- phenixbb - phenix-online.org

Re: [phenixbb] rosetta fragment files -- adjusting residue numbers to combine them
by Thomas C. Terwilliger 16 Jun '11

16 Jun '11

Hi Leonid and others wanting to use phenix.mr_rosetta with large chains, After looking at the Rosetta code and conferring with Frank DiMaio from the Baker laboratory... You can paste several fragment files together to represent your entire chain, but you need to edit all but the first one to set the position in the sequence file that each set of fragments goes with. Here is a little script that will take a fragments file that you have created that started with residue 651 and edit it in a way that you can just add to the end of your fragments file for residues 1-650. Run it with: phenix.python adjust_robetta_resid.py \ fragments_in fragments_adjusted 651 -------------------------------- # adjust_robetta_resid.py # use: phenix.python adjust_robetta_resid.py fragments_in fragments_adjusted 651 # to adjust the first residue of fragments_in to be 651 import sys args=sys.argv[1:] if len(args) != 3: print "USE: phenix.python adjust_robetta_resid.py fragments_in fragments_adjusted <start_resno>" sys.exit() file_in=args[0] file_out=args[1] start_resno=int(args[2]) print "Copying %s to %s offsetting start residue number to %d" %( file_in,file_out,start_resno) f=open(file_out,'w') new_resno=0 for line in open(file_in).readlines(): if line.find('position:') > -1 and line.find('neighbors:')>-1: spl=line.split() current_resno=int(spl[1]) new_resno=current_resno+start_resno print "Residue %d changed to %d" %(current_resno,new_resno) spl[1]=" %d " %(new_resno) new_line=" ".join(spl) else: new_line=line print >>f, new_line.rstrip() f.close() -------------------------------- I will add this to phenix as "phenix.adjust_robetta_resid" as well. However...there still is a problem if you have multiple chains...as mr_rosetta has only one set of fragments files the same fragments files are being applied to all your chains. I will add a way to specify which fragments files go with which chains. All the best, Tom T >> [phenixbb-bounces(a)phenix-online.org] On Behalf Of Leonid Sazanov [sazanov(a)mrc-mbu.cam.ac.uk] >> Sent: 16 June 2011 13:11 >> To: phenixbb(a)phenix-online.org >> Subject: [phenixbb] rosetta fragment files >> >> Hi, I am trying to use mr_rosetta with phenix-1.7.1-743 and rosetta 3.2.1. All rosetta tests passed OK. >> I have several large protein chains in the starting model (already placed). >> So I had to get several pairs of fragment files from robetta server and list all of them in the script. >> Then mr_rosetta fails at the REBUILD_1 stage with the message: >> could not open file (fragment file), although file is definitely there. Is the reason that one can have only two input fragment files (3/9)? Can several fragment files be combined into two 3/9 ones? >> Thanks >> >> -- >> Dr. Leonid A. Sazanov >> Research group leader >> Medical Research Council >> Mitochondrial Biology Unit >> Wellcome Trust / MRC Building >> Hills Road >> Cambridge >> CB2 0XY >> >> _______________________________________________ >> 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 >>

1 0

rosetta fragment files
by Leonid Sazanov 16 Jun '11

16 Jun '11

Hi, I am trying to use mr_rosetta with phenix-1.7.1-743 and rosetta 3.2.1. All rosetta tests passed OK. I have several large protein chains in the starting model (already placed). So I had to get several pairs of fragment files from robetta server and list all of them in the script. Then mr_rosetta fails at the REBUILD_1 stage with the message: could not open file (fragment file), although file is definitely there. Is the reason that one can have only two input fragment files (3/9)? Can several fragment files be combined into two 3/9 ones? Thanks -- Dr. Leonid A. Sazanov Research group leader Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY

3 2

IUCr satellitte
by Gloria Borgstahl 16 Jun '11

16 Jun '11

I am forwarding this information to you on behalf of Marc. Best regards, Gloria The Commission on aperiodic Crystals is organizing a * two days satellite meeting just after the IUCr Congress in Madrid: 'Aperiodic Crystals for Beginners', in Alcala de Henares, 31 August-1st September 2011. ** This school will present in a simple way the methods used for the structural analysis of Aperiodic Crystals*, namely incommensurately modulated phases, incommensurate composites crystals and quasicrystals. It is intended for beginners in the field and will alternate step by step lectures and tutorials. You will find more information in the attached leaflet or on the web site * **http://sig3.ecanews.org/aperbeg2011/aperbeg2011.html*<http://sig3.ecanews.org/aperbeg2011/aperbeg2011.html> Best regards Marc de Boissieu -- -- Marc de Boissieu Sciences de l'Ingéniérie, des Matériaux et des Procédés (SIMaP) Grenoble INP, CNRS, UJF 1130 rue de la piscine BP 75 38402 Saint Martin d'Hères Cedex (France) Tel 33 (0)4 76 82 67 03 Fax 33 (0)4 76 82 66 44 e-Mail: *Marc.de-Boissieu(a)simap.inpg.fr* <Marc.de-Boissieu(a)simap.inpg.fr>

1 0

refinement of twinning dataset
by Ms Chiung-Wen Chang 14 Jun '11

14 Jun '11

hi everyone i have some issues with the refinement of my twinning dataset the dataset has 2.1 A resolution the twin fraction is around 0.43 i did not detwin and ran the refinement directly (with twinning refinement) The attached is the polygon so far the R: 0.1905 Rfree: 0.21 RMSD angles: 0.91 bonds: 0.006 clashscore: 28.176 average B: 45.8 are the clashscore and Average B in the reasonable range ? because the pattern of the polygon is looked wired what can I do more to get them better ? thanks for your help : ) Mary

2 1

[Fwd: Re: elbow.join_cif_files error]
by Maia Cherney 14 Jun '11

14 Jun '11

Hi, I run command line elbow.join_cif_files ligand1.cif ligand2.cif ligand3.cif. As I understand, ligand1.cif and ligand2.cif are cif files present in the directory, the ligand3.cif should be made after joining the first two cifs. I get this error Traceback (most recent call last): File "/usr/local/phenix-1.7.1-743/elbow/elbow/command_line/join_cif_files.py", line 245, in <module> run(filenames, target) File "/usr/local/phenix-1.7.1-743/elbow/elbow/command_line/join_cif_files.py", line 145, in run include_commented_restraints=1, #include_commented_restraints, File "/usr/local/phenix-1.7.1-743/elbow/elbow/formats/monomer_library_cif_parser.py", line 185, in parse_cif raise RuntimeError('long tmp') RuntimeError: long tmp Maia

2 1

Using rosetta for domain search with partial model solution
by Daniel Mattle 14 Jun '11

14 Jun '11

Dear Phenix Developers, Is there a possibility within rosetta searching only for a domain (using hhr files) while one has already a partial pdb model lacking a particular domain? I was unable to find this feature? Do you have implemented that? If this is not implemented yet, would it be possible to add this feature? Best, Daniel

2 1

sca file & anomalous difference map: understanding the story from the scratch,
by Haytham Wahba 13 Jun '11

13 Jun '11

i am new user first Q?? with HKL2000 (with scale anomalous option: ON) the output.sca file is like that (for example): 1 -985 38.064 89.066 51.543 90.000 100.446 90.000 p21 0 0 2 3433.6 77.1 0 0 3 735.6 14.0 0 0 11 1564.7 25.4 0 0 12 5643.2 88.3 0 0 13 541.5 9.7 0 0 14 1701.0 27.4 0 1 1 2060.5 47.0 0 1 2 4115.3 75.3 4257.1 97.5 0 1 3 8782.0 280.6 7728.9 173.9 0 1 5 1760.8 28.4 1778.5 33.5 0 1 6 6650.2 122.2 6843.2 126.0 0 1 7 1935.8 36.6 1794.2 29.1 is that one is merged or unmerged????? if i compare with the output.sca with scale anomalous option (off): 0 0 2 3444.4 77.3 0 0 3 734.9 14.0 0 0 4 1705.0 27.5 0 0 5 2693.8 49.4 0 0 6 8383.1 153.9 ------------------------------------------------------- second Q? using output.sca (with scale anomalous option on) for molecular Replacment generate MR.mtz which shows F,SIGF in data labels under phenix.refine the generated (refine_data.mtz) shows: I-obs(+),SIGI-obs(+),I-obs(-),SIGI-obs(-) what is going on in first and second run? ----------------------------------------------------------------- third Q? i want to generate anomalous difference map using phenix.map but when i use output.sca (with scale anomalous option: ON) as reflections file the data label show ((i-obs,sigma)) how to convert this SCA file (if it is merged) to unmerged sca file to creat anomalous difference map for protein contains Br, Sn and Sulpher?? i want to see peaks for these 3 elements to confirm their presence. N.B: the wavelenght was 1.00900 N.B: resolution 1.78 A N.B: i use GUI phenix i am sorry for that long e-mail. thank you in advance haytham wahba biochemi UdeM Canada

5 7

again: XDS files
by Kay Diederichs 11 Jun '11

11 Jun '11

Hi everybody, it has been possible for many years to produce MTZ files from XDS data; I do that all the time, going through xdsconv (filetype CCP4, or CCP4_F, or CCP4_I depending on what type of data one wants - see the docs). This works very well. Others use the xds/pointless/scala/truncate route or the older xds/combat route or ... - as long as it works that's fine. Thus my message was not meant to discourage people from doing that. Rather I see a new possibility to go _directly_ into Phenix, which clearly may be desirable in some cases (less programs involved means less work and maybe fewer bugs), and I wanted to describe the options. If Autosol can use unmerged data (which was new to me), then going from XDS through pointless to a unmerged MTZ file should be the easiest and best way (http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Pointless). best, Kay

1 0

installation problem on Ubuntu
by Daqi Tu 10 Jun '11

10 Jun '11

Hi, I was trying to install the 32 bit Phenix-dev-782 or the official release 1.7.1-743 onto a virtual ubuntu 10.04 32-bit machine. Both of them failed with this error: /bin/tar: ./build/intel-linux-2.6/base/bin/wx-config: Cannot create symlink to `/net/longnose/scratch2/phenix/phenix-dev-782/build/intel-linux-2.6/base/lib/wx/config/gtk2-ansi-release-2.8': Operation not supported /bin/tar: Exiting with failure status due to previous errors /mnt/hgfs/windubuntu/phenix-installer-dev-782/bin/install-from-binary: 352: /usr/local/phenix-dev-782/build/intel-linux-2.6/base/bin/python: not found Any comments? Thanks. Daqi Tu

3 3

low-resolution refinement
by Jennifer Weinreich 10 Jun '11

10 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

3 2

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".

7 7

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

1 0

Fragment library for mr_rosetta
by riya doreen 09 Jun '11

09 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

2 3

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

4 4

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

1 0

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>

1 0

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 >>>> >>> >

1 0

Polygon error
by Yuri 08 Jun '11

08 Jun '11

Great Pavel, thanks -- Yuri Pompeu

1 0

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 >>> >> >>

1 0

XDS format
by Jianghai Zhu 08 Jun '11

08 Jun '11

Hi, In the manual of version 1.7.1, I found out that only phenix.hyss can read XDS_ASCII files with merged data. Do other phenix tools recognized XDS_ASCII files? If not, I would like to request this feature. For example, let phenix.autosol read XDS_ASCII file with merged or unmerged data. Thanks. -- Jianghai

7 10

Re: [phenixbb] mr_rosetta - homology search with hhr file - Cannot contact EBI DbFetch
by iulek＠interponta.com.br 07 Jun '11

07 Jun '11

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 >

1 0

polygon Error.
by Yuri 07 Jun '11

07 Jun '11

Hello everyone, Keep getting an error when I try to run polygon to validate my model. Here is what i get: RuntimeError : lbfgs error: Line search failed: The step is at the lower bound stpmin(). Traceback: File "/home/local/UFAD/yuri.pompeu/Desktop/PHENIX_installation/phenix-1.7.1-743/cctbx_project/libtbx/thread_utils.py", line 223, in run return_value = self._target(self._args, self._kwargs, self._c) File "/home/local/UFAD/yuri.pompeu/Desktop/PHENIX_installation/phenix-1.7.1-743/cctbx_project/libtbx/runtime_utils.py", line 58, in __call__ result = self.target() File "/home/local/UFAD/yuri.pompeu/Desktop/PHENIX_installation/phenix-1.7.1-743/phenix/phenix/validation/analyze_all.py", line 358, in __call__ result = validation_result(params, tmp_dir) File "/home/local/UFAD/yuri.pompeu/Desktop/PHENIX_installation/phenix-1.7.1-743/phenix/phenix/validation/analyze_all.py", line 139, in __init__ return_fmodel_and_pdb=True) File "/home/local/UFAD/yuri.pompeu/Desktop/PHENIX_installation/phenix-1.7.1-743/cctbx_project/mmtbx/model_vs_data.py", line 806, in run mvd_obj.collect(model_vs_data = show_model_vs_data(fmodel)) File "/home/local/UFAD/yuri.pompeu/Desktop/PHENIX_installation/phenix-1.7.1-743/cctbx_project/mmtbx/model_vs_data.py", line 556, in show_model_vs_data sigmaa_plot = fmodel.sigmaa().show_short(silent=True) File "/home/local/UFAD/yuri.pompeu/Desktop/PHENIX_installation/phenix-1.7.1-743/cctbx_project/mmtbx/f_model.py", line 1464, in sigmaa use_sampling_sum_weights = p.use_sampling_sum_weights) File "/home/local/UFAD/yuri.pompeu/Desktop/PHENIX_installation/phenix-1.7.1-743/cctbx_project/mmtbx/scaling/sigmaa_estimation.py", line 191, in __init__ w_obs=w_obs) File "/home/local/UFAD/yuri.pompeu/Desktop/PHENIX_installation/phenix-1.7.1-743/cctbx_project/scitbx/math/chebyshev_lsq_fit.py", line 72, in __init__ self.minimizer = lbfgs.run(target_evaluator=self) File "/home/local/UFAD/yuri.pompeu/Desktop/PHENIX_installation/phenix-1.7.1-743/cctbx_project/scitbx/lbfgs/__init__.py", line 258, in run log) File "/home/local/UFAD/yuri.pompeu/Desktop/PHENIX_installation/phenix-1.7.1-743/cctbx_project/scitbx/lbfgs/__init__.py", line 143, in run_c_plus_plus if (minimizer.run(x, f, g)): continue Thank you -- Yuri Pompeu

2 2

mr_rosetta - homology search with hhr file - Cannot contact EBI DbFetch
by iulek＠interponta.com.br 07 Jun '11

07 Jun '11

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

2 1

a double conformation residue included in metal coordination file
by Yamei Yu 07 Jun '11

07 Jun '11

HI all, In my structure, there is a double conformation residue and on conformation is coordinated to a metal. I use phenix.metal_coordination to generate a elbow.edits file. In such file the restraint listed as: refinement.geometry_restraints.edits { bond { action = *add atom_selection_1 = name MG and chain B and resname MG and resseq 2001 atom_selection_2 = name OD2 and altid A and chain B and resname ASP and resseq 271 distance_ideal = 2.070000 sigma = 0.100 } } But when I use this file for refinement, I got an error message: Sorry: No atom selected: "name OD2 and altid A and chain B and resname ASP and resseq 271" I also check my PDB file: ATOM 6100 N AASP B 271 -19.420 19.064 51.907 0.50115.36 N ANISOU 6100 N AASP B 271 14002 14643 15186 -598 738 -1235 N ATOM 6101 CA AASP B 271 -18.016 18.977 51.528 0.50127.08 C ANISOU 6101 CA AASP B 271 15508 16123 16656 -585 725 -1202 C ATOM 6102 C AASP B 271 -17.194 19.859 52.460 0.50105.81 C ANISOU 6102 C AASP B 271 12832 13418 13952 -583 730 -1182 C ATOM 6103 O AASP B 271 -17.750 20.593 53.277 0.50 67.89 O ANISOU 6103 O AASP B 271 8027 8614 9153 -586 738 -1193 O ATOM 6104 CB AASP B 271 -17.818 19.429 50.080 0.50154.71 C ANISOU 6104 CB AASP B 271 18986 19641 20157 -560 689 -1204 C ATOM 6105 CG AASP B 271 -18.871 18.868 49.141 0.50167.83 C ANISOU 6105 CG AASP B 271 20622 21317 21830 -559 682 -1230 C ATOM 6106 OD1AASP B 271 -18.804 17.661 48.823 0.50157.05 O ANISOU 6106 OD1AASP B 271 19265 19945 20462 -568 691 -1224 O ATOM 6107 OD2AASP B 271 -19.758 19.638 48.708 0.50156.92 O ANISOU 6107 OD2AASP B 271 19211 19952 20460 -550 666 -1256 O ATOM 6108 N BASP B 271 -19.303 18.972 52.212 0.50115.36 N ANISOU 6108 N BASP B 271 14002 14643 15186 -598 738 -1235 N ATOM 6109 CA BASP B 271 -17.822 18.681 52.128 0.50127.08 C ANISOU 6109 CA BASP B 271 15508 16123 16656 -585 725 -1202 C ATOM 6110 C BASP B 271 -17.006 19.773 52.851 0.50105.81 C ANISOU 6110 C BASP B 271 12832 13418 13952 -583 730 -1182 C ATOM 6111 O BASP B 271 -17.610 20.704 53.419 0.50 67.89 O ANISOU 6111 O BASP B 271 8027 8614 9153 -586 738 -1193 O ATOM 6112 CB BASP B 271 -17.514 18.729 50.592 0.50154.71 C ANISOU 6112 CB BASP B 271 18986 19641 20157 -560 689 -1204 C ATOM 6113 CG BASP B 271 -16.455 17.692 50.152 0.50167.83 C ANISOU 6113 CG BASP B 271 20622 21317 21830 -559 682 -1230 C ATOM 6114 OD1BASP B 271 -16.846 16.720 49.601 0.50157.05 O ANISOU 6114 OD1BASP B 271 19265 19945 20462 -568 691 -1224 O ATOM 6115 OD2BASP B 271 -15.310 17.950 50.520 0.50156.92 O ANISOU 6115 OD2BASP B 271 19211 19952 20460 -550 666 -1256 O Is there something wrong? Thank you very much! yamei yu

2 1

problem with hhr files in phenix_mr.rosetta
by Miguel Ortiz Lombardia 07 Jun '11

07 Jun '11

Dear phenix developers, Trying to run a test job with phenix_mr.rosetta on a Mac (10.6.7) using a command line such as (phenix is the dev-764 version): phenix.mr_rosetta seq_file=this.seq data=P41212.mtz hhr_files=ed593l.hhr hhr_files=ed593g.hhr fragment_files=frag3.gz fragment_files=frag9.gz rescore_mr.relax=False rosetta_models=20 ncs_copies=3 space_group=p41212 use_all_plausible_sg=False nproc=100 group_run_command=qsub I get this kind of error: ******************* ERROR ENDING *************** Uninterpretable: 'Q ss_pred --------------------------------------------------------------------------------\nQ ed593 390 -------------------------------------------------------------------------------- 389 (593)\nQ Consensus 390 -------------------------------------------------------------------------------- 389 (593)\n\nT Consensus 623 ~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 702 (1010)\nT 2xgj_A 623 GKDNYGWGAVVDFAKRINKRNPSAVYTDHESYIVNVVVNTMYIDSPVNLLKPFNPTLPEGIRPAEEGEKSICAVIPITLD 702 (1010)\nT ss_dssp TTEEEEEEEEEEEEECCCSSCTTCCCCTTTTEEEEEEEEEEETTSCGGGCCTTCCCCCTTCCBCCTTCCEEEEEEEECGG\nT ss_pred CccccceeEEEeeccccccCCCCceeeccccceeeeeecccccCCcccccccccccCccccCcccccccceeEEEEeehh\n\n\nQ ss_pred --------------------------------------------------------------------------------\nQ ed593 390 -------------------------------------------------------------------------------- 389 (593)\nQ Consensus 390 -------------------------------------------------------------------------------- 389 (593)\n\nT Consensus 703 ~i~~i~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~ 782 (1010)\nT 2xgj_A 703 SIKSIGNLRLYMPKDIRASGQKETVGKSLREVNRRFPDGIPVLDPVKNMKIEDEDFLKLMKKIDVLNTKLSSNPLTNSMR 782 (1010)\nT ss_dssp GEEEEEEEECCCCSSTTCSSSHHHHHHHHHHHHHHSSSCCCBCCTTTTSCCCCHHHHHHHHHHHHHHHHHTTSHHHHSSS\nT ss_pred hhhcccceEEecCccccChHHHHHHHHHHHHHHHhCccCCcccCchhhccCCcHHHHHHHHHHHHHHHHHhcCccccCcC' ******************* ERROR ENDING *************** I thought that could be due to different line endings in Macs vs. UNIX, so I transformed the hhr files with (unix2mac is unix2dos 5.3 (2011-04-26)from Fink) unix2mac ed593l.hhr unix2mac ed593g.hhr But then the same input line results in: (...) Loading PDB and alignment files from /a/people/miguel/Lab/Rosetta/MR_ROSETTA_6/WORK_1/ed593l_1/ed593l_ed.hhr Log file for mr_model_preparation is: /a/people/miguel/Lab/Rosetta/MR_ROSETTA_6/WORK_1/ed593l_1/mr_model_preparation.log ******************* ERROR ENDING *************** Incorrect file format ******************* ERROR ENDING *************** Any other ideas? Thank you! -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR6098) CNRS, Universités d'Aix-Marseille I & II Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 mailto:[email protected] http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

3 3

meaning of nproc in mr_rosetta
by Miguel Ortiz Lombardía 07 Jun '11

07 Jun '11

Dear Phenix developers, Could you elaborate on the meaning of "nproc" in phenix.mr_rosetta? I tried unsuccessfully to find out in the docs. Please, let me know if I missed something. I sent out a master job to an SGE queue engine, having set nproc=64. At this moment I find 168 jobs submitted and running and the total number of processors in use seems to be around 120. Better understanding of the meaning of nproc would help with the allocation of resources. Best regards, -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR6098) CNRS, Universités d'Aix-Marseille I & II Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 mailto:[email protected] http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

2 3

The SASTBX webserver
by Peter Zwart 03 Jun '11

03 Jun '11

Dear All, I would like to advertise our online server featuring some basic SAXS analyses tools. The website http://sastbx.als.lbl.gov/cgi-bin/index.html has functionality for 1. Model intensity calculation (using a Spherical Harmonic Expansion; sastbx.she ) 2. Shape determination (or better: Shape Recovery; sastbx.shapeup) 3. Model alignment (sastbx.zalign) The applications we have developed are build using the SASTBX, an extension of the CCTBX (http://cctbx.sf.net) framework, dedicated to the analyses of SAXS data. The model intensity calculation engine uses an approach similar to CRYSOL and (in our hands) provides model SAXS data of a similar quality as FOXS and CRYSOL. The shape recovery procedure (shapeup) provides an estimate of the shape typically within 1 minute without the need for preprocessing the data (i.e. just feed it your background subtracted SAXS curve and nothing more). You can provide a known model as well for comparison. Some example shape recovery results can be found here: http://sastbx.als.lbl.gov/grant/shapeup/summary.html The examples were prepared utilizing data provided by Edward Snell and coworkers (Grant, T. D., Luft, J. R., Wolfley, J. R., Tsuruta, H., Martel, A., Montelione, G. T. and Snell, E. H. (2011), Small angle X-ray scattering as a complementary tool for high-throughput structural studies. Biopolymers, 95: 517–530). Feel free to contact me or Haiguang Liu (HGLiu(a)lbl.gov) if you encounter any problems or have questions. Regards, Peter Zwart -- ----------------------------------------------------------------- P.H. Zwart Research Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org SASTBX: http://sastbx.als.lbl.gov -----------------------------------------------------------------

1 0

omit map
by Desi Mail 03 Jun '11

03 Jun '11

Hi everybody, I would like to calculate the omit map around the ligand. I followed the documentation http://www.phenix-online.org/documentation/autobuild.htm#anch159 But the 2Fo density around the ligand is very poor. Any help is appreciated. Thanks Mary Make a SA-omit map around atoms in target.pdb phenix.autobuild data=data.mtz model=coords.pdb omit_box_pdb=target.pdb composite_omit_type=sa_omit Coefficients for the output omit map will be in the file resolve_composite_map.mtz in the subdirectory OMIT/ . An additional map coefficients file omit_region.mtz will show you the region that has been omitted. (Note: be sure to use the weights in both resolve_composite_map.mtz and omit_region.mtz).

6 8

Diamond Light Source phase III beamline proposal - call for support.
by Johan Turkenburg 03 Jun '11

03 Jun '11

Many of you will already have seen the request for Expressions of Interest for the Diamond phase III proposal for "A versatile microfocus beamline with an in-situ side station for macromolecular crystallography at DIAMOND". As one of the co-proposers I would like to urge you to support this proposal and write a letter to this effect. We need as many as possible! Details of the proposal can be found here, with a link where your letter of support can be uploaded: http://www.diamond.ac.uk/Home/Beamlines/PhaseIII/ExpressionsofInterest.html You may already have been contacted by other colleagues in the MX community but this is of high importance to the structural community as a whole, and we especially invite our international colleagues to provide support for this initiative. To help us collate these EOI's and comment on any additional feedback you may have, we would ask you to do this by June 8th. Johan Dr. Johan P. Turkenburg X-ray facilities manager York Structural Biology Laboratory University of York Phone (+) 44 1904 328251 York YO10 5DD UK Fax (+) 44 1904 328266

1 0

elbow question
by wtempel 03 Jun '11

03 Jun '11

Dear colleagues, am I alone in thinking that in my example phenix.elbow gave me more than what I was asking for, specifically atom H11 attached to sulfur? Is it added by elbow, or does it originate from the "--chem=tpp" input? Best regards, Wolfram Tempel command line: phenix.elbow --chem=tpp --mogul phenix version: 1.7.1-743

3 4

GUI for phenix_mr.rosetta
by riya doreen 02 Jun '11

02 Jun '11

Dear phenix developers, Is it possible to run phenix_mr.rosetta from the GUI ? Thanks

2 1

Re: [phenixbb] rosetta_mr autobuild failure - typo fixed
by Thomas C. Terwilliger 02 Jun '11

02 Jun '11

Hi again Joe, Typo below (csh vs bash) fixed in this version of the message. -Tom Hi Joe, I'm sorry for the problems in running mr_rosetta! Getting the set up to work is appearing to be a bit of a challenge, particularly on a mac. So the first problem is this: "dyld: Library not loaded: /Applications/rosetta3.2_bundles/rosetta_source/build/src/release/macos/10.5/64/x86/gcc/libdevel.dylib Referenced from: /usr/local/bin/rosetta/rosetta_source/bin/mr_protocols.default.macosgccrelease Reason: image not found" In the cases that have come up so far, there have been two problems. Here are the solutions to those two problems: 1. The installation of Rosetta cannot be moved after it is compiled. This is because the path to the libraries (as in the error message above) is compiled into Rosetta. So...if you moved this installation around at all, try remaking the installation and keeping it in its original location. 2. In some cases the path to the libraries can be conflicting between PHENIX and some other definition on your system. In this case you can try the following shell command (before running phenix.mr_rosetta): with csh: setenv PHENIX_TRUST_OTHER_ENV 1 or with bash or sh: export PHENIX_TRUST_OTHER_ENV=1 Hopefully...one of those will fix this problem. Now the second problem...I am not sure what the actual error is in this one. The error message you got is not helpful as you say because it refers to a file path on the machine where I created the test. That path does not actually have to exist however (I just ran the test on another machine that is not connected to that directory and it runs fine). This means there is some other problem that is the real one. (I will get rid of this error message so this won't happen in the future). Can you try this: 1. reproduce the problem: phenix_regression.wizards.test_command_line_rosetta_quick_tests \ test_autobuild 2. have a look at the log files: cat run.log # if not empty, may give a big clue more test_autobuild_current.log # look at end of this file for clues 3. the test_autobuild_current.log log file may refer to a sub-process where the actual problem occurs: Log file for autobuilding will be: /Users/terwill/unix/misc/junk/test_autobuild/WORK_1/autobuild.log in this case that autobuild log file, and files in WORK_1/AutoBuild_run_1_/TEMP0 may give additional clues. Let me know what this shows! All the best, Tom T >> >> Hi all, >> >> I wanted to use the rebuilding feature of Rosetta to help improve the R-fators of MR solution in a new space group. I'm using Phenix 1.7.1-743 w/ Rosetta 3.2 on MAC OSX 10.5.8 >> >> installation was succesful, so after editing my .profile to include export PHENIX_ROSETTA_PATH=/usr/local/bin/rosetta, I tried to run the following tests: >> >> 1. phenix_regression.wizards.test_command_line_rosetta_quick_tests test_set_up >> >> 2. phenix_regression.wizards.test_command_line_rosetta test_mr_rosetta >> >> 3. phenix_regression.wizards.test_command_line_rosetta_quick_tests >> >> While the first was successful (ALL COMMAND_LINE TEST OK), the second reported the following error: >> >> Error: test_command_line_rosetta failed >> >> Upon subsequently running the test_mr_rosetta.com script created in the subdirectory, the following error was reported: >> >> coords1.ali >> coords1.pdb >> fobs.mtz >> mr_rosetta_quick.eff >> perfect.mtz >> seq.dat >> test3.gz >> test9.gz >> test_mr_rosetta.com >> test_mr_rosetta.log >> Sorry: mr_rosetta failed... >> >> ******************************************************************************** Sorry, a subprocess has failed... >> >> END OF LOG FILE >> /usr/local/bin/rosetta/test_mr_rosetta/MR_ROSETTA_1/GROUP_OF_RESCORE_MR_1/RUN_FILE_1.log : >> >> SYMMETRY FROM INPUT SOLUTION: CRYST1 25.000 25.000 25.000 90.00 100.00 90.00 P 1 21 1 >> >> Scoring the model >> /usr/local/bin/rosetta/test_mr_rosetta/MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/RUN_1/AutoMR_run_1_/coord_mr.1.pdb Relaxing model at 3.0 A, generating and scoring 1 relaxed models >> >> Error message: >> >> child process stderr output: >> command: 'sh >> /usr/local/bin/rosetta/test_mr_rosetta/MR_ROSETTA_1/GROUP_OF_RESCORE_MR_1/RUN_1/RESCORE_MR_1/WORK_1/run_relax.sh' >> /usr/local/bin/rosetta/test_mr_rosetta/MR_ROSETTA_1/GROUP_OF_RESCORE_MR_1/RUN_1/RESCORE_MR_1/WORK_1/run_relax.sh: >> line 3: 11915 Trace/BPT trap >> /usr/local/bin/rosetta/rosetta_source/bin/mr_protocols.default.macosgccrelease @relax.flags > relax.log 2>&1 >> Failed to run RELAX >> >> >> ******************* ERROR ENDING *************** >> Failed to run RELAX ...see log file in >> /usr/local/bin/rosetta/test_mr_rosetta/MR_ROSETTA_1/GROUP_OF_RESCORE_MR_1/RUN_1/RESCORE_MR_1/WORK_1/relax.log >> >> ******************* ERROR ENDING *************** >> >> >> The resulting log file showed the following: >> >> dyld: Library not loaded: >> /Applications/rosetta3.2_bundles/rosetta_source/build/src/release/macos/10.5/64/x86/gcc/libdevel.dylib >> Referenced from: >> /usr/local/bin/rosetta/rosetta_source/bin/mr_protocols.default.macosgccrelease >> Reason: image not found >> >> phenix_regression.wizards.test_command_line_rosetta_quick_tests failed with the following: >> >> Running test_autobuild >> FALED TO RUN: test_autobuild >> ************************************************************** >> Error: test_command_line_rosetta_quick_test failed >> >> After running the resulting test_autobuild.com script, the log file showed: >> >> S_COORD_0001_ed_0005_ed.pdb >> averaged_map_coeffs.mtz >> coords1.pdb >> fobs.mtz >> relax.pkl >> seq.dat >> test_autobuild.com >> test_autobuild.log >> Sorry: Failed to run autobuild >> ERROR MESSAGE: >> Sorry the file >> /net/sigma/raid1/scratch1/terwill/misc/mr_rosetta/coords1_data.mtz seems not to exist? ( key = input_data_file) >> >> >> The last error message was particularly confusing as that directory indeed does not exist on my machine, put was rather the directory path given as an example in the documentation. >> >> I have two hunches for what could be going wrong, but I unsure how to fix either: >> >> 1. In the phenix documentation it says if using a mac, I might have to download some patches, but I could not find any on the Rosetta dowload page ;(. >> >> 2. The documentation also stipulates to specify a proxy server if behind a firewall using >> export HTTP_PROXY=proxyout.mydomain.edu:8080 >> I am behind a firewall, but on my machine there is no proxy server listed under system prefernces-->advanced-->proxies. I can access my machine using a vpn, but don't know how to tell rosetta to do the same. >> >> Thanks for all your help in advance and sorry that this is so long winded ;) >> >> Cheers, >> >> Joe >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

1 0

rosetta_mr autobuild failure
by Joseph Brock 02 Jun '11

02 Jun '11

Hi all, I wanted to use the rebuilding feature of Rosetta to help improve the R-fators of MR solution in a new space group. I'm using Phenix 1.7.1-743 w/ Rosetta 3.2 on MAC OSX 10.5.8 installation was succesful, so after editing my .profile to include export PHENIX_ROSETTA_PATH=/usr/local/bin/rosetta, I tried to run the following tests: 1. phenix_regression.wizards.test_command_line_rosetta_quick_tests test_set_up 2. phenix_regression.wizards.test_command_line_rosetta test_mr_rosetta 3. phenix_regression.wizards.test_command_line_rosetta_quick_tests While the first was successful (ALL COMMAND_LINE TEST OK), the second reported the following error: Error: test_command_line_rosetta failed Upon subsequently running the test_mr_rosetta.com script created in the subdirectory, the following error was reported: coords1.ali coords1.pdb fobs.mtz mr_rosetta_quick.eff perfect.mtz seq.dat test3.gz test9.gz test_mr_rosetta.com test_mr_rosetta.log Sorry: mr_rosetta failed... ******************************************************************************** Sorry, a subprocess has failed... END OF LOG FILE /usr/local/bin/rosetta/test_mr_rosetta/MR_ROSETTA_1/GROUP_OF_RESCORE_MR_1/RUN_FILE_1.log : SYMMETRY FROM INPUT SOLUTION: CRYST1 25.000 25.000 25.000 90.00 100.00 90.00 P 1 21 1 Scoring the model /usr/local/bin/rosetta/test_mr_rosetta/MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/RUN_1/AutoMR_run_1_/coord_mr.1.pdb Relaxing model at 3.0 A, generating and scoring 1 relaxed models Error message: child process stderr output: command: 'sh /usr/local/bin/rosetta/test_mr_rosetta/MR_ROSETTA_1/GROUP_OF_RESCORE_MR_1/RUN_1/RESCORE_MR_1/WORK_1/run_relax.sh' /usr/local/bin/rosetta/test_mr_rosetta/MR_ROSETTA_1/GROUP_OF_RESCORE_MR_1/RUN_1/RESCORE_MR_1/WORK_1/run_relax.sh: line 3: 11915 Trace/BPT trap /usr/local/bin/rosetta/rosetta_source/bin/mr_protocols.default.macosgccrelease @relax.flags > relax.log 2>&1 Failed to run RELAX ******************* ERROR ENDING *************** Failed to run RELAX ...see log file in /usr/local/bin/rosetta/test_mr_rosetta/MR_ROSETTA_1/GROUP_OF_RESCORE_MR_1/RUN_1/RESCORE_MR_1/WORK_1/relax.log ******************* ERROR ENDING *************** The resulting log file showed the following: dyld: Library not loaded: /Applications/rosetta3.2_bundles/rosetta_source/build/src/release/macos/10.5/64/x86/gcc/libdevel.dylib Referenced from: /usr/local/bin/rosetta/rosetta_source/bin/mr_protocols.default.macosgccrelease Reason: image not found phenix_regression.wizards.test_command_line_rosetta_quick_tests failed with the following: Running test_autobuild FALED TO RUN: test_autobuild ************************************************************** Error: test_command_line_rosetta_quick_test failed After running the resulting test_autobuild.com script, the log file showed: S_COORD_0001_ed_0005_ed.pdb averaged_map_coeffs.mtz coords1.pdb fobs.mtz relax.pkl seq.dat test_autobuild.com test_autobuild.log Sorry: Failed to run autobuild ERROR MESSAGE: Sorry the file /net/sigma/raid1/scratch1/terwill/misc/mr_rosetta/coords1_data.mtz seems not to exist? ( key = input_data_file) The last error message was particularly confusing as that directory indeed does not exist on my machine, put was rather the directory path given as an example in the documentation. I have two hunches for what could be going wrong, but I unsure how to fix either: 1. In the phenix documentation it says if using a mac, I might have to download some patches, but I could not find any on the Rosetta dowload page ;(. 2. The documentation also stipulates to specify a proxy server if behind a firewall using export HTTP_PROXY=proxyout.mydomain.edu:8080 I am behind a firewall, but on my machine there is no proxy server listed under system prefernces-->advanced-->proxies. I can access my machine using a vpn, but don't know how to tell rosetta to do the same. Thanks for all your help in advance and sorry that this is so long winded ;) Cheers, Joe

2 1

Setting phenix_env in ubuntu 10 system
by Jobichen Chacko 01 Jun '11

01 Jun '11

Dear All, I recently downloaded and installed phenix 1.7-1-743 on Ubuntu system. I need to run the command " source/usr/local/phenix**/phenix_env.sh" each time to launch the program when running as a command line. If I close that terminal and type the command in a new terminal, it is giving the reply "command not found". How does one set paths so that phenix.refine will be recognized in a new terminal window? I got some suggestiions to edit either ~/.bashrc or ~/.bash_profile and add the appropriate "source" command to it. But when I edit .bashrc phenix is automatically executed when I open a new terminal. I want to run phenix by typing command like "phenix.refine xx.pdb xx.mtz". Please let me know which file I should edit to get this. If possible can any ubuntu user send me a copy of the .bashrc file/or any other required file with environment path for phenix. Thank you for your time. Jobi

3 2

Autobuild Error
by B. Anand 01 Jun '11

01 Jun '11

Dear All, I am using autobuild to rebuild the model after MR. However, it stops with the following error which am I not able to comprehend. Could you please shed some light on this error. Am using phenix version 1.7.1 (Release tag:743). Thanks. With Best Regards, Anand *************ERROR ENDING ******************* ******************************************************************************** Failed to carry out AutoBuild_multiple_models: ******************************************************************************** Sorry, a subprocess has failed... END OF LOG FILE /home/anand/Autobuild/5/AutoBuild_run_1_/TEMP0/RUN_FILE_1.log : utoBuild Run 1 Tue May 31 01:00:15 2011 Build cycle 1 of 16 method:rebuild Initial rebuild cycle: just combining previous models or copying over initial PDB file Using edited_pdb.pdb for rebuild, copied to unrefined.pdb_1 Refining model: unrefined.pdb_1 No refinement carried out (may need free R flags) Error message from phenix.refine: 'function' object has no attribute 'as_mtz_dataset' Refinement failed... *************ERROR ENDING ******************* ******************************************************************************** Failed to carry out AutoBuild_build_cycle: Initial phenix refinement of AutoBuild_run_1_/edited_pdb.pdb with exptl_fobs_phases_freeR_flags.mtz failed...quitting... /home/anand/Autobuild/5/AutoBuild_run_1_/TEMP0/AutoBuild_run_1_/LAST.LOG may have additional information... 'function' object has no attribute 'as_mtz_dataset' ******************************************************************************** *************ERROR ENDING ******************* ******************************************************************************** *************ERROR ENDING ******************* -- B. Anand, Ph. D. Assistant Professor Department of Biotechnology Indian Institute of Technology Guwahati Guwahati 781039 Assam, India Email: banand(a)iitg.ernet.in anandbasub(a)gmail.com Phone: +91-361-258 2223 Fax: +91-361-258 2249 Web: http://www.iitg.ernet.in/banand/

2 1

Re: [phenixbb] Refining sucrose
by Yuri 01 Jun '11

01 Jun '11

All coot needs to run its real-space refinement is a .cif file as Nigel pointed out. You can also get this file from other ligand library websites (proDrg, hic-cup, etc...). The only catch here is. The name of your sucrose atoms must match, exactly, those in the file. Once you have such file go to the the file drop-down menu and click on Import CIF dictionary in coot. That should enable to rotate the rotatable bonds of your ligand -- Yuri Pompeu

5 5

heavy atoms
by ChenTiantian 01 Jun '11

01 Jun '11

Hi, I am dealing with a complex structure which the ligand contains a atom Iodine, I guess it's because Iodine is heavy atom, the electron density of Iodine turns red after 5 cycles refinement. Anybody coped with similar issue? How to let phenix know that the Iodine atom is part of the ligand? Best, Tiantian -- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Address: Room 101, 646 Songtao Road, Zhangjiang Hi-Tech Park, Pudong New Area, Shanghai, 201203, P.R. China

2 1

Phenix MTZ files,
by Saba Ferdous 154-FAS/BSBI/F05 01 Jun '11

01 Jun '11

Dear Phenix users I am new to Phenix..probably my question might be childish to you. so with appologies, I have predicted protein structure by using modeller, i want to refine my structure but i am unable to know that what is MTZ files n CIF files because i have only my PDB. And i want to fix beta deviations and outliers, bad angles and bad bonds in my structure. kindly help me and suggest me that what can i do to refine my structure. Best Regards -- Saba Ferdous Research Scholar (M. Phil) National Center for Bioinformatics Quaid-e-Azam University, Islamabad Pakistan

2 1

ligand cif file
by ChenTiantian 31 May '11

31 May '11

Hi there, Now I use phenix.elbow to produce the cif file of the ligand instead of using Prodrg. but I find a problem with this cif file, the C=N bond is not right, it becomes C-N in the cif file, so it does not fit the electron density, what should I do to modify the cif file to chage C-N to C=N ? Best Regards, Tiantian -- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Address: Room 101, 646 Songtao Road, Zhangjiang Hi-Tech Park, Pudong New Area, Shanghai, 201203, P.R. China

3 3

mr_rosetta test failure
by Laurie Betts 31 May '11

31 May '11

We installed latest phenix and latest rosetta last week. I ran test script: phenix_regression.wizards.test_command_line_rosetta_quick_tests and got the test failing at the prerefine because of missing shared libraries, as shown below in the FAQ (italics). I tried again in both bash & csh after setting or exporting the environment variables shown below, but got the same exact error. If I do printenv the shell sees the new env var. What should I try next? THanks so much Laurie Betts & CD Poon University of North Carolina *Why does mr_rosetta bomb and say "error while loading shared libraries: libdevel.so: cannot open shared object file: No such file or directory ? This may indicate that somewhere your system is defining the shared libraries that Rosetta needs, and these are for a place that is not where Rosetta expects them to be. You can try to ignore the previous definitions this way: If you are using the bash or sh shells: export PHENIX_TRUST_OTHER_ENV=1 or csh (C-shell): setenv PHENIX_TRUST_OTHER_ENV 1 in the script where you run mr_rosetta, or before you run it from the command line. *

2 1

Re: [phenixbb] strategy suggestion ???
by Michael Thompson 31 May '11

31 May '11

I once used the following strategy to search for ligands when the apo structure had already been determined. I was using Refmac at the time, but I don't see why you couldn't do it with phenix.refine. After you process your data, if your crystals with and without the ligands are isomorphous, then you don't necessarily need to do molecular replacement to get phases. After you process the data from your crystals with the ligands, you can take the mtz file and start refining with the pdb file for your apo structure. You can start with a rigid body refinement to account for any small shifts or rotations that may have taken place when you added the ligand. Then after that refine according to your protocol of choice. The main place you can run into trouble is if you have a polar space group. If you do the rigid body refinement and get a horrible R-factor, the there's a good chance you have indexed the two data sets in opposite orientations. This can be corrected by reindexing, I think the phenix tool for this is xmanip but someone can correct me if I'm wrong. Good luck, Mike ----- Original Message ----- From: "ChenTiantian" <chentiantian2010(a)gmail.com> To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> Sent: Monday, May 30, 2011 6:31:51 PM GMT -08:00 US/Canada Pacific Subject: [phenixbb] strategy suggestion ??? Hi, I just started learning crystallography months ago, and the software I used most is XDS, HKL2000, phenix and coot. Now I am working on a series of datasets-----the same target protein with various ligands. The following is my refinement workflow: 1, Processing data with XDS (or HKL2000 for some of the datasets) 2,Molecule replacement with phaser. 3,Check and modify the structure residue by residue with COOT, 4,phenix.refine with the following command line: phenix.refine protein.1.mtz protein.pdb \ strategy=individual_sites+individual_sites_real_space+individual_adp+tls \ simulated_annealing=true simulated_annealing.start_temperature=1000 \ simulated_annealing.cool_rate=10 main.number_of_macro_cycles=5 \ ordered_solvent=true refinement.input.xray_data.labels="F,SIGF" \ output.prefix=myprotein 5,Fit the ligand and redo step 3&4; stop refining when the Rwork and Rfree looks reasonable. 6,Chage the strategy line to strategy=individual_adp adp.individual.isotropic=all \ to remove the ANISOU lines in pdb file. Any suggestion for this workflow ? or how do you always deal with the similar case ? cause I'm new about this field,maybe I did something stupid. Ps, the value of Rwork and Rfree are too close, like, Final: r_work = 0.1741 r_free = 0.1817 bonds = 0.036 angles = 1.818 Is that reasonable ? -- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Address: Room 101, 646 Songtao Road, Zhangjiang Hi-Tech Park, Pudong New Area, Shanghai, 201203, P.R. China _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles miket(a)chem.ucla.edu

1 0

strategy suggestion ???
by ChenTiantian 31 May '11

31 May '11

Hi, I just started learning crystallography months ago, and the software I used most is XDS, HKL2000, phenix and coot. Now I am working on a series of datasets-----the same target protein with various ligands. The following is my refinement workflow: 1, Processing data with XDS (or HKL2000 for some of the datasets) 2,Molecule replacement with phaser. 3,Check and modify the structure residue by residue with COOT, 4,phenix.refine with the following command line: phenix.refine protein.1.mtz protein.pdb \ strategy=individual_sites+individual_sites_real_space+individual_adp+tls \ simulated_annealing=true simulated_annealing.start_temperature=1000 \ simulated_annealing.cool_rate=10 main.number_of_macro_cycles=5 \ ordered_solvent=true refinement.input.xray_data.labels="F,SIGF" \ output.prefix=myprotein 5,Fit the ligand and redo step 3&4; stop refining when the Rwork and Rfree looks reasonable. 6,Chage the strategy line to strategy=individual_adp adp.individual.isotropic=all \ to remove the ANISOU lines in pdb file. Any suggestion for this workflow ? or how do you always deal with the similar case ? cause I'm new about this field,maybe I did something stupid. Ps, the value of Rwork and Rfree are too close, like, Final: r_work = 0.1741 r_free = 0.1817 bonds = 0.036 angles = 1.818 Is that reasonable ? -- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Address: Room 101, 646 Songtao Road, Zhangjiang Hi-Tech Park, Pudong New Area, Shanghai, 201203, P.R. China

4 3

Inconsistent R-factors in PDB file
by Schubert, Carsten [PRDUS] 30 May '11

30 May '11

Hi, Not sure if this has been asked before but recently I noticed phenix seems to report inconsistent R-values after each refinement. The final values reported in the screen output after refinement match the values reported in the 'Quick Facts' section, but are not matched by the values in the PDB deposition section. Attached is an example: ... REMARK ******************** REFINEMENT SUMMARY: QUICK FACTS ******************* REMARK Start: r_work = 0.1907 r_free = 0.2151 bonds = 0.004 angles = 0.727 REMARK Final: r_work = 0.1838 r_free = 0.2141 bonds = 0.005 angles = 0.832 REMARK ************************************************************************ ... REMARK IF THIS FILE IS FOR PDB DEPOSITION: REMOVE ALL FROM THIS LINE UP. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (phenix.refine: 1.7.1_743) REMARK 3 AUTHORS : Adams,Afonine,Chen,Davis,Echols,Gopal, REMARK 3 : Grosse-Kunstleve,Headd,Hung,Immormino,Ioerger,McCoy, REMARK 3 : McKee,Moriarty,Pai,Read,Richardson,Richardson,Romo, REMARK 3 : Sacchettini,Sauter,Smith,Storoni,Terwilliger,Zwart REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.950 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.113 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.33 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.21 REMARK 3 NUMBER OF REFLECTIONS : 29410 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.1894 REMARK 3 R VALUE (WORKING SET) : 0.1877 REMARK 3 FREE R VALUE : 0.2122 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.74 REMARK 3 FREE R VALUE TEST SET COUNT : 1982 For regular work I really don't care as long as the values are consistent and tell me if the refinement reached convergence, but for a deposition it matters a bit more. So which values should I report for a paper? Cheers, Carsten

2 1

Iterative build composite omit hanging
by José Trincão 30 May '11

30 May '11

Hello, I tried to run an iterative build composite omit for my protein - P1, 1350 residues/monomer, 4 molecules in the A.U.. After about 1.5 weeks running almost all was done except one omit region which was stuck. I had two processes running indefinitely (reduce and python) with no output. I tried to rerun that region alone but it gets stuck also with reduce producing no output. What should I do to get the complete map (I am going to merge all the other regions together, but would like to know why this particular one is problematic). Thanks! Jose José Trincão, PhD CQFB@FCT-UNL 2829-516 Caparica, Portugal "It's very hard to make predictions... especially about the future" - Niels Bohr

2 1

isotropic
by ChenTiantian 30 May '11

30 May '11

-- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Address: Room 101, 646 Songtao Road, Zhangjiang Hi-Tech Park, Pudong New Area, Shanghai, 201203, P.R. China

1 0

sigmaA-weigted 2FoFc maps by only mtz file
by zhangh1＠umbc.edu 27 May '11

27 May '11

Hi, If I only provide a mtz file with Fo, Fc and phase data, and do NOT have the pdb file, can any phenix utility calculate the sigmaA-weigted 2FoFc maps? Thanks! Hailaing

2 6

SA omit map for ligand
by Tjaard Pijning 27 May '11

27 May '11

Hi, I am trying to make an SA-omit Fo-Fc map for a sugar ligand (chain B) bound to protein (structure solved by MR), without doing any rebuilding of protein or ligand – just calculate an Fo-Fc map that I can load into PyMol. So far I used the AutoBuild – Create omit map module with these settings : - input files : model (protein+ligand+waters), data (.mtz), restraints for sugar ligand (.cif) - omit map type : simulated annealing - omit region : omit selection - omit map options : keep input waters, omit chain list : omit_chain_list chainB However, the ligand gets modified even though I use “omit_chain_list chainB”. What are the parameters to set to keep the model (protein, ligand, waters) from being rebuilt ? Furthermore, what is the procedure to load the SA Fo-Fc omit map into pymol ? Phenix version is 1.6.4-486. Thanks in advance, Tjaard Ing. Tjaard Pijning Research Assistant Protein Crystallography Group Nijenborgh 7 9747 AG Groningen The Netherlands (31)(0)50 363 43 85

4 3

get_cc_mtz_pdb results
by Jerome Nwachukwu 27 May '11

27 May '11

Hi: I am using get_cc_mtz_pdb to compare some structural models and found differences in overall CC around ~0.0056 and local CC around 0.0033. How much difference in local and overall CC values between two models is generally considered significant? Thank you, -Jerome Jerome C. Nwachukwu, PhD Dept. of Cancer Biology The Scripps Research Institute-Florida 130 Scripps Way, 2C1 Jupiter, FL 33458

2 2

a new PDB clustering tool available in phenix from nightly build dev-756
by Francois Berenger 26 May '11

26 May '11

Dear Phenix users, Starting from the nightly build dev-756, a new clustering tool called DURANDAL is included in Phenix. It performs exact clustering of proteins in PDB format, fast. It is primarily aimed at people working in protein structure prediction and having to deal with a lot of protein models. The correspondence used to compute CARMSD for a pair of proteins is 1 to 1. If two proteins A and B are to be optimally superposed, both PDB files (A.pdb and B.pdb) must have the same numbers of alpha carbons. The first alpha carbon in A.pdb will be matched to the first alpha carbon in B.pdb, and so on. Clustering up to 20,000 PDB files should work on most machines. Workstations with a lot of memory will be able to cluster even more files. Examples: --------- * to perform exact clustering using a fixed cutoff value of 3.0 Angstroms: durandal.cluster_pdbs -i [file_containing_one_PDB_filename_per_line]\ -d 3.0 -o out -s -v * there is also another tool included, to compute CARMSD of many files versus a reference one (the first in the list is considered the reference): durandal.rank_pdbs [file_containing_one_PDB_filename_per_line] If you want to know more about how the software is working, you can have a look at http://bioinformatics.oxfordjournals.org/content/27/7/939 Don't hesitate to ask if you encounter any problem while using the software. Best regards, Francois Berenger.

1 0

ADP refinement
by Christian Roth 26 May '11

26 May '11

Dear all, I am sorry for this very stupid question, but I probably overlooked the relevant text in the documentation. I requested the refinement of a heavy atom (chloride) with anisotropic ADP. In the log than isotropic refined ADP were set for 0 atoms. I guess I have to define all other chains as isotropic. Is that right. I have a lot of chains, it would be possible but a pain (more than 40 chains). Is there a something like refine anisotropic chain x and all others isotropic? Thanks and best Regards Christian

2 1