- phenixbb - phenix-online.org

Low resolution refinement
by Appu kumar 26 Apr '14

26 Apr '14

Hello All, I want to refine the low resolution structure (6.5A). It is a membrane protein and we are able to phase it. It will be great help if any one can guide me how to proceed further with the refinement. People uses Phenix to refine low resolution structure, so phenix is really a good program to proceed for refinement against low resolution. Thank in advance Appu

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Build Phenix from Source Code
by Chen Zhao 25 Apr '14

25 Apr '14

Dear all, I would like to try phenix.rosetta_refine and it is said in the online tutorial that the phenix should be built from source code in linux. However I ran into some errors, and I am too far from a linux export to figure it out. I am using Debian Wheezy with kernel 3.2.0-4-amd64. I download the source installer (phenix-installer-1.9-1683-source.tar) and run the installer as: # ./install --prefix=/usr/local/src --nproc=8 --no-gui (it seems from README-DEV that there is no --python-shared flag as described in the online tutorial) After while, I receive the following error message: ************************************************************************************************************************* Installing Imaging... log file is /workspace/setup/phenix-installer-1.9-1683/build-source/intel-linux-2.6-x86_64/cz-thinkpadw530-debian/tmp/Imaging_install_log getting package Imaging-1.1.7.tar.gz... using /workspace/setup/phenix-installer-1.9-1683/base/Imaging-1.1.7.tar.gz Traceback (most recent call last): File "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install", line 9, in <module> install_cctbx_base.installer(args=sys.argv, log=sys.stdout) File "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py", line 95, in __init__ self.build_cctbx_dependencies() File "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py", line 134, in build_cctbx_dependencies self.build_imaging() File "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py", line 349, in build_imaging confirm_import_module="Image") File "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py", line 325, in build_python_module_simple log=pkg_log) File "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py", line 150, in call return call(args, log=log) File "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/installer_utils.py", line 51, in call raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc)) RuntimeError: Call to '/usr/local/src/phenix-1.9-1683/build/intel-linux-2.6-x86_64/base/bin/python setup.py build ' failed with exit code 1 FATAL ERROR: aborting installation. ************************************************************************************************************************* I looked into Imaging_install_log, and at the end, I have the following errors: ************************************************************************************************************************* /usr/bin/ld: /usr/local/lib/libpython2.7.a(abstract.o): relocation R_X86_64_32S against `_Py_NotImplementedStruct' can not be used when making a shared object; recompile with -fPIC /usr/local/lib/libpython2.7.a: could not read symbols: Bad value collect2: error: ld returned 1 exit status error: command 'gcc' failed with exit status 1 *************************************************************************************************************************** Could anybody help me out? Thank you so much, Chen

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Re: [phenixbb] Build Phenix from Source Code
by Chen Zhao 25 Apr '14

25 Apr '14

I switched to version 1.8.4-1496 and this time the same error didn't occur. Also --python-shared/--with-rosetta flag works. But I ran it as # ./install --prefix=/usr/local/src --nproc=8 --no-gui --phython-shared then regenerate the dispatchers by running libtbx.refresh as shown in the message after installation. However, the installation is not complete, and if I source phenix_env.sh, the error message as below will show up: *************************************************************************************************************** bash: /usr/local/src/phenix-1.8.4-1496/bin/machine_type: No such file or directory bash: /usr/local/src/phenix-1.8.4-1496/bin/machine_version: No such file or directory bash: /usr/local/src/phenix-1.8.4-1496/bin/find-installation: No such file or directory *************************************************************************************************************** What else should I run to complete building phenix? PS. Because the first time I didn't append --python-shared flag, I build it again after deleting the original directory. I guess there might be files elsewhere that are changed, since I didn't have this error the first time. Thanks a lot, Chen On Thu, Apr 24, 2014 at 11:10 PM, Chen Zhao <c.zhao(a)yale.edu> wrote: > OK, thank you for your suggestion! I will do that. But as a perfectionist, > I will try to finish with the installation. I later found that the flag is > --with-rosetta but not --python-shared... I have to build it again... > Crying... > > Best, > Chen > > > On Thu, Apr 24, 2014 at 11:06 PM, Meng, Wuyi <wuyi.meng(a)yale.edu> wrote: > >> Sbgrid version means the version compiled by sbgrid (on 130.132.25.142and other cbic Mac Pros). The Mac Pro runs 2x fast than csb and yale hpc >> computers of same phenix refinement, they have 8 cores too. Rosetta runs >> usually take days to weeks to finish, it is wise to do it on yale hpc >> cluster. >> >> Wuyi, >> >> On Apr 24, 2014, at 10:49 PM, Chen Zhao <c.zhao(a)yale.edu> wrote: >> >> Dear Wuyi, >> >> Thank you for your warm help as always! But actually SBGrid is not >> "installed" in this machine (don't laugh, it is my laptop...) Do you mean >> phenix-1.8.4-1496 when saying the SBGrid version? I did try this version >> after you mentioned and at least it passed the step that gave me the error >> before. I will wait and see how the compilation goes. And if this works, >> hopefully there will be no error when running >> rosetta.build_phenix_interface. I will try the one on130.132.25.142 if >> nothing works. >> >> Thank you so much again! >> >> Good night, >> Chen >> <130.132.25.142> >> >> >> On Thu, Apr 24, 2014 at 10:35 PM, Meng, Wuyi <wuyi.meng(a)yale.edu> wrote: >> >>> phenix.rosetta_refine should work on 130.132.25.142 according to >>> following statement from sbgrid: >>> >>> Linux 64-bit We have installed and configured nightly versions >>> of Phenix and Rosetta to support the newly announced Phenix-Rosetta >>> refinement mentioned in Nature Methods. These experimental versions are not >>> the default, so you'll need to add version >>> overrides in your ~/.sbgrid.conf file: P HE N I X _ X = n i g h t l y R >>> O S E T T A _ X = n i g h t l y You can refresh your memory for setting >>> version overrides on our website. These new features are only available on >>> 64-bit Linux at this time. Phenix >>> generally has very good support for OS X, but Macs >>> seem to be a second tier platform for the Rosetta >>> developers. >>> >>> Wuyi, >>> >>> > On Apr 24, 2014, at 10:14 PM, Chen Zhao <c.zhao(a)yale.edu> wrote: >>> > >>> > Dear all, >>> > >>> > I would like to try phenix.rosetta_refine and it is said in the online >>> tutorial that the phenix should be built from source code in linux. However >>> I ran into some errors, and I am too far from a linux export to figure it >>> out. I am using Debian Wheezy with kernel 3.2.0-4-amd64. I download the >>> source installer (phenix-installer-1.9-1683-source.tar) and run the >>> installer as: >>> > >>> > # ./install --prefix=/usr/local/src --nproc=8 --no-gui (it seems from >>> README-DEV that there is no --python-shared flag as described in the online >>> tutorial) >>> > >>> > After while, I receive the following error message: >>> > >>> > >>> ************************************************************************************************************************* >>> > Installing Imaging... >>> > log file is >>> /workspace/setup/phenix-installer-1.9-1683/build-source/intel-linux-2.6-x86_64/cz-thinkpadw530-debian/tmp/Imaging_install_log >>> > getting package Imaging-1.1.7.tar.gz... >>> > using >>> /workspace/setup/phenix-installer-1.9-1683/base/Imaging-1.1.7.tar.gz >>> > Traceback (most recent call last): >>> > File >>> "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install", >>> line 9, in <module> >>> > install_cctbx_base.installer(args=sys.argv, log=sys.stdout) >>> > File >>> "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py", >>> line 95, in __init__ >>> > self.build_cctbx_dependencies() >>> > File >>> "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py", >>> line 134, in build_cctbx_dependencies >>> > self.build_imaging() >>> > File >>> "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py", >>> line 349, in build_imaging >>> > confirm_import_module="Image") >>> > File >>> "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py", >>> line 325, in build_python_module_simple >>> > log=pkg_log) >>> > File >>> "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py", >>> line 150, in call >>> > return call(args, log=log) >>> > File >>> "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/installer_utils.py", >>> line 51, in call >>> > raise RuntimeError("Call to '%s' failed with exit code %d" % >>> (args, rc)) >>> > RuntimeError: Call to >>> '/usr/local/src/phenix-1.9-1683/build/intel-linux-2.6-x86_64/base/bin/python >>> setup.py build ' failed with exit code 1 >>> > FATAL ERROR: aborting installation. >>> > >>> ************************************************************************************************************************* >>> > >>> > I looked into Imaging_install_log, and at the end, I have the >>> following errors: >>> > >>> > >>> ************************************************************************************************************************* >>> > /usr/bin/ld: /usr/local/lib/libpython2.7.a(abstract.o): relocation >>> R_X86_64_32S against `_Py_NotImplementedStruct' can not be used when making >>> a shared object; recompile with -fPIC >>> > /usr/local/lib/libpython2.7.a: could not read symbols: Bad value >>> > collect2: error: ld returned 1 exit status >>> > error: command 'gcc' failed with exit status 1 >>> > >>> *************************************************************************************************************************** >>> > >>> > Could anybody help me out? >>> > >>> > Thank you so much, >>> > Chen >>> > >>> > _______________________________________________ >>> > phenixbb mailing list >>> > phenixbb(a)phenix-online.org >>> > http://phenix-online.org/mailman/listinfo/phenixbb >>> > >>> > >>> > The information in this e-mail is intended only for the person to whom >>> it is >>> > addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> > contains patient information, please contact the Partners Compliance >>> HelpLine at >>> > http://www.partners.org/complianceline . If the e-mail was sent to >>> you in error >>> > but does not contain patient information, please contact the sender >>> and properly >>> > dispose of the e-mail. >>> >> >> >

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HELP. semelno met refinement not working.
by Kenneth A. Satyshur 24 Apr '14

24 Apr '14

When I refine my seleno met residues in Phenix (1.8.4-1496) ALL my MSE are restrained to ONE conformer, in coot terms ptp #11 with a Chi 1 of 60 deg. This happens at the start of the second cycle when it does 'rsrl'. I can watch it happen in coot. POP! There is goes. Some of the MSE are in this conformation, but not all of them. This refinement is wrong, so how do I correct it? thanks kas -- Kenneth A. Satyshur, M.S.,Ph.D. Senior Scientist University of Wisconsin Madison, Wisconsin 53706 608-215-5207

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BCA/CCP4 Summer School in Protein Crystallography at Diamond
by Airlie McCoy 24 Apr '14

24 Apr '14

Applications are now open for the BCA/CCP4 Summer School in Protein Crystallography to be held at Diamond (UK) from Tuesday 26th August to Sunday 31st August 2014. Applications close 1st May 2014. References are due by 8th May 2014. The BCA/CCP4 Protein Crystallography Summer School is intended for students and researchers new to crystallography. Its dual aims are to provide comprehensive training in crystallography and to promote best practise within the British crystallographic community. The lectures cover the gamut of techniques required for a structure solution, from protein expression through to structure validation. Intensively supervised computer tutorials enable students to relate the theory presented in the lectures to practice. Although CCP4 programs will primarily be used in these tutorials, the aim will be to approach crystallographic questions in a software-agnostic manner. There will also be a crystal manipulation and cooling workshop. Note that the course is scheduled during Diamond synchrotron downtime, so there will not be active data collection at the Diamond beamlines. For more information on eligibility, cost, and applications see: http://www.diamond.ac.uk/Home/Events/BCA-Summer-School.html Application form: http://extranet2.diamond.ac.uk/ISV/EventWidget/BCA/ApplicationsForm.aspx

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inputing tNCS into phenix?
by Yarrow Madrona 23 Apr '14

23 Apr '14

Hello, I recently posted a question about stalled R-factors and and obtained excellent help resulting in the realization that I have tNCS even though it is not picked up by X-triage. I know the transformation matrix of one molecule onto another but I am not sure how to input this into phenix (both the translation and the rotation) to improve refinement. Is there a way to do this? I'm sorry if this has already been covered. -Yarrow

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Trouble Refining Ligand in Phenix
by Chris Fage 22 Apr '14

22 Apr '14

Hi Everyone, I am trying to refine a structure with a phosphorylated amino acid. After refining in Phenix, the Fo-Fc density (green) overlaps the 2Fo-Fc density for all atoms of the derivatized amino acid in Coot, almost as if I had not built in the residue. I am loading a .cif for the derivative when I run phenix.refine. I have also tried ReadySet, but when I click the "Run in phenix.refine" button, I see the message Error interpreting command line argument as parameter definition: "refine_65-coot-2.metal.edits" RuntimeError: Unexpected end of output. Am I just seeing noise, or is Phenix not actually refining this portion of the model? I would appreciate any suggestions. Best, Chris

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Saenger class in nucleic acids
by Chen Zhao 22 Apr '14

22 Apr '14

Dear all, Could anybody point me to a reference for the saenger_class and leontis_westhof_class in nucleic acids? I just failed to find it in the long reference list in the phenix.refine online tutorial. Thanks a lot in advance, Chen

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inputing tNCS into phenix?
by Yarrow Madrona 21 Apr '14

21 Apr '14

Hello, I recently posted a question about stalled R-factors and and obtained excellent help resulting in the realization that I have tNCS even though it is not picked up by X-triage. I know the transformation matrix of one molecule onto another but I am not sure how to input this into phenix (both the translation and the rotation) to improve refinement. Is there a way to do this? I'm sorry if this has already been covered. -Yarrow

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Re: [phenixbb] Phenix composite omit map
by Chen Zhao 21 Apr '14

21 Apr '14

Dear all, Thank you all for your help and the program is running now. However, I met a AttributeError as " 'twin_model_manager' object has no attribute 'f_model_scaled_with_k1' ". Sorry for so many problems. Thank you so much, Chen On Mon, Apr 21, 2014 at 1:13 PM, Chen Zhao <c.zhao(a)yale.edu> wrote: > Dear Engin, > > Thank you so much for your reply! Yes, this is the problem because I am > using phenix-1.8.4-1496. I will download the newest version! > > Best, > Chen > > > On Mon, Apr 21, 2014 at 1:10 PM, Engin Özkan <eozkan(a)uchicago.edu> wrote: > >> Dear Chen, >> >> What version of Phenix are you using? phenix.composite_omit_map was >> recently added (post 1.8.4 release). Are you using a recent nightly >> (presumably dev-1579 as you suggest or even newer, like the release >> candidate for 1.9)? >> >> Engin >> >> >> On 4/21/14, 12:05 PM, Chen Zhao wrote: >> >> Thank you Tom, >> >> I understand what "command not found" mean, but I already sourced >> "phenix_env" in my bashrc. "phenix.list" works, also I have already run >> "phenix.autosol", "phenix.autobuild", "phenix.refine" without any problems. >> >> Thank you so much again! >> >> Sincerely, >> Chen >> >> >> On Mon, Apr 21, 2014 at 1:01 PM, Terwilliger, Thomas C < >> terwilliger(a)lanl.gov> wrote: >> >>> Hi Chen, >>> >>> "command not found" usually means the shell cannot find a particular >>> command. It often can be fixed by sourcing the right setup commands. >>> >>> If you type: >>> >>> phenix.list >>> >>> does it also say "command not found"? If so, you just need to source >>> the phenix version you want. When you install it phenix lists where this >>> directory is...If you are on a mac you will say something like this: >>> >>> >>> source /Applications/PHENIX-1.8.3-1479/Contents/phenix-1.8.3-1479/phenix_env >>> >>> and you can put that in your .cshrc file too (if you are using csh). >>> >>> Let me know if that doesn't do it! >>> All the best, >>> Tom T >>> >>> >>> >>> >>> On Apr 21, 2014, at 10:53 AM, Chen Zhao wrote: >>> >>> Dear all, >>> >>> Hello! I am now running into a simple technical problem but I just >>> cannot figure it out. I am trying to create a composite omit map by phenix, >>> but when I typed in the command phenix.composite_omit_map XXX.eff based >>> on the instructions on >>> http://www.phenix-online.org/version_docs/dev-1579/composite_omit_map.htm, >>> I got the error message "command not found". Could anybody help me out? >>> >>> Thank you so much in advance! >>> >>> Sincerely, >>> Chen >>> >>> >>> >> >> >> _______________________________________________ >> phenixbb mailing [email protected]://phenix-online.org/mailman/listinfo/phenixbb >> >> >> -- >> Assistant Professor >> Dept of Biochemistry and Molecular Biology >> University of Chicago >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> >> >

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