[phenixbb] Rosetta refinement and MR_Rosetta
miyatake
miyatake at riken.jp
Mon Jan 5 07:12:45 PST 2015
Thank you so much, Tom.
All trials except "env" were failed.
When I typed env, I saw below;
I don't know the reason why the typo "PHENIX_ROSETTA_PHATH" is still there...
[HM-MacBook-Pro:~] miyatake% env
TMPDIR=/var/folders/dk/hqlbh9_j7px4vx7hw9lbrc6m0000gn/T/
XPC_FLAGS=0x0
Apple_PubSub_Socket_Render=/private/tmp/com.apple.launchd.dQS6stgFCF/Render
LANG=ja_JP.UTF-8
TERM=xterm-256color
DISPLAY=/private/tmp/com.apple.launchd.IIe7wDCBoC/org.macosforge.xquartz:0
SSH_AUTH_SOCK=/private/tmp/com.apple.launchd.woFKBJTh94/Listeners
SECURITYSESSIONID=186a6
TERM_PROGRAM=Apple_Terminal
XPC_SERVICE_NAME=0
TERM_PROGRAM_VERSION=343
TERM_SESSION_ID=2F944CE0-4F21-4698-8932-38A8D060BFCF
__CF_USER_TEXT_ENCODING=0x1F5:0x1:0xE
SHELL=/bin/bash
HOME=/Users/miyatake
LOGNAME=miyatake
USER=miyatake
PATH=/Users/miya0817/sharp-2.6.0/adm/bin:/Applications/Phenix-dev-1894/Contents/phenix-dev-1894/build/bin:/Applications/Lafire-4.0/commands/:/Applications/cns_solve_1.3.2/mac-intel-darwin/bin:/Applications/cns_solve_1.3.2/mac-intel-darwin/utils:/Applications/arp_warp_7.5/bin/bin-x86_64-Darwin:/Applications/ccp4-6.5/etc:/Applications/ccp4-6.5/bin:/Applications/ccp4-6.5/share/xia2/Applications:/Users/miya0817/sharp-2.6.0/adm/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin
HOSTTYPE=intel-mac
VENDOR=apple
OSTYPE=darwin
MACHTYPE=x86_64
SHLVL=4
PWD=/Users/miyatake
GROUP=staff
HOST=HM-MacBook-Pro.local
REMOTEHOST=
CCP4_OPEN=UNKNOWN
SYMOP=/usr/local/lib/solve//symop.lib
SYMINFO=/usr/local/lib/solve//syminfo.lib
SOLVEDIR=/usr/local/lib/solve/
CCP4_MASTER=/Applications
CCP4=/Applications/ccp4-6.5
CCP4_SCR=/tmp/miyatake
CCP4I_TCLTK=/Applications/ccp4-6.5/bin
BALBES_ROOT=/Applications/ccp4-6.5/share/balbes/BALBES/Package
GFORTRAN_UNBUFFERED_PRECONNECTED=Y
CBIN=/Applications/ccp4-6.5/bin
CLIB=/Applications/ccp4-6.5/lib
CLIBD=/Applications/ccp4-6.5/lib/data
CETC=/Applications/ccp4-6.5/etc
CINCL=/Applications/ccp4-6.5/include
CHTML=/Applications/ccp4-6.5/html
CEXAM=/Applications/ccp4-6.5/examples
CCP4I_TOP=/Applications/ccp4-6.5/share/ccp4i
MMCIFDIC=/Applications/ccp4-6.5/lib/ccp4/cif_mmdic.lib
CRANK=/Applications/ccp4-6.5/share/ccp4i/crank
CLIBD_MON=/Applications/ccp4-6.5/lib/data/monomers/
CCP4_HELPDIR=/Applications/ccp4-6.5/help/
MANPATH=/Applications/ccp4-6.5/share/man:/Applications/ccp4-6.5/share/man:/Applications/ccp4-6.5/share/man:/Applications/ccp4-6.5/share/man:/Applications/ccp4-6.5/share/man:/Applications/ccp4-6.5/share/man:/Applications/ccp4-6.5/share/man
warpbin=/Applications/arp_warp_7.5/bin/bin-x86_64-Darwin
warpdoc=/Applications/arp_warp_7.5/manual
CNS_SOLVE=/Applications/cns_solve_1.3.2/
CNS_ARCH=mac-intel-darwin
OMP_STACKSIZE=256m
CNS_LIB=/Applications/cns_solve_1.3.2/libraries
CNS_MODULE=/Applications/cns_solve_1.3.2/modules
CNS_TOPPAR=/Applications/cns_solve_1.3.2/libraries/toppar
CNS_CONFDB=/Applications/cns_solve_1.3.2/libraries/confdb
CNS_XTALLIB=/Applications/cns_solve_1.3.2/libraries/xtal
CNS_NMRLIB=/Applications/cns_solve_1.3.2/libraries/nmr
CNS_XRAYLIB=/Applications/cns_solve_1.3.2/libraries/xray
CNS_XTALMODULE=/Applications/cns_solve_1.3.2/modules/xtal
CNS_NMRMODULE=/Applications/cns_solve_1.3.2/modules/nmr
CNS_HELPLIB=/Applications/cns_solve_1.3.2/helplib
CNS_INST=/Applications/cns_solve_1.3.2/mac-intel-darwin
CNS_SOURCE=/Applications/cns_solve_1.3.2/mac-intel-darwin/source
LAFIRE_DIR=/Applications/Lafire-4.0
LAFIRE_PYTHON_BIN=/Applications/Lafire-4.0/bin/python
PHENIX=/Applications/Phenix-dev-1894/Contents/phenix-dev-1894
PHENIX_VERSION=dev-1894
PHENIX_ROSETTA_PHATH=/Applications/rosetta_2014.35.57232_bundle
ROSETTA3_DB=/Applications/rosetta_2014.35.57232_bundle/main/database
HTTP_PROXY=proxyout.mydomain.edu:8080
BDG_home=/Users/miya0817/sharp-2.6.0
PHENIX_ROSETTA_PATH=/Applications/rosetta_2014.35.57232_bundle
On Mon, 5 Jan 2015 13:49:46 +0000
"Terwilliger, Thomas Charles" <terwilliger at lanl.gov> wrote:
> Hi Miyatake,
>
> I think we are getting close. That error message means the directory (exactly as typed on the terminal) does not exist or could not be found somehow.
>
> What do you get if you type:
>
> ls /Applications/rosetta_2014.35.57232_bundle
>
> If you get a directory listing, can you do this:
>
> echo $PHENIX_ROSETTA_PATH
> ls $PHENIX_ROSETTA_PATH
>
> Does that give you a directory listing? If yes, then try:
>
>
> rosetta.build_phenix_interface
>
> again. If that fails, try:
>
>
> rosetta.build_phenix_interface rosetta_path=$PHENIX_ROSETTA_PATH
>
> If that still fails, then can you type:
>
> env
>
> and then can you send me the terminal output for all of this?
>
> Thanks!
> -Tom T
>
>
> ________________________________________
> From: miyatake [miyatake at riken.jp]
> Sent: Monday, January 05, 2015 12:21 AM
> To: Terwilliger, Thomas Charles
> Cc: miyatake; phenixbb at phenix-online.org; irees at lbl.gov; Paul Adams
> Subject: Re: [phenixbb] Rosetta refinement and MR_Rosetta
>
> Dear Tom,
>
> Thank you so much for your help.
>
> However, I still see the error message below:
>
>
>
> [HM-MacBook-Pro:/Applications/ccp4-6.5] miyatake% rosetta.build_phenix_interface
> Traceback (most recent call last):
> File "/Applications/Phenix-dev-1894/Contents/phenix-dev-1894/build/../modules/phenix/phenix/command_line/rosetta_build_phenix_interface.py", line 106, in <module>
> run(sys.argv[1:])
> File "/Applications/Phenix-dev-1894/Contents/phenix-dev-1894/build/../modules/phenix/phenix/command_line/rosetta_build_phenix_interface.py", line 51, in run
> raise RuntimeError("Rosetta path invalid:\n%s" % rosetta_path)
> RuntimeError: Rosetta path invalid:
> /Applications/rosetta_2014.35.57232_bundle
> [HM-MacBook-Pro:/Applications/ccp4-6.5] miyatake% rosetta.build_phenix_interface
> Traceback (most recent call last):
> File "/Applications/Phenix-dev-1894/Contents/phenix-dev-1894/build/../modules/phenix/phenix/command_line/rosetta_build_phenix_interface.py", line 106, in <module>
> run(sys.argv[1:])
> File "/Applications/Phenix-dev-1894/Contents/phenix-dev-1894/build/../modules/phenix/phenix/command_line/rosetta_build_phenix_interface.py", line 51, in run
> raise RuntimeError("Rosetta path invalid:\n%s" % rosetta_path)
> RuntimeError: Rosetta path invalid:
> /Applications/rosetta_2014.35.57232_bundle
> [HM-MacBook-Pro:/Applications/ccp4-6.5] miyatake% rosetta.build_phenix_interface nproc=8
> Traceback (most recent call last):
> File "/Applications/Phenix-dev-1894/Contents/phenix-dev-1894/build/../modules/phenix/phenix/command_line/rosetta_build_phenix_interface.py", line 106, in <module>
> run(sys.argv[1:])
> File "/Applications/Phenix-dev-1894/Contents/phenix-dev-1894/build/../modules/phenix/phenix/command_line/rosetta_build_phenix_interface.py", line 51, in run
> raise RuntimeError("Rosetta path invalid:\n%s" % rosetta_path)
> RuntimeError: Rosetta path invalid:
> /Applications/rosetta_2014.35.57232_bundle
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> On Sun, 4 Jan 2015 13:45:31 +0000
> "Terwilliger, Thomas Charles" <terwilliger at lanl.gov> wrote:
>
> > Hi Miyatake,
> >
> > I notice that the Phenix web site I pointed you to at
> >
> > http://www.phenix-online.org/documentation/reference/rosetta_refine.html#installation
> >
> > has a typo and says setenv PHENOX_ROSETTA_PATH; perhaps that was what the problem was! We have fixed the typo for future releases.
> >
> > So in case that wasn't the problem, here is how to set the shell variable PHENIX_ROSETTA_PATH:
> >
> > 1. Notice the location of your Rosetta installation. For example it might be at:
> >
> > /usr/local/rosetta_2014.16.56682_bundle
> >
> > 2. Then set your shell variables. The command depends on whether you are using csh or
> >
> > For sh or bash shells you say:
> >
> > export PHENIX_ROSETTA_PATH=/usr/local/rosetta_2014.16.56682_bundle
> > export ROSETTA3_DB=/usr/local/rosetta_2014.16.56682_bundle/main/database
> >
> > or for csh/tcsh shells:
> >
> > setenv PHENIX_ROSETTA_PATH "/usr/local/rosetta_2014.16.56682_bundle"
> > setenv ROSETTA3_DB "/usr/local/rosetta_2014.16.56682_bundle/main/database"
> >
> > You can check that it worked by saying
> >
> > echo $PHENIX_ROSETTA_PATH
> > echo $ROSETTA3_DB
> >
> > and you should get back the paths that you defined. Then your rosetta.build_phenix_interface command should work.
> >
> > Let me know if that doesn't do it!
> > All the best,
> > Tom T
> >
> > ________________________________________
> > From: miyatake [miyatake at riken.jp]
> > Sent: Saturday, January 03, 2015 9:17 PM
> > To: Terwilliger, Thomas Charles
> > Cc: miyatake; phenixbb at phenix-online.org
> > Subject: Re: [phenixbb] Rosetta refinement and MR_Rosetta
> >
> > Dear Tom,
> >
> > Thank you for your reply.
> >
> > When I execute the command line,
> >
> > rosetta.build_phenix_interface nproc=8
> >
> > I see the error message below;
> >
> >
> > Traceback (most recent call last):
> > File "/Applications/Phenix-dev-1894/Contents/phenix-dev-1894/build/../modules/phenix/phenix/command_line/rosetta_build_phenix_interface.py", line 106, in <module>
> > run(sys.argv[1:])
> > File "/Applications/Phenix-dev-1894/Contents/phenix-dev-1894/build/../modules/phenix/phenix/command_line/rosetta_build_phenix_interface.py", line 49, in run
> > or set environment variable PHENIX_ROSETTA_PATH.""")
> > RuntimeError: Path to Rosetta not found. Please specify rosetta_path=PATH on command line,
> > or set environment variable PHENIX_ROSETTA_PATH.
> >
> >
> >
> >
> > Why did it happen?
> >
> > Best regards,
> >
> > H. Miyatake
> >
> >
> >
> >
> >
> > On Sat, 3 Jan 2015 17:29:58 +0000
> > "Terwilliger, Thomas Charles" <terwilliger at lanl.gov> wrote:
> >
> > > Hi Miyatake,
> > >
> > > Can you possibly make sure that you have 2 installations of Rosetta, one for mr_rosetta and one separately configured for rosetta_refine...The second one you set up with:
> > >
> > > rosetta.build_phenix_interface
> > >
> > > You can see the full instructions for this at:
> > >
> > > http://www.phenix-online.org/documentation/reference/rosetta_refine.html#installation
> > >
> > > Let me know if that doesn't do it!
> > > All the best,
> > > Tom T
> > >
> > > ________________________________________
> > > From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of miyatake [miyatake at riken.jp]
> > > Sent: Saturday, January 03, 2015 7:34 AM
> > > To: phenixbb at phenix-online.org
> > > Subject: [phenixbb] Rosetta refinement and MR_Rosetta
> > >
> > > Dear Phenix users,
> > >
> > > Hello,
> > >
> > > I run MR_Rosetta without any problems.
> > >
> > > When I run, however, Rosetta refinement, it stopped with
> > > a message "can't find rosetta_bin".
> > >
> > > Why did it happen?
> > >
> > > H. Miyatake
> > > _______________________________________________
> > > phenixbb mailing list
> > > phenixbb at phenix-online.org
> > > http://phenix-online.org/mailman/listinfo/phenixbb
> >
>
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