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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 23 Oct '09

23 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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