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Re: [phenixbb] phenixbb Digest, Vol 48, Issue 2
by Xuewu Zhang 03 Nov '09

03 Nov '09

You are right. It started in the 2nd macro cycle. I should have been a little more patient. Sorry about it. Thanks, Xuewu On Tue, Nov 3, 2009 at 2:00 PM, <phenixbb-request(a)phenix-online.org> wrote: > Send phenixbb mailing list submissions to > phenixbb(a)phenix-online.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.phenix-online.org/mailman/listinfo/phenixbb > or, via email, send a message with subject or body 'help' to > phenixbb-request(a)phenix-online.org > > You can reach the person managing the list at > phenixbb-owner(a)phenix-online.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of phenixbb digest..." > > > Today's Topics: > > 1. Re: optimization of wxc and wxu (Xuewu Zhang) > 2. Re: optimization of wxc and wxu (Pavel Afonine) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 3 Nov 2009 08:28:58 -0600 > From: Xuewu Zhang <xuewu.zhang(a)gmail.com> > Subject: Re: [phenixbb] optimization of wxc and wxu > To: phenixbb(a)phenix-online.org > Message-ID: > <926abad50911030628h31d09c53m59c2c84f1d024596(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > 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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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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