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Re: [phenixbb] unknown space group problems
by Banumathi Sankaran 02 Mar '06

02 Mar '06

can u send me the drs phone number pa Tom, If this lady does indeed send you the data, Would you be so kind to run the latest version of xtriage on it to see wheter or not tyhe spacegroup is correct? Thomas C. Terwilliger wrote: >Hi Angela, > >I think the solution to the first problem is to index your data in the >space group H3 instead of R3 (the hexagonal setting of R3 rather than the >rhombohedral setting). This is the convention these days in many >programs, including in the AutoSol wizard. > >The second problem I'm a little less clear on. Can you send me some output >where this happens (or if you like, a tar file with the data) and I'll >have a look at it? >Regards, >Tom T > > > > >>I am trying to sovle MAD data using the PHENIX software. I am using the >>AutoSol >>wizard. My data is integrated in R3. Phenix keeps spitting out the error >>that >>this space group is either unknown or the cell dimensions are >>inappropriate to >>the space group (the are a=b=c=159 and alpha=beta=gamma=109). Is there a >>glitch >>with thi space group or am I doing something wrong. Phaser tends to have >>the >>same problem with this space group and I can not seem to get around it. >> >>If I provide data in a different space group I can get past this problem >>only to >>be confronted with another problem regarding the column labels in my mtz >>files. >>I have six data sets collected. Two for each of three different >>wavelengths. >>Each of the two for a single wavelength is scaled seperately and then >>merged >>together using ccp4. I have taken a lot of effort to make sure that the >>column >>labels do not repeat in these files, yet I continually get column label >>errors >>when I run three mtz files in the AutoSol wizard (one mtz file for each >>wavelength). I am getting the same errors in ccp4 as well. There must be >>something basic that I am doing wrong with regards to processing my data >>and >>merging the mtzs together. >> >>Thanks you for your help. >>Angela >> >>_______________________________________________ >>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 > > _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://www.phenix-online.org/mailman/listinfo/phenixbb

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Re: [phenixbb] unknown space group problems
by Banumathi Sankaran 02 Mar '06

02 Mar '06

I am sorry i sent my previous mail by mistake Banu Tom, If this lady does indeed send you the data, Would you be so kind to run the latest version of xtriage on it to see wheter or not tyhe spacegroup is correct? Thomas C. Terwilliger wrote: >Hi Angela, > >I think the solution to the first problem is to index your data in the >space group H3 instead of R3 (the hexagonal setting of R3 rather than the >rhombohedral setting). This is the convention these days in many >programs, including in the AutoSol wizard. > >The second problem I'm a little less clear on. Can you send me some output >where this happens (or if you like, a tar file with the data) and I'll >have a look at it? >Regards, >Tom T > > > > >>I am trying to sovle MAD data using the PHENIX software. I am using the >>AutoSol >>wizard. My data is integrated in R3. Phenix keeps spitting out the error >>that >>this space group is either unknown or the cell dimensions are >>inappropriate to >>the space group (the are a=b=c=159 and alpha=beta=gamma=109). Is there a >>glitch >>with thi space group or am I doing something wrong. Phaser tends to have >>the >>same problem with this space group and I can not seem to get around it. >> >>If I provide data in a different space group I can get past this problem >>only to >>be confronted with another problem regarding the column labels in my mtz >>files. >>I have six data sets collected. Two for each of three different >>wavelengths. >>Each of the two for a single wavelength is scaled seperately and then >>merged >>together using ccp4. I have taken a lot of effort to make sure that the >>column >>labels do not repeat in these files, yet I continually get column label >>errors >>when I run three mtz files in the AutoSol wizard (one mtz file for each >>wavelength). I am getting the same errors in ccp4 as well. There must be >>something basic that I am doing wrong with regards to processing my data >>and >>merging the mtzs together. >> >>Thanks you for your help. >>Angela >> >>_______________________________________________ >>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 > > _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://www.phenix-online.org/mailman/listinfo/phenixbb

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unknown space group problems
by Angela Hoffort 01 Mar '06

01 Mar '06

I am trying to sovle MAD data using the PHENIX software. I am using the AutoSol wizard. My data is integrated in R3. Phenix keeps spitting out the error that this space group is either unknown or the cell dimensions are inappropriate to the space group (the are a=b=c=159 and alpha=beta=gamma=109). Is there a glitch with thi space group or am I doing something wrong. Phaser tends to have the same problem with this space group and I can not seem to get around it. If I provide data in a different space group I can get past this problem only to be confronted with another problem regarding the column labels in my mtz files. I have six data sets collected. Two for each of three different wavelengths. Each of the two for a single wavelength is scaled seperately and then merged together using ccp4. I have taken a lot of effort to make sure that the column labels do not repeat in these files, yet I continually get column label errors when I run three mtz files in the AutoSol wizard (one mtz file for each wavelength). I am getting the same errors in ccp4 as well. There must be something basic that I am doing wrong with regards to processing my data and merging the mtzs together. Thanks you for your help. Angela

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installing phenix
by Kielkopf, Clara L. 10 Feb '06

10 Feb '06

I'm a linux novice installing Phenix on our linux boxes, running Fedora Core 3 in the bash shell. THe install script runs without error, and the new phenix-1.1a directory is created in /usr/local. However, I have to switch to csh before running the program. Even after setting the environmental variables correctly, the program wouldn't run in the bash shell. Is there a simple modification to run in bash? Thank you.

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Problems in installation Phenix1.1a on Linux redhat F4
by Cheng Luo, Ph.D. 06 Jan '06

06 Jan '06

Dear Phenix users, I am a new user of phenix. When I install it in a new machine installed Linux F4, I meet a problem in gtk. I paste the information( the reported err is in red words). " generating PHENIX environment setup script creating /marmor9/pub/bin/phenix-1.1a/phenix_env generating libtbx environment additions creating $PHENIX_BUILD/dispatcher_include_phenix.sh setting environment configuring PHENIX components /marmor9/pub/bin/phenix-1.1a/build/intel-linux/python/bin/gtk-query-immodules-2.0: error while loading shared libraries: /marmor9/pub/bin/phenix-1.1a/build/intel-linux/python/lib/libgdk-x11-2.0.so.0: cannot restore segment prot after reloc: Permission denied generating gdk-pixbuf.loaders file" .....other is ok After installation, i source the env and run with phenix command, it told me these errors: File "/marmor9/pub/bin/phenix-1.1a/phenix/wxGUI/wxPhenix.py", line 11, in ? from wxPython.wx import * File "/marmor9/pub/bin/phenix-1.1a/build/intel-linux/python/lib/python2.4/site-packages/wx-2.5.3-gtk2-ansi/wxPython/__init__.py", line 10, in ? import _wx File "/marmor9/pub/bin/phenix-1.1a/build/intel-linux/python/lib/python2.4/site-packages/wx-2.5.3-gtk2-ansi/wxPython/_wx.py", line 3, in ? from _core import * File "/marmor9/pub/bin/phenix-1.1a/build/intel-linux/python/lib/python2.4/site-packages/wx-2.5.3-gtk2-ansi/wxPython/_core.py", line 15, in ? import wx._core File "/marmor9/pub/bin/phenix-1.1a/build/intel-linux/python/lib/python2.4/site-packages/wx-2.5.3-gtk2-ansi/wx/__init__.py", line 42, in ? from wx._core import * File "/marmor9/pub/bin/phenix-1.1a/build/intel-linux/python/lib/python2.4/site-packages/wx-2.5.3-gtk2-ansi/wx/_core.py", line 4, in ? import _core_ ImportError: /marmor9/pub/bin/phenix-1.1a/build/intel-linux/python/lib/libgdk-x11-2.0.so.0: cannot restore segment prot after reloc: Permission denied Then I share this disk and source and run in another machine install red-hat 9, it did work. So maybe some library configurations are different, but since I have no too much experience about it. Is it possible for your expert give me some suggestion? Thank you in advance for your any suggestions! Best regards, Cheng Luo, Ph.D. Cheng Luo, Ph.D. Marmorstein's Lab Room 327,3601 Spruce StreetThe Wistar Institute PA(19104) USA Tel:215-898-2304 2006-01-06

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test
by Paul Adams 14 Aug '05

14 Aug '05

-- ========================================================== | Paul Adams | | Staff Scientist, Physical Biosciences Division | | Head, Berkeley Center for Structural Biology | | Deputy PI, Berkeley Structural Genomics Center | |--------------------------------------------------------| | Building 64, Room 248 | Lawrence Berkeley Laboratory, | | Tel: 510-486-4225 | 1 Cyclotron Road, | | FAX: 510-486-5909 | BLDG 64R0121, | | mailto:[email protected] | Berkeley, CA 94720, USA. | ==========================================================

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