sciences No.2, Yuan Ming Yuan West Road Haidian District?Beijing?China?100094 Tel: +86-10-62732672 > > > Message: 2 > Date: Fri, 16 Jul 2010 22:10:32 -0700 > From: Pavel Afonine <pafonine(a)lbl.gov> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] sum(occ)<1? > Message-ID: <4C413B48.305(a)lbl.gov> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Ed, > > > Reset occupancies that are outside the [0,1] range at every step of > > minimization. > > this simply will not work: this will invalidate the internal memory of > LBFGS minimizer that we use in phenix.refine and as result it will drive > it crazy. > > Pavel. > > > > ------------------------------ > > Message: 3 > Date: Fri, 16 Jul 2010 22:24:35 -0700 > From: Pavel Afonine <pafonine(a)lbl.gov> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] how to fix a secondary structure? > Message-ID: <4C413E93.6010002(a)lbl.gov> > Content-Type: text/plain; charset=UTF-8; format=flowed > > Hi Xinghua, > > you can use secondary structure restrains that are available in > phenix.refine. It will automatically figure out secondary structure and > apply proper restrains. This should preserve your helix geometry and > still refine it. > > Example: > > phenix.refine model.pdb data.mtz main.secondary_structure_restraints=true > > > Recently I am trying to fix a helice, but found that it is so hard > > for me because of the poor resolution(3.2A) and also a unvisible loop > > near it, so is there any way to just fix a helice ? can I get it out > > of the whole structure to refine it? > > If you still prefer not refining that helix over applying > secondary-structure restrains, then you can do that too: > > phenix.refine model.pdb data.mtz refine.sites.individual="not (chain A > and resseq 123:156)" > > where atom selection > > chain A and resseq 123:156 > > selects your helix, and prefix "not" means you exclude it from refinement. > > Of course you can do all this from PHENIX GUI. > > Let me know if you have any questions. > > Pavel. > > > ------------------------------ > > Message: 4 > Date: Fri, 16 Jul 2010 22:48:52 -0700 > From: Pavel Afonine <pafonine(a)lbl.gov> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] how to fix a secondary structure? - P.S. > Message-ID: <4C414444.8080208(a)lbl.gov> > Content-Type: text/plain; charset="utf-8"; Format="flowed" > > By the way, more information about secondary structure restraints in > phenix.refine you can find in recent PHENIX Newsletter (pages 12-17): > > http://www.phenix-online.org/newsletter/CCN_2010_07.pdf > > Pavel. > > > On 7/16/10 5:52 PM, xinghua qin wrote: > > Hi phenixers: > > Recently I am trying to fix a helice, but found that it is so hard > > for me because of the poor resolution(3.2A) and also a unvisible loop > > near it, so is there any way to just fix a helice ? can I get it out > > of the whole structure to refine it? > > > > Best regards > > > > Xinghua Qin > > > > -- > > Xinghua Qin > > College of Biological Sciences > > No.2, Yuan Ming Yuan West Road > > Haidian District?Beijing?China?100094 > > Tel: +86-10-62732672 > > > > > > ------------------------------ > > >

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sum(occ)<1?
by Ed Pozharski 17 Jul '10

17 Jul '10

Let's say there are two orientations of a ligand for which occupancies need to be refined. By default, the sum of the two will be fixed at 1.0. From quick look at the manual, the only way to have the sum(occ) at lower level is to reset main.occupancy_max. However, this will probably affect all the atoms for which occupancies are refined, which is undesirable (while ligand may have total occupancy of <1, alternate conformers for protein residues should always add up to 1). Am I missing something or the only way to get this done is to refine twice - once only for ligand occupancy, and then for the rest of the model. And what if total occupancy of the ligand is unknown? Is there a way to allow sum(occ) to be anywhere between 0 and 1? -- "I'd jump in myself, if I weren't so good at whistling." Julian, King of Lemurs

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how to fix a secondary structure?
by xinghua qin 16 Jul '10

16 Jul '10

Hi phenixers: Recently I am trying to fix a helice, but found that it is so hard for me because of the poor resolution(3.2A) and also a unvisible loop near it, so is there any way to just fix a helice ? can I get it out of the whole structure to refine it? Best regards Xinghua Qin -- Xinghua Qin College of Biological Sciences No.2, Yuan Ming Yuan West Road Haidian District，Beijing，China，100094 Tel: +86-10-62732672

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How to manually define NCS group for phenix.autobuild?
by J J 15 Jul '10

15 Jul '10

Hello everyone, It is easy to manually define NCS group in phenix.refine, but how to manually define it in phenix.autobuild? phenix.simple_ncs_from_pdb will generate an .ncs_spec file which can be used in autobuild, but what if I want to define ncs group myself, say removing some residues from the automatically detected one. I can manually remove them from the .ncs_spec file, but the operations defined in the .ncs_spec is no longer valid? Thanks in advance Jason U Pitt

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How to define multiple rebuilding region?
by J J 15 Jul '10

15 Jul '10

Dear All, I am trying to use phenix.autobuild to rebuild some poor regions in my model. Since I know which part should be rebuilt, I was thinking using rebuild_chain_list in combination with rebuild_res_end_list and rebuild_res_start_list. The manual suggested: " You can specify more than one region by using the Parameter Group Options button to add lines." What is this Parameter Group Options button? I am running through an .eff file. I have tried something like this: rebuild_chain_list= " 'A, 'B' " rebuild_res_end_list= 50 rebuild_res_start_list=10 However, it does not work. It becomes more obscure to me what if I want to rebuild more than one region in a single chain? Thanks in advance. Jason ------------------------------------------------ University of Pittsburgh School of Medicine 3501 Fifth Avenue Pittsburgh, PA 15261 ------------------------------------------------

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Rwork/Rfree and aniso ADPs
by Roberto Battistutta 15 Jul '10

15 Jul '10

Dear All, I have noticed a (too much?) increment in the difference between Rwork and Rfree upon introduction of anisotropic ADPs, from 18.6/21.6 (isotropic ADPs) to 14.5/20.0. The max resolution is 1.6 A with good statistics. What could be the reason for that? Is 1.6 A too low for anisotropic ADPs in phenix? I would like to keep Rwork/Rfree values nearer, how could I do? Thank you. Bye, Roberto. Roberto Battistutta Associate Professor Department of Chemistry University of Padua via Marzolo 1, 35131 Padova - ITALY tel. +39.049.8275265/67 fax. +39.049.8275239 roberto.battistutta(a)unipd.it www.chimica.unipd.it/roberto.battistutta/ VIMM (Venetian Institute of Molecular Medicine) via Orus 2, 35129 Padova - ITALY tel. +39.049.7923236 fax +39.049.7923250 www.vimm.it

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Selecting ellipsoid of data
by Frank von Delft 14 Jul '10

14 Jul '10

Hi, is there a tool in phenix that allows me to select an ellipsoid of data -- specified e.g. by the highest resolutions in three reciprocal lattice directions. (Yes, I'm playing with anisotropy, "playing" being the operative word.) phx

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Interpreting new ligands
by Monique Gangloff 13 Jul '10

13 Jul '10

Hi, I have not managed to refine glycans such as beta-L-fucose (FUL) that are not listed in the PHENIX library. I am not sure what the problem is. eLBOW works fine and creates a cif file for FUL. elbow.ligand_linking file.pdb crashes with the following error message: "Fatal problems interpreting PDB file". The refinement works fine when I remove FUL from my pdb file. Any suggestion would be very welcome. Cheers, Monique

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Re: [phenixbb] Occupancy Refinement of substrate and product occupying the same coordinates.
by Joseph Brock 13 Jul '10

13 Jul '10

Hi Ralf and Pavel, Thanks so much for the quick response and advice. I have tried both of your suggestions: To assign different altloc identifiers, with the same res ID, chain ID and different resnames (Ralf) and with the same resname (Pavel). I had thought of this but was afraid it would cause confusion with the associated .cif files. Unfortunately, this appears to be the case. For your strategy Ralf, the .cif and .pdb files created by "phenix.ready_set modified.pdb" and the .cif file created by "phenix.elbow modified.pdb" were all accepted by phenix.refine, however the two molecules were still driven away from each other =( For your strategy Pavel, I could not get phenix.refine to run with either the pehnix.ready_set, or the phenix.elbow outputs. It consistently gives the following .cif file error: Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown nonbonded energy type symbols: 52 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. Also note that phenix.ready_set and phenix.elbow are available for creating restraint definitions (CIF files). I will send to you the appropriate sections of both modified pdb files off list and the associated .cif files. Thanks so much again to both of you for all of your help. Cheers, Joe. _________________________________________________________________ View photos of singles in your area! Looking for a hot date? http://clk.atdmt.com/NMN/go/150855801/direct/01/

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Occupancy Refinement of substrate and product occupying the same coordinates.
by Joseph Brock 12 Jul '10

12 Jul '10

Dear Phenix community, I have a crystal structure which I believe involves the substrate and product of the enzymatic reaction occupying the same space within the active site. Ideally, I would like to refine their occupancies to sum to a value less than or equal to 1, as one would for alternate conformations of the same molecule. Phenix does not recognize that they both have partial occupancies however, and the steric repulsion consequently drives them apart during refinement. Does anyone have any advice on achieving this? This is a 1.6Å structure using Phenix version 1.6.1-353. Many thanks for all your help in advance, Joe. _________________________________________________________________ Browse profiles for FREE! Meet local singles online. http://clk.atdmt.com/NMN/go/150855801/direct/01/

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