- phenixbb - phenix-online.org

Re: [phenixbb] optimization of wxc and wxu
by Xuewu Zhang 03 Nov '09

03 Nov '09

Hi phenix developers/gurus, I am using the latest night build of phenix on OS X snow leopard. I found that phenix ignores these lines in my custom refinement file: refinement.target_weights.optimize_wxc="True" refinement.target_weights.optimize_wxu="True" Manually setting up the scale factors however works. I am not sure whether this is a bug or a platform related issue. Thanks, Xuewu Zhang

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GUI and X servers
by Leo Sazanov 02 Nov '09

02 Nov '09

Hi, I am accessing our linux server (where phenix sits) via Exceed X server from Windows machine, and everything used to work fine until recent (I think from v.1-5-2) versions of phenix. Now if I launch new GUI, mouse position is not recognised anymore not only by phenix, but then also by other programs - so if I click on something, something else completely gets activated. I did not change any Exceed settings, so the problem seems to be due to phenix. Also, same thing happens with Xming server. If I access from Mac machine, everything seems to be OK. Has anybody seen it and what could be the reason for that? Thanks! -- Dr. Leonid A. Sazanov Research group leader Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-mbu.cam.ac.uk Tel: +44-1223-252910 Fax: +44-1223-252915

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Error message when starting phenix gui
by Folmer Fredslund 30 Oct '09

30 Oct '09

Dear all Should I be concerned about this error message when starting phenix 1.5-2?: Gtk-Message: Failed to load module "canberra-gtk-module": libcanberra-gtk-module.so: cannot open shared object file: No such file or directory Best regards, Folmer Fredslund

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Converting .mtz to xplor or having phenix output to xplor file
by Sam Stampfer 28 Oct '09

28 Oct '09

Hi, This isn't exactly phenix-related but someone might know an easy solution. I'm trying to open an electron density map in pymol. It won't open .mtz files and the .xplor files I generated from ccp4i don't seem to work either. I need to have my density as a .xplor file in order for pymol to open it (I think). How would I generate a .xplor file from .mtz? Or, alternately, how can I set phenix to output a .xplor file? I've had it output to a cns file instead of .mtz but that didn't help me get it in .xplor format. Thanks! -Sam

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external program interference : libwx_gtk2ud-2.8.so.0 not found on ubuntu 64 bit
by hari jayaram 27 Oct '09

27 Oct '09

I just downloaded and installed phenix 1.5.2 . I want to run phenix with the GUI on my 64 ubuntu 8.04 box When I run phenix I get the following error: hari@charlie:~$ phenix Traceback (most recent call last): File "/usr/local/phenix-1.5-2/phenix/wxGUI2/command_line/main.py", line 13, in <module> run(sys.argv[1:]) File "/usr/local/phenix-1.5-2/phenix/wxGUI2/command_line/main.py", line 7, in run from wxGUI2 import App File "/usr/local/phenix-1.5-2/phenix/wxGUI2/__init__.py", line 109, in <module> import wx File "/rawdata12/wx-widgets-read-only/wxPython/wx/__init__.py", line 45, in <module> from wx._core import * File "/rawdata12/wx-widgets-read-only/wxPython/wx/_core.py", line 4, in <module> import _core_ ImportError: libwx_gtk2ud-2.8.so.0: cannot open shared object file: No such file or directory I know that I should not be getting this error because I have wxwidgets and wxpython installed and I have wx working on this machine for other apps. Consequently I do have a libwx_gtk2ud-2.8.so.0 on my LD_LIBRARY_PATH. I tried with and without a libwx_gtk2ud-2.8.so.0 in my LD_LIBRARY_PATH and I still got the same error. Any ideas why phenix GUI does not start? Thanks Hari hari@charlie:~$ which phenix /usr/local/phenix-1.5-2/build/intel-linux-2.6-x86_64/bin/phenix hari@charlie:~$ echo $LD_LIBRARY_PATH /home/hari/ccp4-6.0.99e/lib::/home/hari/ccp4-6.0.99e/extralib

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Command to call/read external file when running phenix.refine from
by Ashley Pike 23 Oct '09

23 Oct '09

Hi, I am running phenix.refine(v.1.5.2) from the command line using a batch file containing all my customised options ie. phenix.refine my_parameters. From this batch file (my_parameters) I also want to include additional geometric and NCS restraints. Rather than have them clutter things up, I want to call/invoke them from an external file instead. I had been told that this is possible using the command 'include file <filename>' but it seems that this is not doing what I had hoped. When run in this way phenix.refine doesn't complain but is not using the restraints. Needless to say everything is fine when I actually include the information directly in the batch file. Any hints what I am doing wrong? Cheers, Ashley

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1.5.2 and validation
by Mark Collins 23 Oct '09

23 Oct '09

Hi I just installed 1.5.2 and tried it out for a few hours this afternoon. Is it possible to run the phenix programs from the command line without being forced to launch the shiney new gui? I have 3 structures I had considered finished by R/Rfree and Molprobity. I was playing around with polygons (great way to quickly assess the structure) and found that 2 of the 3 strucutres are "bad" with very low RMSDs for bonds, angles, chirality, dihedrals and planarity. All were refined with phenix 1.3, but they are all fairly small ~80-90 residues. So do I need to go back and revisit these, advice much appreciated? Also I found that I can edit the validate_0.eff (from phenix/project_data/ ) and run the file from the command line. But is there a way to actually change keys_to_show and fiters for polygon in the gui? Also it seems that the *twinned crashed the validation when run this way (bug reported). Thanks Mark

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The new GUI is really nice!
by Laurie Betts 23 Oct '09

23 Oct '09

I think I initially sent this to the wrong address, sorry. Just wanted to say: I just downloaded the new version of PHENIX (1.5-2) on my Mac; I had a lot of trouble with previous versions using the GUI (but really like the command line driven flexibility), but now playing around with the new one, I think I will become hooked. Thank you all VERY much from all of us phenix-o-philes. Laurie Betts

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new GUI is really nice
by Laurie Betts 22 Oct '09

22 Oct '09

I just downloaded the new version of PHENIX (1.5-2) on my Mac; I had a lot of trouble previously using the GUI (but really like the command line driven flexibility), but now playing around with the new one, I think I will become hooked. Thank you all VERY much from all of us phenix-o-philes. Laurie

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Re: [phenixbb] AutoMR and capsids
by SIPPEL,KATHERINE H 22 Oct '09

22 Oct '09

Dear Randy, > If you're sure that there are 3 full copies (and that you > couldn't, say, have six half-copies sitting on crystallographic > 2-folds), the best would be to search for full capsids. Now, for > each copy there are 60 different ways that the capsid could be > oriented, but the version of Phaser distributed with the latest > Phenix release should recognize the internal symmetry -- let us > know if it doesn't! I'm pretty sure its not actually full copies. The unit cell is 262.9, 262.9, 609.1 with an R32 space group. I'm downloading the latest release at the moment. > If it turns out that a capsid is sitting on a symmetry axis, > Phaser will probably reject it because of an outrageous number of > clashes. In that case, you should turn off the clash test, just > look for one copy, and then examine the overlapped solution to > see which part of the capsid is crystallographically unique. Thanks for the tips on the ASU, I wouldn't have thought of that. > Hi Katherine, > Back when I did this with HBV I had one capsid per > crystallographic AsU and I >used Amore (pre-phaser or phenix). I > searched with the icosohedral ASU >looking for 60 copies, and was > surprised how easily the solution fell out. If >you use this > strategy, you really just need one icos ASU per capsid and you > >can then expand the rest using standard icos symmetry. > I think the answer will be do what's easiest, and if it's 99% ID > it should >fall out pretty easily anyway. Bear in mind that > depending on what you've >done to these capsids the icos ASU's > may have slightly re-oriented (in my case >I had added a drug > that kept the icos ASU identical but had tilted the whole >thing > relative to the plane of the capsid). This may also guide your > strategy. > Good luck, > Christina Our standard protocol is Amore with CNS. When Amore failed I thought I might try something different. I have really enjoyed Phenix for my small proteins and thought that I might take advantage of that lovely NCS feature in phenix.refine. I just wasn't sure how to proceed within the AutoMR program. Obviously in the end I will go with what works. > PS- Isn't Mavis around in Florida somewhere, or are you even in > her lab? She >and Rob are a great resource.... I do work for Rob and Mavis and they are a fabulous resource. Best bosses ever (and no they won't see this, its just the truth). Thanks for the help, Katherine > On Oct 22 2009, SIPPEL,KATHERINE H wrote: > >> Dear all, >> >> I am currently trying to use AutoMR to do molecular replacement >> on an icosahedral virus capsid. It is a T=1 capsid so there are >> 60 copies of the monomer per capsid and based on the Matthews >> coefficient there are ~3 capsids in the unit cell. The search >> model is 99% identical (thank God) but I am unsure how to >> approach this. >> >> Do I used the 60-mer as the model and search for three copies? >> Do I use a monomer for the model and search for 180 copies? >> Should I break the model down to smaller pieces (i.e. a 30-mer >> and copies=6, or 12-mer and copies=15)? >> >> I would appreciate any help I can get on this one. >> >> Thanks, >> >> Katherine >> >> -- >> SIPPEL,KATHERINE H >> Ph. D. candidate >> Department of Biochemistry and Molecular Biology >> College of Medicine >> University of Florida >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >> > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb > > -- SIPPEL,KATHERINE H Ph. D. candidate McKenna Lab Department of Biochemistry and Molecular Biology College of Medicine University of Florida

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Another questions: water for adp and partial occupancy
by Young-Jin Cho 22 Oct '09

22 Oct '09

Hi, I thought we should put water molecules as isotropic and full occupancies. However, I saw different cases. So I am wondering the reasons for putting waters as anisotropic and with partial occupancies in an active sites. Does any one have this kind of experience or can you explain the advantage or disadvante of this types of strategy? Thanks in advance, Young-Jin Cho

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AutoMR and capsids
by SIPPEL,KATHERINE H 22 Oct '09

22 Oct '09

Dear all, I am currently trying to use AutoMR to do molecular replacement on an icosahedral virus capsid. It is a T=1 capsid so there are 60 copies of the monomer per capsid and based on the Matthews coefficient there are ~3 capsids in the unit cell. The search model is 99% identical (thank God) but I am unsure how to approach this. Do I used the 60-mer as the model and search for three copies? Do I use a monomer for the model and search for 180 copies? Should I break the model down to smaller pieces (i.e. a 30-mer and copies=6, or 12-mer and copies=15)? I would appreciate any help I can get on this one. Thanks, Katherine -- SIPPEL,KATHERINE H Ph. D. candidate Department of Biochemistry and Molecular Biology College of Medicine University of Florida

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Partially occupied SO4 and waters
by Chris Waddling 20 Oct '09

20 Oct '09

I have a partially occupied sulfate ion that is refining to 55% along with one of two arginine side chains. Associated with the second conformation of the arginine, there is positive density for three partially occupied waters. In Shelxl, I can use the PART identifier to specify that the sulfate ion and the waters are not present simultaneously and are associated with their respective Arg side chain conformation. Is there a way to do this in Phenix? Thanks, Chris -- Dr. Christopher A. Waddling, Ph.D. University of California at San Francisco

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Re: [phenixbb] Molprobity percentile statistic
by hari jayaram 20 Oct '09

20 Oct '09

Thanks Nat and Pavel for your emails, Thanks for the suggestion of using phenix.polygon. The comparative analysis of my structure relative to others at my resolution was what I was after. And thats the reason I liked the molprobity statistics expressed as percentile since it helped me realize how far I have to go relative to other structures at the PDB. If its not too difficult can I cast my vote to report it inside the phenix GUI. Its just that running the full analysis inside of phenix is significantly faster than running it on the duke webservers. In molprobity If I remember correctly the overall score is some weighted average, and the molprobity paper also cautions against taking it too literally. Also If I remember the molprobity percentiles are absolute and not only composed of structures at similar resolutions . Regardless thanks for the hint about phenix.polygon . I just looked at my phenix.polygon report and I am afraid its a little asymmetric. Hari On Mon, Oct 19, 2009 at 9:58 PM, hari jayaram <harijay(a)gmail.com> wrote: > Thanks Nat and Pavel for your emails, > Thanks for the suggestion of using phenix.polygon. The comparative > analysis of my structure relative to others at my resolution was what > I was after. > > And thats the reason I liked the molprobity statistics expressed as > percentile since it helped me realize how far I have to go relative to > other structures at the PDB. If its not too difficult can I cast my > vote to report it inside the phenix GUI. Its just that running the > full analysis inside of phenix is significantly faster than running it > on the duke webservers. > > In molprobity If I remember correctly the overall score is some > weighted average, and the molprobity paper also cautions against > taking it too literally. Also If I remember the molprobity percentiles > are absolute and not only composed of structures at similar > resolutions . > > Regardless thanks for the hint about phenix.polygon . > I am attaching a snapshot of my polygon ..I an afraid its a little > asymmetric. > > Hari > > On Mon, Oct 19, 2009 at 7:48 PM, Pavel Afonine <PAfonine(a)lbl.gov> wrote: >> Hi Hari, >> >> if you run phenix.model_vs_data you will get those numbers (namely: >> Ramachandran outliers, clashscores, CB-deviations; although you will not >> get "Molprobity score" simply because I don't know what it is and so I >> didn't add it): >> >> phenix.model_vs_data model.pdb data.mtz >> >> Nat: every time time you run model_vs_data for whatever purpose (getting >> fmodel, etc...) you get an object that contains all these numbers. >> >> Pavel. >> >> >> On 10/19/09 3:32 PM, hari jayaram wrote: >>> Hi i just started using the phenix GUI front-end to Molprobity . Its >>> really nice the way it plugs into coot and displays all the statistics >>> etc. >>> Is there any place that it also reports the percentile clashscore and >>> percentile Molprobity score for overall model quality a la the >>> webserver at molprobity.biochem.duke.edu >>> >>> Thanks >>> Hari >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://www.phenix-online.org/mailman/listinfo/phenixbb >>> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >> >

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Molprobity percentile statistic
by hari jayaram 19 Oct '09

19 Oct '09

Hi i just started using the phenix GUI front-end to Molprobity . Its really nice the way it plugs into coot and displays all the statistics etc. Is there any place that it also reports the percentile clashscore and percentile Molprobity score for overall model quality a la the webserver at molprobity.biochem.duke.edu Thanks Hari

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Re: [phenixbb] pseudo-merohedral twinning or pseudo-symmetry?
by Gino Cingolani 16 Oct '09

16 Oct '09

Laurie, I had a similar problem. Scaling statistics in P212121 were OK, and - of course - no twinning was detected ... but nothing made sense during refinement. Looking at the data more carefully I found that if one rescales in P21, the b-angle was stably refined to 90.20 with ~30% better Rsym than in orthorhombic. When running xtriage on the P21 data, I found the data were indeed "pseudomerohedrally-twinned" with twinning fraction ~0.38. Good luck! Gino

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pseudo-merohedral twinning or pseudo-symmetry?
by Laurie Betts 16 Oct '09

16 Oct '09

Hi - We have a data set that seems to process well in primitive orthorhombic. a=80, b=87, c=114. The data has overall Rsymm around 10% to 2.6 Angstrom, where I/sigI > 2, and Chi-squared is around 1.4. Phenix.xtriage shows some pathology in intensity statistics such that the L-test indicates <|L|> = 0.414 and <L^2> = 0.241, with the L-test Z score = 7.334. The Wilson ratio for acentric refls is 1.774. According the xtriage, There were no "pseudomerohedral" twin laws found, and the comments at the end say "As there are no twin laws possible given the crystal symmetry, there could be a number of reasons......" Is it more likely that this is a case of pseudo-symmetry, or would one not expect the intensity statistics to have the values they do in that case. Also, is the absence of twin laws defined by the fact that proper merohedral twinning is not possible for P222 space groups? Still confused, Laurie Betts

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autobuild
by Colin Levy 16 Oct '09

16 Oct '09

Hi, can autobuild be setup to use kicked maps when starting from a molecular replacement model? Thanks Colin

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Re: [phenixbb] grouped occupancy definitions
by Dr. Mark Mayer 15 Oct '09

15 Oct '09

Hi Pavel, I'm digging in docs and list serv but could not find out, and figured you probably know faster. I need to make an occ.params file for some groups of non adjacent side chains which interact with each other, and associated waters. 1) How do I select ACs 2) How do I constrain water occupancies so that their Q + that of coupled protein atomes does not exceed 1. If I match the AC flags for the waters and side chains will this take care of it. e.g. if residues 2 and 21 have coupled ACs and waters 101 and 102 move in when residue 21 is in one of its ACs how would I define below? refinement { refine { occupancies { constrained_group { selection = chain A and resseq 2 selection = chain A and resseq 21 selection = chain W and resseq 101 selection = chain W and resseq 102 } } Thanks !!! -- +++++++++++++++++++++++++++++++++++++++++++++++++++++++ Mark Mayer Ph.D.

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low resolution refinement question
by Peter Grey 15 Oct '09

15 Oct '09

Dear Phenix users, I refine a large complex with three monomers in ASU at very low resolution - 4.5A - and would like to ask two questions. - Could you give some tips about refinement at this resolution other than rigid body refinement - Can TLS and grouped B-factors work at this poor resolution ? - I would really prefer that rigid body refinement will strictly obey the NCS that was found in the molecular replacement solution. I understand constrained NCS does not exist yet in phenix but is there something approximate that can be used in rigid body refinement ? I tried the conventional restrained NCS and the result was just like without restrains. Thank you for your time , Peter.

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Why is CIF monomer data split into individual files?
by Joe Krahn 14 Oct '09

14 Oct '09

Is there a good reason not to merger all monomer data into a single file, similar to PDB's components.cif? My first thought is that it is a performance issue. However, I wrote a simple CIF parser in Tcl, and found that carefully designed regexp processing can index data segments very fast. The entire components.cif takes just a few seconds. (The key is to use a regexp that matches an entire data block, and not tokenize the whole file.) So, I am thinking that a single merged file might be better. With separate files, there is already a need for a list of residues (mon_lib_list.cif) which could just as well be file offsets. So, even if parsing is not so fast, it is not an issue because we already have an index file. One problem with separate files is that it relies on the 3-letter residue name to be unique. With a merged file, a different database key can be used without concern for filename restrictions. The PDB format was originally designed so that HET 3-letter codes only need a file scope, where HETNAM defines the full name of each HET residue in a file. Everyone has been using HET codes the same as standard residues, which has cause the 3-letter codes to become meaningless database keys rather than useful abbreviations. Eventually, we will run out of 3-letter codes, and will have to change. Why not start sooner rather than later? Even now, there are potential conflicts. For example, CCP4 has DNA residues using a lower-case d, which may not provide a unique filename for non-POSIX case-insensitive operating systems. If anyone actually wants a Tcl CIF parser, I can share it. I only wrote it as a simple and efficient way to read CIF files from a CCP4i script. Joe Krahn

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Re: [phenixbb] Autobuild for very elongated models
by Gino Cingolani 14 Oct '09

14 Oct '09

Thanks Tom! Gino ****************************************************************************** Gino Cingolani, Ph.D. Associate Professor Thomas Jefferson University Dept. of Biochemistry & Molecular Biology 233 South 10th Street - Room 826 Philadelphia PA 19107 Office (215) 503 4573 Lab (215) 503 4595 Fax (215) 923 2117 E-mail: gino.cingolani(a)jefferson.edu ****************************************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e conoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120) ---- Original message ---- >Date: Wed, 14 Oct 2009 08:28:09 -0600 >From: Tom Terwilliger <terwilliger(a)lanl.gov> >Subject: Re: [phenixbb] Autobuild for very elongated models >To: Gino.Cingolani(a)jefferson.edu,PHENIX user mailing list <phenixbb(a)phenix-online.org> > >Hi Gino, > >Here is how to specify a mask in phenix.autobuild (see https://www.phenix-online.org/documentation/faqs.htm >#anch68): > >----------------- >How can I specify a mask for density modification in AutoSol/AutoBuild? >If you want to specify a mask, add this command: > >resolve_command_list=" 'model ../../coords.pdb' 'use_model_mask' " >where there are " and ' quotes and coords.pdb is the model to use for >a mask. Note the "../../" because coords.pdb is in your working >directory but when resolve runs the run directory is 2 directories >lower, so relative to that directory your coords.pdb is at "../../ >coords.pdb". You will know it is working if your resolve_xx.log says: >"Using model mask calculated from coordinates" >----------------- >I am not so sure this is the problem, however. I would suggest that >you do a quick composite omit map before refinement on your mr model: >phenix.autobuild data=data.mtz model=MR.1.pdb >composite_omit_type=simple_omit >It is important that this start with you MR unrefined model so that >you have no worries about model bias. This procedure will omit a >region, refine, calculate a 2Fo-Fc map for the omitted region, then >repeat for all other parts of your model and paste them all together >and put it in >AutoBuild_run_1_/OMIT/resolve_composite_map.mtz >which you can use to calculate a map with LABIN="FP=FP PHIB=PHIM >FOM=FOMM" (you need to include the FOM). >If this map shows density for your whole model...you are in great >shape and the problem may indeed be the mask. If it does not...then >the model may not be very close and it may be difficult to proceed. >All the best, >Tom T > >On Oct 14, 2009, at 7:57 AM, Gino Cingolani wrote: > >> Hi Everyone, >> >> I am trying to solve a very elongated structure (~180A-long) formed >> by two long a-helices. I have a good MR solution (Log-Likelihood >> Gain ~168.537 to 3.0A resolution), which refines OK immediately >> after MR (Rfactor/Rfree 46/50%). The electron density has clear side >> chain features and high res data is available to ~2.1A resolution. >> >> Logically, I should be able to plug everything into Autobuild and >> get a good final model (or at least something better than my input >> MR solution). I have tried a million time using different parameters >> and datasets, but Autobuild always breaks up my long helical model >> into short helical bundles, that refine to random Rfree. In other >> words, if my starting MR model is a continuous >> 80aa-long helix, Autobuild fragments it into three helices of ~30aa >> each packed laterally (I see back my initial model if I visualize >> symmetry-related atoms in Coot). >> >> In parallel, I have made the following observation. >> If I use DM to improve my phases, prior to Autobuild, I noticed that >> something similar happens. DM gives great density for less than half >> of my long helix while the rest is flattened. >> If I look at the solvent mask generated by DM, it basically flattens >> half of my elongated model. It seems that at least DM fails to >> generate a solvent mask that makes sense with such an elongated >> structure (by the way, the unit cell is a=25, b=37, c=220 in >> P212121). This problem can be circumvented in DM where >> an outside solvent mask can be inputted, but what about in phenix? >> >> Is it possible that Autobuild is failing because Resolve also makes >> a poor solvent mask? Is there a way to see and/or edit the solvent >> mask generated by Resolve? Or even better, can I input a new solvent >> mask in Autobuild? >> >> Thanks in advance for the feedback! >> >> Gino >> >> >> ****************************************************************************** >> Gino Cingolani, Ph.D. >> Associate Professor >> Thomas Jefferson University >> Dept. of Biochemistry & Molecular Biology >> 233 South 10th Street - Room 826 >> Philadelphia PA 19107 >> Office (215) 503 4573 >> Lab (215) 503 4595 >> Fax (215) 923 2117 >> E-mail: gino.cingolani(a)jefferson.edu >> ****************************************************************************** >> "Nati non foste per viver come bruti, ma per seguir virtute e >> conoscenza" >> ("You were not born to live like brutes, but to follow virtue and >> knowledge") >> Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120) >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb > > >Thomas C. Terwilliger >Mail Stop M888 >Los Alamos National Laboratory >Los Alamos, NM 87545 > >Tel: 505-667-0072 email: terwilliger(a)LANL.gov >Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov >PHENIX web site: http:www.phenix-online.org >ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu >TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB >CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss > > > > >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://www.phenix-online.org/mailman/listinfo/phenixbb

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Autobuild for very elongated models
by Gino Cingolani 14 Oct '09

14 Oct '09

Hi Everyone, I am trying to solve a very elongated structure (~180A-long) formed by two long a-helices. I have a good MR solution (Log-Likelihood Gain ~168.537 to 3.0A resolution), which refines OK immediately after MR (Rfactor/Rfree 46/50%). The electron density has clear side chain features and high res data is available to ~2.1A resolution. Logically, I should be able to plug everything into Autobuild and get a good final model (or at least something better than my input MR solution). I have tried a million time using different parameters and datasets, but Autobuild always breaks up my long helical model into short helical bundles, that refine to random Rfree. In other words, if my starting MR model is a continuous 80aa-long helix, Autobuild fragments it into three helices of ~30aa each packed laterally (I see back my initial model if I visualize symmetry-related atoms in Coot). In parallel, I have made the following observation. If I use DM to improve my phases, prior to Autobuild, I noticed that something similar happens. DM gives great density for less than half of my long helix while the rest is flattened. If I look at the solvent mask generated by DM, it basically flattens half of my elongated model. It seems that at least DM fails to generate a solvent mask that makes sense with such an elongated structure (by the way, the unit cell is a=25, b=37, c=220 in P212121). This problem can be circumvented in DM where an outside solvent mask can be inputted, but what about in phenix? Is it possible that Autobuild is failing because Resolve also makes a poor solvent mask? Is there a way to see and/or edit the solvent mask generated by Resolve? Or even better, can I input a new solvent mask in Autobuild? Thanks in advance for the feedback! Gino ****************************************************************************** Gino Cingolani, Ph.D. Associate Professor Thomas Jefferson University Dept. of Biochemistry & Molecular Biology 233 South 10th Street - Room 826 Philadelphia PA 19107 Office (215) 503 4573 Lab (215) 503 4595 Fax (215) 923 2117 E-mail: gino.cingolani(a)jefferson.edu ****************************************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e conoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120)

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use get_cc_mtz_pdb to calculate the cc between model and map
by 丁玮 13 Oct '09

13 Oct '09

Hi, everyone: When I use get_cc_mtz_pdb to calculate the cc between model and map, two values is output: （1）Overall map correlation: （2）Map correlation in region of model: What is the different between them? Whether the "Map correlation in region of model" is the correlation between model and the density map superimposing on it and the "Overall map correlation" is the correlation between model and the overall density map? Thanks a lot! dream dingding830106(a)sina.com 2009-10-14

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autosol import failed
by Jan Abendroth 13 Oct '09

13 Oct '09

Hi all, I am trying to run Phenix AutoSol on a SAD data set. Sadly enough, it fails on me during reading in the mtz file with the error message below. The same happens with both intensities or amplitudes. phenix version 1.5-2 run through the gui where I read in the mtz file and specified I+, I-, ... Any ideas? Thanks Jan ~~~~~~~~~~~~~ error message: ImportRawData_output_files ImportRawData Run 3 Tue Oct 13 18:14:37 2009 NOTE: Input labels currently restricted to: I(+),SIGI(+),I(-),SIGI(-) Note also: a group of labels needs to be enclosed with quotes Skipping labels I(+) SIGI(+) I(-) SIGI(-) which do not match requested labels **************************************** AutoSol Input failed -- Jan Abendroth deCODE biostructures Seattle / Bainbridge Island WA, USA work: JAbendroth_at_decode.is home: Jan.Abendroth_at_gmail.com

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New GUI, MTZ, multiple data sets
by Graeme Winter 12 Oct '09

12 Oct '09

Hi Folks, I just tried reading an MTZ file full of MAD data (from xia2) with the new GUI, and it seems like you can't read more than one data set from a given file - is this the case? It did correctly find all of the columns that were in there. Reading in scalepack format files, one per wavelength, seemed to work fine. Browse then selecting the same file again didn't seem to work, couldn't find the "add another dataset" button... it of course works just fine from the command-line with the .eff file. Thanks, Graeme

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Re: [phenixbb] Does PHENIX exclude Rfree reflections in maps?
by Thomas C. Terwilliger 12 Oct '09

12 Oct '09

Hi Pavel and Joe, I carried out a test to see if (1) excluding a super-free set completely from automated structure solution affects the results and (2) if the super-free R that results is different from the standard free R obtained with all data and excluding the free set only from refinement. Here are the results: A = structure B, C and D are for the run with a super-free set excluded from all calculations. B and C are work and free R for the reflections included in the calculation. D is the R for the super-free set. E and F are work and free R for the same datasets, run in the same way, but without any super-free set. A B C D E F ---super-free-run---- --standard run-- structure work free super-free work free 1029B 0.31 0.38 0.41 0.29 0.36 1038B 0.22 0.26 0.26 0.24 0.28 1071B 0.28 0.33 0.35 0.26 0.30 rab3a-sad 0.31 0.35 0.38 0.29 0.34 rnase-p 0.28 0.32 0.31 0.28 0.29 calmodulin 0.26 0.27 0.27 0.27 0.29 cobd-sad 0.24 0.26 0.26 0.24 0.28 insulin 0.27 0.30 0.29 0.25 0.26 nsf-n 0.23 0.26 0.26 0.21 0.24 ut-synthase 0.24 0.29 0.28 0.24 0.28 mean 0.26 0.30 0.31 0.26 0.29 Conclusions: (1) super-free is very nearly the same as free in the matched set. (2) leaving out super-free data does not make a lot of difference in these actual cases. (Perhaps it might in worse data sets) (3) so it would be ok to take out super-free set, but it is not necessary. All the best, Tom T >> Hi Pavel and Joe, >> >> I'm glad you put that option in, Pavel. However for model-building it is >> not so straightforward. Normally we are building into density-modified >> maps. Density modification works poorly when a significant set of >> reflections is excluded, so this becomes impractical. We could exclude >> those reflections in the map only, but they will have been used in density >> modification so they are no longer truly free. I don't have a good >> solution for that. >> >> I am guessing that for model-building, the free R is hardly affected, >> compared to refinement against the map, though I haven't tested this. >> >> All the best, >> Tom T >> >>>> Hi Joe, hi Tom, >>>> >>>> until recently, all reflections (work and test) were used in map >>>> calculation. When I added a real-space refinement option to >>>> phenix.refine I spent a day thinking hard about why Rfree was almost >>>> always equal to Rwork after real-space refinement, until I realized >>>> that >>>> I have to exclude test reflections from map calculation, and that fixed >>>> the problem. >>>> >>>> I think it depends on the task: >>>> >>>> - for things like real-space refinement (where the map is heavily used) >>>> or automated model building, the test reflections have to be excluded >>>> from map calculation; >>>> >>>> - for catching a tiny detail (looking at weak ligand density = slight >>>> map use) or fixing a few side chains, all reflections should be used, >>>> since 10% of data put aside may sometime significantly affect map >>>> quality. >>>> >>>> Pavel. >>>> >>>> >>>> On 9/30/09 11:51 AM, Tom Terwilliger wrote: >>>>> Hi Joe, >>>>> In PHENIX R-free reflections are included in your maps. >>>>> All the best, >>>>> Tom T >>>>> >>>>> On Sep 30, 2009, at 12:47 PM, Joe Krahn wrote: >>>>> >>>>>> Does PHENIX exclude R-free reflections when computing maps? IMHO, it >>>>>> is >>>>>> bad to use test reflections in maps, or anywhere else other than >>>>>> computing R-free, but opinions vary. If some people still want test >>>>>> reflections in maps, maybe it could be an option. >>>>>> >>>>>> Thanks, >>>>>> Joe Krahn >>>> _______________________________________________ >>>> phenixbb mailing list >>>> phenixbb(a)phenix-online.org >>>> http://www.phenix-online.org/mailman/listinfo/phenixbb >>>> >> >>

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Re: [phenixbb] FreeR set reduced by half in twin crystal refinement?
by lauren 08 Oct '09

08 Oct '09

Hi all Thanks for all your reply, really helpful Joe wrote, >My first guess is that the R-free set generated in CCP4 is not set to follow twin laws, so you have work and free reflections associated by twinning. However, I would expect PHENIX >to check this. >As for the reduced size, that probably comes from the way the twinned test set is calculated. Maybe it is a bug. Are you using anomalous data? No anomalous >What is the PHENIX version? Peter wrote, >- you have at least n% of free flags, but not more then 2000+epsilon >(typically) >- it follows any possible twin law (not user specified, it follows symmetry of the lattice) After I change the setting "xray_data.r_free_flags.max_free ", and set it up to 5000. xray_data.r_free_flags.fraction=0.05, the results look normal. Final: r_work = 0.1782 r_free = 0.2285 bonds = 0.007 angles = 1.186 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.1807 REMARK 3 R VALUE (WORKING SET) : 0.1782 REMARK 3 FREE R VALUE : 0.2285 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.07 REMARK 3 FREE R VALUE TEST SET COUNT : 2776 Best Regards Lauren

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parallel phaser?
by Francis E Reyes 07 Oct '09

07 Oct '09

Did phaser get OpenMP/parallelized or was I just having a dream? If so, how's it work? Thanks FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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FreeR set reduced by half in twin crystal refinement?
by lauren 07 Oct '09

07 Oct '09

Hi everyone, I have a P31 twin crystal, resolution 2.0, and with twin fraction 0.451. I use phenix.refine to refine the structure and with freeR set to 8%. % phenix.refine data.sca model.pdb twin_law="h,-h-k,-l" xray_data.r_free_flags.generate=True xray_data.r_free_flags.fraction=0.08 Result: Final: r_work = 0.1793 r_free = 0.2258 bonds = 0.011 angles = 1.557 REMARK 3 FREE R VALUE : 0.2258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.67 REMARK 3 FREE R VALUE TEST SET COUNT : 2013 After the refinement, it seems like my freeR set size reduced by half (3.67%). Is it due to the twin effect, or something is wrong with my refinement? And if I use ccp4 program "scalpeak2mtz " to convert the .sca to .mtz and with freeR fraction set to 8%. Then refine it with phenix. % phenix.refine data.mtz model.pdb twin_law="h,-h-k,-l" Final: r_work = 0.1669 r_free = 0.1970 bonds = 0.010 angles = 1.406 REMARK 3 FREE R VALUE : 0.2022 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.80 REMARK 3 FREE R VALUE TEST SET COUNT : 4326 It turns out, my test set is still 8%, and R/Rfree looks even better than the first one. So I am wondering which one is the correct one and why? Thanks! Lauren

3 2

difference map peaks
by RAVINDRA D MAKDE 07 Oct '09

07 Oct '09

Hi everyone, I would like to have commnets from experts on the following issues. I am refining DNA-protein complex at 3 A resolution and my current Rfree is 21.5 % (phenix.refine). 1. I am getting difference map peaks (in Coot) of magnitude less than -5 sigmas (0.24 e/A3) (~10 or more peaks) and equal number of positive peaks of same magnitudes.The positive peaks hardly have 2fo-fc of more than 1.0 sigma level. I presumed this well could be due to bulk solvent or improper mask. Therefore I optimized the mask parameters (by giving option under "General refinement parameters" in phenix.refine GUI). I could get my R free lower as expected but I still got these peaks back. Although I am not absolutely sure, but positive peaks are more in polar pocket of protein and negative peaks are more in non-polar and aromatic pockets. I have PEG, Na acetate in my crystal soup. What these negative peaks represent for? 2. During addition of atoms like Na+, Cl- in map, do one need to careful about of the its coordination valency in surrounding pocket. ? I will be highly thankful to you for the same. Ravi Ravindra D. Makde, PhD Postdoctoral fellow, Tan lab, The Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802 USA

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prime_and_switch, error in input mtz label assignment
by Tatyana Sysoeva 06 Oct '09

06 Oct '09

Dear all, I have a question to your kindest attention. We were trying to run today phenix on distant cluster (phenix-1.3) with next command line *phenix.autobuild data=data.mtz solvent_fraction=0.6 ps_in_rebuild=True \ input_pdb_file=model.pdb maps_only=True* Autobuild failed with these last lines in the Autobuild_run_1_1.log Failed to carry out AutoBuild_multiple_models: *Sorry, subprocess failed...message is: ******************************************************************************** phenix.autobuild \ write_run_directory_to_file=/home/btn1/tn_phenix/refine/final_loops/with_ncs_H/no_wateradd_noH/prime_switch/AutoBuild_run_1_/TEMP0/INFO_FILE_1 Reading effective parameters from /home/btn1/tn_phenix/refine/final_loops/with_ncs_H/no_wateradd_noH/prime_switch/AutoBuild_run_1_/TEMP0/PARAMS_1.eff Sending output to AutoBuild_run_1_/AutoBuild_run_1_1.log ******************************************************************************** Failed to carry out AutoBuild_build_cycle: failure ******************************************************************************** * in Autobuild_run_1_/TEMP0/Autobuild_run_1_/Autobuold_run_1_1.log the failure message is next: *Columns of data in AutoBuild_run_1_/TEMP0/TEMP.mtz: H K L FMODEL PHIFMODEL FP SIGFP 2FOFCWT PH2FOFCWT child process stderr output: command: 'AutoBuild_run_1_/TEMP0/temporary.com' resolve_giant: Error in label assignments Failed to run resolve ---------------------------------- TRIED resolve_giant ...but not OK ******************************************************************************** Failed to carry out AutoBuild_build_cycle: failure ******************************************************************************** * There are temporary.com and temporary.com.bak in the folder and there is only difference, except that in temporary.com there is "labin FP=FP FC=FMODEL PHIC=PH2FOFCWT FWT=2FOFCWT" in temporary.com.bak there is "labin FP=FP FC=FMODEL PHIC=PHI2FOFCWT FWT=2FOFCWT" Prime_and_switch.log file ends with *Reading SG information from TEMP.mtz Space group name: P21212 Point group: 222 Space group number : 18 Symmetry operators: 4 Number of columns: 9 H K L FMODEL PHIFMODEL FP SIGFP 2FOFCWT PH2FOFCWT *** Warning From LRASSN : User input label PHI2FOFCWT does not match any file label  resolve_giant: Error in label assignments </pre>   </html> * I checked created TEMP.mtz, it looks like: * Column Labels : H K L FMODEL PHIFMODEL FP SIGFP 2FOFCWT PH2FOFCWT So the question is next: Why is prime_and_switch process looking for the "right" labels (PH2FOFCWT), which are present in previously created TEMP.mtz file, but sees them wrong (PHI2FOFCWT)? Is this possible that we have somewhat wrong inputs or is there problem with the set of commands? Sincerely, Tanya * *

2 1

log file
by Young-Jin Cho 06 Oct '09

06 Oct '09

Hi, While I refining I found the following is included in the .log file. I am using different pdb files. When I looked up residue number 175, it looked ok to me. Do you guys have any idea how to deal with this? Conformer: "C" Number of residues, atoms: 175, 1321 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 14, 'TRANS': 159, 'PCIS': 1} Chain breaks: 24 Unresolved chain link angles: 14 Unresolved chain link dihedrals: 28 Unresolved chain link planarities: 14 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 1313 Thanks in advance, Young-Jin

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PHENIX 1.5 and exploding residues
by Antony Oliver 06 Oct '09

06 Oct '09

Dear all, I am currently refining a structure using PHENIX 1.5-3 and have encountered some problems with "exploding residues". I have attached a image (small PNG file) highlighting the problem. Has anyone had a similar experience? Or know the solution to the problem? Change weighting in favour of geometry ? Many thanks, Tony Oliver . The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.

4 4

question about constrain ncs
by crystallogrphy 06 Oct '09

06 Oct '09

Hi, I am refining a 3.6A data set. There are 5 monomers per asymetric unit. I am considering to use constrained NCS to increase the ratio of reflection/parameter. Does phenix.refine has a script to put contrained ncs or I just use simple_ncs_from_pdb to determine the best NCS?

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Latest phenix from command line
by Graeme Winter 05 Oct '09

05 Oct '09

Hi Folks, I'm one of those people who use the command-line for everything, and I just found my "phenix mad spell" phenix.autosol sites=8 atom_type=Se infl.data=TS03_12287_free.mtz \ infl.f_prime=-9.9 infl.f_double_prime=3.9 low.data=TS03_12287_free.mtz \ low.f_prime=-3.3 low.f_double_prime=0.5 \ infl.labels='F_INFL SIGF_INFL DANO_INFL SIGDANO_INFL' \ low.labels='F_LREM SIGF_LREM DANO_LREM SIGDANO_LREM' no longer appears to work: Traceback (most recent call last): File "/dls_sw/apps/phenix/1.5-2c/phenix-1.5-2/phenix/phenix/command_line/autosol.py", line 585, in <module> run_autosol=run_autosol(args=sys.argv[1:]) File "/dls_sw/apps/phenix/1.5-2c/phenix-1.5-2/phenix/phenix/autosol/wizard_command_line.py", line 300, in __init__ self.Sorry(line) File "/dls_sw/apps/phenix/1.5-2c/phenix-1.5-2/phenix/phenix/autosol/wizard_command_line.py", line 1238, in Sorry raise AssertionError,e AssertionError: Sorry, unknown file or keyword: infl.data=TS03_12287_free.mtz Possibilities... (use 'phenix.autosol --help all' to get full help): general.data_quality=TS03_12287_free.mtz data=TS03_12287_free.mtz Looked at the doc and saw: MAD dataset The inputs for a MAD dataset need to specify f_prime and f_double_prime for each wavelength. You can use a parameters file "mad.eff" to input MAD data. You run it with "phenix.autosol mad.eff". Here is an example of a parameters file for a MAD dataset. You can set many additional parameters as well (see the list at the end of this document). autosol { seq_file = seq.dat sites = 2 atom_type = Se wavelength { data = peak.sca lambda = .9798 f_prime = -8.0 f_double_prime = 4.5 } wavelength { data = inf.sca lambda = .9792 f_prime = -9.0 f_double_prime = 1.5 } So I make mad.eff from information above, then -bash-3.2$ phenix.autosol mad.eff Traceback (most recent call last): File "/dls_sw/apps/phenix/1.5-2c/phenix-1.5-2/phenix/phenix/command_line/autosol.py", line 585, in <module> run_autosol=run_autosol(args=sys.argv[1:]) File "/dls_sw/apps/phenix/1.5-2c/phenix-1.5-2/phenix/phenix/autosol/wizard_command_line.py", line 155, in __init__ self.process_wizard_params(args) File "/dls_sw/apps/phenix/1.5-2c/phenix-1.5-2/phenix/phenix/command_line/autosol.py", line 562, in process_wizard_params self.Sorry("Unrecognized file or keyword: "+str(arg)) File "/dls_sw/apps/phenix/1.5-2c/phenix-1.5-2/phenix/phenix/autosol/wizard_command_line.py", line 1238, in Sorry raise AssertionError,e AssertionError: Unrecognized file or keyword: mad.eff As listed in the instructions. Any clues, anyone? Many thanks in advance, Graeme

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PHENIX parallel computing?
by Joe Krahn 03 Oct '09

03 Oct '09

A parallel version of PHENIX was discussed before. I know that parallelization of refinement is difficult, and probably not worth the effort when there is still a lot of function/methods work. However, running parallel independent tasks could pay off without a lot of work. For example, optimization of WXU and WXC can spawn multiple tasks with different test weights. Annealing tasks could also run multiple jobs, and pick the best result, or even merge results based on real-space fit analysis. Joe Krahn

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Does PHENIX exclude Rfree reflections in maps?
by Joe Krahn 02 Oct '09

02 Oct '09

Does PHENIX exclude R-free reflections when computing maps? IMHO, it is bad to use test reflections in maps, or anywhere else other than computing R-free, but opinions vary. If some people still want test reflections in maps, maybe it could be an option. Thanks, Joe Krahn

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installing phenix 1.5-2
by Tirumala Kumar Chowdary 02 Oct '09

02 Oct '09

Hi, My 1.5-2 build installation is failing with this error 'installing binary components making directory build-binary/intel-linux-2.6-x86_64/beryl/tmp/binary gzip: /nfs/home/chowdary/Download/phenix-installer-1.5-2/bundles/bundle-1.5-2-intel-linux-2.6-x86_64.tar.gz: invalid compressed data--format violated finding installed versions finding binary versions cat: build/intel-linux-2.6-x86_64/version: No such file or directory no pre-existing binary components detected installing new binary package configuring PHENIX components Error configuring: see /nfs/home/chowdary/Download/phenix-installer-1.5-2/build-binary/intel-linux-2.6-x86_64/beryl/log/binary.log for details' and the log file shows this error. /bin/tar: Unexpected EOF in archive /bin/tar: Unexpected EOF in archive /bin/tar: Error is not recoverable: exiting now /nfs/home/chowdary/Download/phenix-installer-1.5-2/bin/install-from-binary: line 349: /nfs/home/chowdary/phenix/phenix-1.5-2/build/intel-linux-2.6-x86_64/base/bin/python: No such file or directory. Earlier builds (1.4.175) are installing and running fine on the same machine. Help please.. Tirumal

2 1

RESOLVE question
by Peter Grey 01 Oct '09

01 Oct '09

Hello, We use iterative cycles of manual building (coot) - refinement (phenix) - density modification to improve maps for the next building step (RESOLVE). Should we use FMODEL,PHIFMODEL from phenix or FCALC,PHIFCALC in the input to RESOLVE. MODEL structure factors are closer to experimental ones but are they better for density modification purposes ? I think that if the program uses , as in DM, only Fobs and phases to calculate the maps then PHIFCALC is better (no contribution of solvent) but if the programs calculates 2Fo-Fc maps then FMODEL,PHIFMODEL is better since it was shown that these maps are beter when bulk solvent correction is used. Could you please comment whether this reasoning is correct and give information as to which is the case in resolve. Thanks, -- Peter

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Re: [phenixbb] refining sugars
by Jose M Casasnovas 01 Oct '09

01 Oct '09

Dear Ralf. I just solved the problem with the sugar refinement. Somehow the way the BETA1-4 cif defines the link is in the reverse order to the NAG-ASN cif link (at least to way I was used to do it). In the NAG-ASN cif, residue_selection_1 in the phenix.refine input must be the NAG and residue_selection_2 the ASN, such as I was used to do in CNS. However, the BETA1-4 cifs follows the opposite way: residue_selection_1 must be the first sugar residue (linked through O4) and residue_selection_2 the second sugar (linked through the C1), which is the most distant residue to the Asn. Thanks so much for your help and to all who sent comments and suggestions. Jose M Casasnovas -- Centro Nacional de Biotecnología (lab. B16) CSIC, Campus UAM Darwin 3 28049 Madrid Spain Ph. 34 915854917(8) Fax. 34 915854506 email: jcasasnovas(a)cnb.csic.es

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Re: [phenixbb] refining sugars
by Engin Ozkan 30 Sep '09

30 Sep '09

I just answered Jose's question on this yesterday. The reason you are having trouble is that there is no NAG-NAG link. It is a BETA1-4. Read the post to see what data_link names are allowed, and use them for your sugars. Below is a copy-paste of my post from yesterday: >That's because there is no such data link as NAG-NAG-B-D. Instead, you >should use a BETA1-4 link. This is similar to what CNS used, if you are >familiar with that (I think it was B14 in CNS). >If you want to know where all the phenix link definitions are, type > >phenix.where_mon_lib_list_cif > >and read the file that's listed. > >It is good to read this to know which residue selection is selection_1 >and which is selection_2. In it you'll see this or something like this. > >data_link_BETA1-4 ># >loop_ >_chem_link_bond.link_id >_chem_link_bond.atom_1_comp_id >_chem_link_bond.atom_id_1 >_chem_link_bond.atom_2_comp_id >_chem_link_bond.atom_id_2 >_chem_link_bond.type >_chem_link_bond.value_dist >_chem_link_bond.value_dist_esd > BETA1-4 1 O4 2 C1 single 1.439 0.020 >loop_ >_chem_link_angle.link_id >_chem_link_angle.atom_1_comp_id >_chem_link_angle.atom_id_1 >_chem_link_angle.atom_2_comp_id >_chem_link_angle.atom_id_2 >_chem_link_angle.atom_3_comp_id >_chem_link_angle.atom_id_3 >_chem_link_angle.value_angle >_chem_link_angle.value_angle_esd > BETA1-4 1 C4 1 O4 2 C1 108.700 3.000 > BETA1-4 1 O4 2 C1 2 O5 112.300 3.000 > BETA1-4 1 O4 2 C1 2 C2 109.470 3.000 > BETA1-4 1 O4 2 C1 2 H1 109.470 3.000 >loop_ >_chem_link_tor.link_id >_chem_link_tor.id >_chem_link_tor.atom_1_comp_id >_chem_link_tor.atom_id_1 >_chem_link_tor.atom_2_comp_id >_chem_link_tor.atom_id_2 >_chem_link_tor.atom_3_comp_id >_chem_link_tor.atom_id_3 >_chem_link_tor.atom_4_comp_id >_chem_link_tor.atom_id_4 >_chem_link_tor.value_angle >_chem_link_tor.value_angle_esd >_chem_link_tor.period > BETA1-4 BETA_1 1 O4 2 C1 2 C2 2 C3 0.00 20.0 1 > BETA1-4 BETA_2 1 C4 1 O4 2 C1 2 C2 0.00 20.0 1 > BETA1-4 BETA_3 1 C3 1 C4 1 O4 2 C1 0.00 20.0 1 >loop_ >_chem_link_chir.link_id >_chem_link_chir.atom_centre_comp_id >_chem_link_chir.atom_id_centre >_chem_link_chir.atom_1_comp_id >_chem_link_chir.atom_id_1 >_chem_link_chir.atom_2_comp_id >_chem_link_chir.atom_id_2 >_chem_link_chir.atom_3_comp_id >_chem_link_chir.atom_id_3 >_chem_link_chir.volume_sign > BETA1-4 2 C1 1 O4 2 O5 2 C2 positiv > >Engin On 9/30/09 10:56 AM, Tirumala Kumar Chowdary wrote: > Thanks for the reply, > > here is part of the log file, which shows the parameter input for nag > refinement > > > Monomer Library directory: > "/usr/local/phenix/phenix-1.4-125/chem_data/mon_lib" > Total number of atoms: 6260 > apply_cif_link: > data_link: NAG-ASN > mod_id_1: DEL-O1 > mod_id_2: DEL-HD22 > residue_selection_1: chain C and resname NAG and resid 1670 > residue_selection_2: chain A and resname ASN and resid 670 > apply_cif_link: > data_link: NAG-ASN > mod_id_1: DEL-O1 > mod_id_2: DEL-HD22 > residue_selection_1: chain C and resname NAG and resid 1784 > residue_selection_2: chain A and resname ASN and resid 784 > apply_cif_link: > data_link: NAG-NAG > residue_selection_1: chain C and resname NAG and resid 1784 > residue_selection_2: chain C and resname NAG and resid 1785 > Number of models: 1 > Model: "" > Number of chains: 3 > Chain: "A" > Number of atoms: 5125 > Number of conformers: 1 > Conformer: "" > Number of residues, atoms: 681, 5125 > > I am presuming that it read what ever it needs to make the ASN-NAG > bonds and NAG-NAG bonds. > > what am I missing here ? > > Tirumal > > > Quoting Engin Ozkan<eozkan(a)stanford.edu>: > >> You don't need to create cif files; phenix has them. NAG is definitely >> there, and you can have two NAGs linked by any biologically-relevant >> glycosidic bond you want. You need to define the links, however. I think >> posting the cif_link.params may get you more help. >> >> Engin >> >> On 9/30/09 8:49 AM, Tirumala Kumar Chowdary wrote: >>> Hi, >>> >>> My question is related to the 'refining sugars in phenix' questions >>> that have been appearing on the bb for the last two days. >>> >>> I am trying to refine my NAGs and somehow phenix is ignoring the sugars >>> in my structure. Neither it is making a bond between my ASN and NAG nor >>> NAG-NAG bond. My nag-nag.cif and cif_link.params are read properly, >>> though. >>> >>> I am using in version 1.4.125 still. Is this the problem ? Does >>> upgrading to any of the later build will help ? >>> >>> >>> Tirumal >>> >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://www.phenix-online.org/mailman/listinfo/phenixbb >>> >> >> >> -- >> Engin Özkan >> Post-doctoral Scholar >> Howard Hughes Medical Institute >> Dept of Molecular and Cellular Physiology >> 279 Campus Drive, Beckman Center B173 >> Stanford School of Medicine >> Stanford, CA 94305 >> ph: (650)-498-7111 >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >> > > > -- Engin Özkan Post-doctoral Scholar Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 ph: (650)-498-7111

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GUI fonts
by Frank von Delft 30 Sep '09

30 Sep '09

Hi, I've just been poking around the new GUIs - neat!! But the font is absolutely enormous, which is terrifically annoying. Where do I change it? (I didn't see it in the preferences.) Cheers phx

2 2

refining sugars
by Tirumala Kumar Chowdary 30 Sep '09

30 Sep '09

Hi, My question is related to the 'refining sugars in phenix' questions that have been appearing on the bb for the last two days. I am trying to refine my NAGs and somehow phenix is ignoring the sugars in my structure. Neither it is making a bond between my ASN and NAG nor NAG-NAG bond. My nag-nag.cif and cif_link.params are read properly, though. I am using in version 1.4.125 still. Is this the problem ? Does upgrading to any of the later build will help ? Tirumal

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N-linked glycans in phenix.refine
by Jose Casasnovas 30 Sep '09

30 Sep '09

Dear Phenix users. I am trying to refine N-linked glycans in phenix. The Asn-NAG link appears to be recognize by the program, but the NAG-NAG link is not. I guess the cif_link must be missing. Monomer Library directory: "/home/soft/phenix/phenix-1.4-3/ext_ref_files/mon_lib" Total number of atoms: 8947 apply_cif_link: data_link: NAG-ASN mod_id_1: DEL-O1 mod_id_2: DEL-HD22 residue_selection_1: chain N and resname NAG and resid 5161 residue_selection_2: chain E and resname ASN and resid 516 apply_cif_link: data_link: NAG-NAG-B-D Sorry: Missing CIF link: data_link_NAG-NAG-B-D Please check for spelling errors or specify the file name with the link as an additional argument. How can I get the required cif_link file and where to place it?? Any suggestion. Thanks. Jose

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Phenix version 1.5 Released
by Paul Adams 29 Sep '09

29 Sep '09

The Phenix developers are pleased to announce that version 1.5 of Phenix is now available. Binary installers for Linux, and Mac OSX platforms are available at the download site: http://phenix-online.org/download/ Just some of the new features in this version (1.5-2) are: - A new Graphical User Interface (accessed by typing phenix at the command line) - Two-way communication with Coot - The latest version of Phaser (2.2) - A development version of torsion angle dynamics available in phenix.refine - Real space refinement in phenix.refine - New GUIs for Autosol, AutoBuild and LigandFit wizards - A number of MolProbity and other validation tools now available - Fast loop building with phenix.fit_loops - Improved ligand geometry generation with phenix.elbow - Inclusion of Nicholas Sauter's LABELIT system for autoindexing and more For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Acting Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Patty Jimenez [ PAJimenez(a)lbl.gov ] [ 1-510-486-7963 ] --

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anomalous difference map demonstration in pymol
by crystallogrphy 29 Sep '09

29 Sep '09

Hi, I have used anomalous data to do refinement. The crystal diffracts to 3.5A. The resulting mtz file shows good anomalous density around the heavy atoms. Now I want to demonstrate the density in Pymol. Does anyone know how to generate the map use the map file in MTZ format in Pymol? Thanks!

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transfering R-free flags
by Tirumala Kumar Chowdary 28 Sep '09

28 Sep '09

Hi, I am trying to refine my model against a higher resolution file. I want to transfer my R-free flags generated by phenix.refine from the lower resolution mtz to the higher resolution file. Is there a way to transfer the R-free flags in Phenix ? If not, where can I find the mtz file from my earlier refinement with R-free flags generated ? Does phenix.refine generate this file and save it for me somewhere ? Thanks Tirumal

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NCS restraints with TLS
by Joe Krahn 28 Sep '09

28 Sep '09

I am using NCS restraints with TLS. It seems that the NCS B-factor restraints are applied to the overall B-factor, rather than just the non-TLS part. Is this correct? In my structure, the disorder varies quite a bit among equivalent molecules, and I don't get good results unless the b_factor_weight is about 1e-3 or less. I am experimenting with NCS restraints in CNS, where each pair of coordinates allows an LSQ fit of B-factor scale and offset to be excluded from the B restraints. It would probably work even better with TLS, which CNS does not have. I don't know if anyone has tried this, but I think that overall molecular B-factor differences are fairly common. Joe Krahn

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NCS averaged maps?
by Francis E Reyes 26 Sep '09

26 Sep '09

With all the recent talk about kicked and filled maps, can we have phenix output an ncs averaged map for those of us who have NCS? Thanks FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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