- phenixbb - phenix-online.org

low resolution, high B, low R
by gerwald jogl 03 Nov '09

03 Nov '09

Hi All, I am working on a 4.2 A structure and feel somewhat uneasy about my refinement results. First, my R/Rfree at the moment is 0.18/0.25. The refinement is not complete and weights are not optimized, so the gap may get smaller. It's just that at 4.2 A, I don't quite expect such low R factors... There is nothing funny with the data, no messing around, no conversions - straightforward data set and a basic rigid body, individual_sites+group_adps, simulated annealing, no tls yet, no ncs. I am aware that one possible answer is that phenix is just really good... The other issue is about B factors. Phenix will happily refine B factors to values of 300 if there is no density in the region and that brings up the question about how to deal with disordered regions in general. Are there any current opinions out there about what would constitute 'reasonable' B factors? Conversely, when would a B factor indicate that it is better to remove the residue from the model instead of leaving it and calling it disordered. Also, this is after group_adp at 4.2 A - should I maybe take this as an indication that this is asking too much from the data and go back to a single adp per chain and tls? All comments are appreciated. Thanks! Gerwald

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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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