- phenixbb - phenix-online.org

low-resolution refinement
by Jennifer Weinreich 11 Jun '11

11 Jun '11

Hello, I am refining a low-resolution structure of a protein complex (4.4 Å). The structure was solved by molecular replacement using structures of individual subunits as search models. Here are some of the questions that I have (and also points raised by our reviewers.) Your thoughts and suggestions on how to proceed with this will be very much appreciated. 1) The B factors are very high (300-400). The Wilson B calculated by phenix.xtriage is ~200. Is this something I should be concerned about? 2) What is the expected (or 'acceptable') gap between R and Rfree at this resolution. (Current R = 27%, Rfree = 33%) Does this sound reasonable? 3) It has been suggested to me that I should try adding riding hydrogens during the last round of refinement (to help with geometry). Is this something I should do? And if so, should I remove them when I deposit the file to the PDB. (Hydrogens at 4.5A are probably going to raise a lot of eyebrows... 4) What is the 'acceptable' coordinate and phase errors for structures at this resolution. (They are now 1.4Å and 36˚) 5) I have been using secondary structure restraints during the refinement, which seems to work reasonably well. I also tried refinement using reference model (the structure of the individual components). But refining with reference models seems to result in high RMSD bonds/angles. Is there something I'm missing? Short of growing better crystals, are there other strategies I should be trying with the existing data? Thank you! Jenn

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XDS files in Phenix
by Kay Diederichs 10 Jun '11

10 Jun '11

Dear Ralf, dear all, Recently there was some discussion about reading of XDS output files here on PhenixBB, and I'd like to try and shed some light on this. First, I'm glad to hear this is possible in principle! However, the caveat is, that three types of "native" output files are written by programs from the "XDS program package": a) the main program ("xds", or "xds_par") writes only one type of file, called XDS_ASCII.HKL. This has _unmerged_ observations, and this is therefore currently _unsuitable_ for reading by Phenix programs (since the Phenix routine expects merged, unique reflections). If this is nevertheless tried, I see the danger that Phenix might "eat" all observations of a unique reflections except one, possibly without telling about this problem (? - I didn't try!!) - this is definitely not what you want! b) the program "xscale" can write an output file with unmerged observations. This is the default, and corresponds to MERGE=FALSE in XSCALE.INP . As for a), this is also not what you want! c) the program "xscale" can write an output file with merged observations. This is not the default, but can be obtained by using MERGE=TRUE in XSCALE.INP . This is what you want to read with Phenix programs. Thus only possibility c) will give you a "native XDS" file that is ready to be read by Phenix programs. In addition to this possibility, one can use of course use "xdsconv" to go from XDS_ASCII.HKL (or any file written by "xscale") to a (non-native XDS) filetype that Phenix programs can read. The most general should be to write a MTZ file, but CNS/X-PLOR type files can also be produced. If someone would implement merging of observations in the Phenix routines (it should be straightforward: negative sigmas indicate that observations should not be used; otherwise the standard formulas could be used; symmetry-related reflections of course have to be handled correctly but they are already sorted by unique reflection), then possibilities a) and b) would also work. But until this is implemented, c) should be used. Hope this helps, Kay P.S. The filetypes and everything else around XDS is accurately documented at http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/ -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: Kay.Diederichs(a)uni-konstanz.de Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz This e-mail is digitally signed. If your e-mail client does not have the necessary capabilities, just ignore the attached signature "smime.p7s".

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Possible Twinned data
by Yuri 10 Jun '11

10 Jun '11

Dear Peter, I sent you my log file off list. I realize now that p43 21 2 doesnt allow for twil law. I reprocessed my data in P222 and P4, dont know if it was the right move, but xtriage now gives me the possible PM and M twin laws, respectively. (Would be happy to send you those log as well). If anyone has input on this issue please join in. I am not greatly experienced on twinned crystals. cheers, -- Yuri Pompeu

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Fragment library for mr_rosetta
by riya doreen 10 Jun '11

10 Jun '11

Hi Everyone, I am trying to generate a fragment library for my sequence of interest to use with mr_rosetta. The Robetta server has a sequence limit of 650 amino acids. For longer sequence, will it make sense to divide the sequence into 650 amino acid fragments and generate multiple fragment files ? Thanks Thanks

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Possible Twinned data
by Yuri 09 Jun '11

09 Jun '11

Hello phenixers, I am a little bit at loss since this is the first time I have encountered this situation. I just collected preliminary data on a ligand soaked crystal. It goes to about 1.85 A. The centrics and acentrics reflections tests look a little deviant from ideal untwinned. I was looking at my xtriage log file and it seemed to me like I have some twinned fraction. Phenix says not. I realize too my completeness is not good. Any educated insight would be helpful as I have never dealt with twinning (if this actually the case). Log file section: Wilson ratio and moments Acentric reflections <I^2>/<I>^2 :1.650 (untwinned: 2.000; perfect twin 1.500) <F>^2/<F^2> :0.839 (untwinned: 0.785; perfect twin 0.885) <|E^2 - 1|> :0.649 (untwinned: 0.736; perfect twin 0.541) Centric reflections <I^2>/<I>^2 :2.099 (untwinned: 3.000; perfect twin 2.000) <F>^2/<F^2> :0.749 (untwinned: 0.637; perfect twin 0.785) <|E^2 - 1|> :0.703 (untwinned: 0.968; perfect twin 0.736) NZ test (0<=z<1) to detect twinning and possible translational NCS ----------------------------------------------- | Z | Nac_obs | Nac_theo | Nc_obs | Nc_theo | ----------------------------------------------- | 0.0 | 0.000 | 0.000 | 0.000 | 0.000 | | 0.1 | 0.052 | 0.095 | 0.171 | 0.248 | | 0.2 | 0.126 | 0.181 | 0.285 | 0.345 | | 0.3 | 0.197 | 0.259 | 0.371 | 0.419 | | 0.4 | 0.271 | 0.330 | 0.440 | 0.474 | | 0.5 | 0.334 | 0.394 | 0.499 | 0.520 | | 0.6 | 0.394 | 0.451 | 0.553 | 0.561 | | 0.7 | 0.447 | 0.503 | 0.600 | 0.597 | | 0.8 | 0.497 | 0.551 | 0.629 | 0.629 | | 0.9 | 0.541 | 0.593 | 0.660 | 0.657 | | 1.0 | 0.581 | 0.632 | 0.697 | 0.683 | ----------------------------------------------- | Maximum deviation acentric : 0.062 | | Maximum deviation centric : 0.078 | | | | <NZ(obs)-NZ(twinned)>_acentric : -0.050 | | <NZ(obs)-NZ(twinned)>_centric : -0.021 | ----------------------------------------------- L test for acentric data using difference vectors (dh,dk,dl) of the form: (2hp,2kp,2lp) where hp, kp, and lp are random signed integers such that 2 <= |dh| + |dk| + |dl| <= 8 Mean |L| :0.441 (untwinned: 0.500; perfect twin: 0.375) Mean L^2 :0.270 (untwinned: 0.333; perfect twin: 0.200) The distribution of |L| values indicates a twin fraction of 0.00. Note that this estimate is not as reliable as obtained via a Britton plot or H-test if twin laws are available. Cheers, -- Yuri Pompeu

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March 15, 2010 deadline- User proposal submission for Collaborative Crystallography at BCSB
by Banumathi Sankaran 08 Jun '11

08 Jun '11

Dear Users, Please note: Due to an extended shutdown, proposals will not be solicited in May for the July-August 2011 beamtime. The next cycle will be September-October 2011. The deadline to submit proposals will be July 15th. Regards Banu

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Fwd: Neutrons in Biology 2011 - REGISTRATION NOW OPEN
by Nathaniel Echols 08 Jun '11

08 Jun '11

---------- Forwarded message ---------- From: Teixeira Susana <teixeira(a)ill.fr> To: phenixbb(a)phenix-online.org Date: Wed, 08 Jun 2011 17:10:52 +0200 Subject: Neutrons in Biology 2011 - REGISTRATION NOW OPEN Dear Colleagues, We are pleased to introduce an intensive 3-day hands-on *Neutrons in Biology 2011 School* (Oct. 21-23, 2011) at the European Photon and Neutron Science Campus (Grenoble, France) - a satellite school to the *Neutrons in Biology and Biotechnology meeting *(Oct. 19-20, 2011). During the course of this school participants will be tutored in the joint use of X-ray and neutron scattering techniques applicable to structural biology – Macromolecular Crystallography (PHENIX), Small Angle Scattering and Reflectometry - with emphasis on their complementary nature. The students will be given "hands-on" training in the use of state-of-the-art data analysis and modelling software. By the close of the course the participants should be able to access the suitability of neutron scattering techniques for their scientific projects using large scale facilities. Pre-registration deadline is August 15, 2011 – a limited number of applications will be accepted! Please visit the website for more information: http://www.ill.eu/nib2011 Best regards, The organisers -- ------------------------------ *Susana TEIXEIRA*, Institut Laue Langevin, LSS Group [image: View Susana Teixeira's profile on LinkedIn]<http://fr.linkedin.com/in/scmteixeira> <http://fr.linkedin.com/in/scmteixeira>

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Re: [phenixbb] mr_rosetta - homology search with hhr file - Cannot contact EBI DbFetch
by iulek＠interponta.com.br 08 Jun '11

08 Jun '11

That must make things easier for me, say, to prepare a single script to use, eg, the 10 best alignments from the hhr file. If I understand well, the "simple alignment file" proposed below must suite both sculptor and mr_rosetta. Many thanks. I will go to download the latest nightly build. J. > Hi Jorge, > > In your version of phenix yes, you need a special format for the alignment > files. I just changed it to allow a simple alignment file: > >> target > sequence-of-target >> template > sequence-of-template > > which is also used by sculptor. This is available in a current nightly > build. You can then just paste the alignment from hhpred into such a > file. > > I hope that helps! > -Tom T > > >>>> Thanks, Tom. >>> Yes, phenix.mr_model_preparation fails just like phenix.mr_rosetta: >>> >>> " >>> Traceback (most recent call last): >>> File >>> "/usr/local/phenix-1.7.1-743/phaser/phaser/command_line/mr_model_preparation.py", >>> line 9, in<mod ule> >>> mr_model_preparation.run( args = sys.argv[1:], out = sys.stdout ) >>> File >>> "/usr/local/phenix-1.7.1-743/phaser/phaser/mr_model_preparation.py", >>> line 255, in run >>> proxy = proxy.DbfetchHTTP( database = "pdb", format = "pdb" ) >>> File "/usr/local/phenix-1.7.1-743/phaser/phaser/proxy.py", line 108, in >>> __init__ >>> raise RuntimeError, "Cannot contact %s" % str( self ) >>> RuntimeError: Cannot contact EBI DbFetch service >>> " >>> >>> I think I will have to go to phenix sculptor. This seems to require >>> the alignment in ".aln (CLUSTAL format), .pir (PIR-format) and .ali >>> (relaxed PIR-like format)" maybe I could prefer to keep the hhr >>> alignment but I will have to check if there is an easy way to translate >>> one format into the other. Apart from this, phenix.mr_rosetta, seems to >>> require the alignment "MODELLER-style". >>> Therefore, to keep the alignment as output by hhr (is this wise? >>> Does this use multialignment and maight this be better that pairwise >>> alignment?) I have to translate it to either aln/pir/ali (for phenix >>> sculptor) and then to MODELLER-style for phenix.mr-rosetta. >>> A suggestion to make this more straight forward? >>> >>> J. >>> >>>> Hi Jorje, >>>> >>>> Yes, you can prepare your model separately from mr_rosetta. You can do >>>> this (for example) with: >>>> >>>> phenix.mr_model_preparation 3800765_mod_ed.hhr >>>> >>>> If that fails with the same download problem, you can create an >>>> alignment >>>> file and use phenix.sculptor to edit your model. >>>> >>>> Then as you suggest, you can use your edited model directly as a >>>> "search_model" and skip the .hhr files entirely. >>>> >>>> Let me know if that doesn't do it! >>>> All the best, >>>> Tom T >>>> >>>>>> Dear all, >>>>>> >>>>>> >>>>>> I would like to use mr_rosetta with homolgy search. I followed >>>>>> the >>>>>> instructions at >>>>>> http://www.phenix-online.org/documentation/mr_rosetta.htm , generated >>>>>> the hhr and the fragment files, but at submitting the job I receive >>>>>> the >>>>>> message: >>>>>> >>>>>> ******************* ERROR ENDING *************** >>>>>> Cannot contact EBI DbFetch service >>>>>> >>>>>> ******************* ERROR ENDING *************** >>>>>> >>>>>> after both loading the file 3800765_mod_ed.hhr and generating the log >>>>>> file mr_model_preparation.log. >>>>>> >>>>>> Concerning this problem, I saw >>>>>> http://www.phenix-online.org/documentation/faqs.htm#anch8 . But I am >>>>>> not >>>>>> behind a proxy and even disabling completely the firewall, the message >>>>>> still appears. >>>>>> Maybe this is more linux related, I use openSuSE 11.4. >>>>>> One workaround would be that I write a script to wget the pdb >>>>>> files >>>>>> (listed in .hhr) and select the due chains, putting these in a certain >>>>>> location and indicating in my script where they are. But I am a kind >>>>>> of >>>>>> confused, might >>>>>> >>>>>> search_models= >>>>>> >>>>>> do this. I am not sure I could use a hhr file together with it. >>>>>> Anyway, >>>>>> this might be a desirable solution for me yet I use to run my stuff in >>>>>> a >>>>>> laptop which goes around by. >>>>>> >>>>>> Thanks, >>>>>> >>>>>> Jorge >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> phenixbb mailing list >>>>>> phenixbb(a)phenix-online.org >>>>>> http://phenix-online.org/mailman/listinfo/phenixbb >>>>>> >>>> _______________________________________________ >>>> phenixbb mailing list >>>> phenixbb(a)phenix-online.org >>>> http://phenix-online.org/mailman/listinfo/phenixbb >>>> >>> >

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Polygon error
by Yuri 08 Jun '11

08 Jun '11

Great Pavel, thanks -- Yuri Pompeu

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Re: [phenixbb] mr_rosetta - homology search with hhr file - Cannot contact EBI DbFetch
by Thomas C. Terwilliger 08 Jun '11

08 Jun '11

Hi Jorge, In your version of phenix yes, you need a special format for the alignment files. I just changed it to allow a simple alignment file: >target sequence-of-target >template sequence-of-template which is also used by sculptor. This is available in a current nightly build. You can then just paste the alignment from hhpred into such a file. I hope that helps! -Tom T >>> Thanks, Tom. >> Yes, phenix.mr_model_preparation fails just like phenix.mr_rosetta: >> >> " >> Traceback (most recent call last): >> File >> "/usr/local/phenix-1.7.1-743/phaser/phaser/command_line/mr_model_preparation.py", >> line 9, in <mod ule> >> mr_model_preparation.run( args = sys.argv[1:], out = sys.stdout ) >> File >> "/usr/local/phenix-1.7.1-743/phaser/phaser/mr_model_preparation.py", >> line 255, in run >> proxy = proxy.DbfetchHTTP( database = "pdb", format = "pdb" ) >> File "/usr/local/phenix-1.7.1-743/phaser/phaser/proxy.py", line 108, in >> __init__ >> raise RuntimeError, "Cannot contact %s" % str( self ) >> RuntimeError: Cannot contact EBI DbFetch service >> " >> >> I think I will have to go to phenix sculptor. This seems to require >> the alignment in ".aln (CLUSTAL format), .pir (PIR-format) and .ali >> (relaxed PIR-like format)" maybe I could prefer to keep the hhr >> alignment but I will have to check if there is an easy way to translate >> one format into the other. Apart from this, phenix.mr_rosetta, seems to >> require the alignment "MODELLER-style". >> Therefore, to keep the alignment as output by hhr (is this wise? >> Does this use multialignment and maight this be better that pairwise >> alignment?) I have to translate it to either aln/pir/ali (for phenix >> sculptor) and then to MODELLER-style for phenix.mr-rosetta. >> A suggestion to make this more straight forward? >> >> J. >> >>> Hi Jorje, >>> >>> Yes, you can prepare your model separately from mr_rosetta. You can do >>> this (for example) with: >>> >>> phenix.mr_model_preparation 3800765_mod_ed.hhr >>> >>> If that fails with the same download problem, you can create an >>> alignment >>> file and use phenix.sculptor to edit your model. >>> >>> Then as you suggest, you can use your edited model directly as a >>> "search_model" and skip the .hhr files entirely. >>> >>> Let me know if that doesn't do it! >>> All the best, >>> Tom T >>> >>>>> Dear all, >>>>> >>>>> >>>>> I would like to use mr_rosetta with homolgy search. I followed >>>>> the >>>>> instructions at >>>>> http://www.phenix-online.org/documentation/mr_rosetta.htm , generated >>>>> the hhr and the fragment files, but at submitting the job I receive >>>>> the >>>>> message: >>>>> >>>>> ******************* ERROR ENDING *************** >>>>> Cannot contact EBI DbFetch service >>>>> >>>>> ******************* ERROR ENDING *************** >>>>> >>>>> after both loading the file 3800765_mod_ed.hhr and generating the log >>>>> file mr_model_preparation.log. >>>>> >>>>> Concerning this problem, I saw >>>>> http://www.phenix-online.org/documentation/faqs.htm#anch8 . But I am >>>>> not >>>>> behind a proxy and even disabling completely the firewall, the message >>>>> still appears. >>>>> Maybe this is more linux related, I use openSuSE 11.4. >>>>> One workaround would be that I write a script to wget the pdb >>>>> files >>>>> (listed in .hhr) and select the due chains, putting these in a certain >>>>> location and indicating in my script where they are. But I am a kind >>>>> of >>>>> confused, might >>>>> >>>>> search_models= >>>>> >>>>> do this. I am not sure I could use a hhr file together with it. >>>>> Anyway, >>>>> this might be a desirable solution for me yet I use to run my stuff in >>>>> a >>>>> laptop which goes around by. >>>>> >>>>> Thanks, >>>>> >>>>> Jorge >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> phenixbb mailing list >>>>> phenixbb(a)phenix-online.org >>>>> http://phenix-online.org/mailman/listinfo/phenixbb >>>>> >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://phenix-online.org/mailman/listinfo/phenixbb >>> >> >>

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