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Re: [phenixbb] bug? iotbx.reflection_statistics apparent
by Ralf W. Grosse-Kunstleve 06 Mar '06

06 Mar '06

> I tried supplying the space group in the command line using the > --symmetry I think there is another bug there - the command line > symmetry does not override the (wrong) symmetry that the routine gets > from the .sca file I am afraid you are right again. I forgot to include the plumbing for the --force_symmetry option. Sorry, this is getting ugly. To use your unmerged reflection file, edit this Python script in the iotbx tree: echo `libtbx.show_dist_paths iotbx`/iotbx/scalepack/no_merge_original_index.py Replace all "force_symmetry=False" with "force_symmetry=True", then try again.

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Re: [phenixbb] bug? iotbx.reflection_statistics apparent space group error reading scalepack .sca file
by Ralf W. Grosse-Kunstleve 06 Mar '06

06 Mar '06

> iotbx.reflection_statistics returns space group 195 > for a scalepack 'no merge original index' .sca file for > space group 123 (i.e space group 197) > > the first line of the .sca file is > 12 i23 You are right, this is a bug. Sorry. However, it went unnoticed because we usually supply the correct space group (along with the missing unit cell parameters) via --symmetry=some_other_file You could also use --unit_cell=10,20,30,90,90,90 --space_group=197 Mostly I prefer --symmetry because there is less of a chance to mistype. Also, quite often the space group in a reflection file is not correct anyway (e.g. P222 vs. P212121). > the CCP4 program scala can output a 'no merge original index' format > file, which has all 24 i23 symmetry operators in the header - but > iotbx.reflection_statistics cannot read that either I think you should be able to use the .sca file with the --symmetry or --space_group option. I've never tried to work with scala 'no merge original index' files. If you could send me your files I will look into fixing both problems. Peter Zwart wrote: > Note that iotbx.reflection statistics itself performs a merging step, > which is less sophisticated then those available in SCALA or scalepack. > Therefor, it might be worthwile considering supplying merged data to > iotbx.reflection_statistics. That's right. The simple merging in the cctbx is meant to be a stop-gap measure. It is best to merge externally with a program specifically designed for this purpose. Thanks for reporting the bug! Cheers, Ralf

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bug? iotbx.reflection_statistics apparent space group error reading scalepack .sca file
by Peter Metcalf 06 Mar '06

06 Mar '06

Hi - I hope this is the right place to post this iotbx.reflection_statistics returns space group 195 for a scalepack 'no merge original index' .sca file for space group 123 (i.e space group 197) the first line of the .sca file is 12 i23 the CCP4 program scala can output a 'no merge original index' format file, which has all 24 i23 symmetry operators in the header - but iotbx.reflection_statistics cannot read that either cheers Peter Metcalf

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Re: [phenixbb] unknown space group problem
by Thomas C. Terwilliger 03 Mar '06

03 Mar '06

Hi Angela, Thanks for sending me the data. I'm sorry about the problem reading your mtz files. The problem with reading the files is that some of the amplitudes in the mtz files are very big, leading to overflows written out as "****" when AutoSol converts them to .sca files. This problem is fixed in the current version of AutoSol, but that doesn't help you much. In the meantime, the solution is to convert the mtz files to sca and scale them so they don't overflow. I used phenix to do this with iotbx.reflection_file_converter idhrem_i23.mtz --label='F_refm101(+)' --sca=rem.sca to do this. The 3 .sca files seem to run ok now. I'm having trouble sending attachments so I didn't attach it, but if you have trouble reproducing my result I'll be happy to send you the converted files. All the best, Tom T > > > ----- Original Message ----- > From: Tom Terwilliger <terwilliger(a)lanl.gov> > Date: Thursday, March 2, 2006 4:48 pm > Subject: Re: [phenixbb] unknown space group problem > >> Hi Angela, >> Thanks! Yes, could you please rename the zip file to ".txt" and re- >> send? >> Our email system deletes all zip files! >> Thanks! >> -Tom T >> >> >> >> 3/2/2006 -0600, you wrote: >> >I am sending the output where the label error occurs as well as a zip >> >file with the three merged mtz files. I hope a zip file is okay, >> if it >> >isn't, let me know and I can try and get a tar file. These data sets >> >have been integrated in I23. >> > >> >I have been trying to reintegrate the data in H3 as suggested, but >> >Mosflm is giving me a lot of problems with this space group. The >> >predictions don't align with the reflections and sometimes it crashes >> >(this was not a problem with R3 or I23). >> > >> >Thanks, >> >Angela >> > >> >X-PMX-Wrap: 60 >> > >> >An executable email attachment called idhpk_i23.zip >> >(content_type:application/x-zip-compressed, size:7039478 bytes) >> was >> >removed from this message by LANL network as a security precaution. >> > >> >Please see http://network.lanl.gov/email/virus-scan.shtml for >> additional >> >information. >> >> >> >> >> 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.govTB Structural Genomics Consortium web site: >> http://www.doe-mbi.ucla.edu/TB >> >> >

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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. 07 Jan '06

07 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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