a question related to Phaser-MR

Wind Sui

1 Jan 2015 1 Jan '15

5:18 a.m.

Dear All, In the Phenix Phaser-MR (simple interface, will you please tell me what should I input for the "sequence identities"? I am looking forward to getting your reply. Wind

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Randy Read

1 Jan 1 Jan

9:58 a.m.

That would be the sequence identity between the model you’re providing and the protein in the crystal, which Phaser needs to know how good the model is expected to be. Best wishes, Randy Read ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 Wellcome Trust/MRC Building Fax: +44 1223 336827 Hills Road E-mail: [email protected] Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk On 1 Jan 2015, at 13:18, Wind Sui wrote:

...

Dear All,

In the Phenix Phaser-MR (simple interface, will you please tell me what should I input for the "sequence identities"?

I am looking forward to getting your reply.

Wind

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

miyatake

3 Jan 3 Jan

6:34 a.m.

New subject: 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

Terwilliger, Thomas Charles

9:29 a.m.

New subject: Rosetta refinement and MR_Rosetta

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#ins... Let me know if that doesn't do it! All the best, Tom T ________________________________________ From: [email protected] [[email protected]] on behalf of miyatake [[email protected]] Sent: Saturday, January 03, 2015 7:34 AM To: [email protected] 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 [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

miyatake

8:17 p.m.

New subject: 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" 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#ins...

Let me know if that doesn't do it! All the best, Tom T

________________________________________ From: [email protected] [[email protected]] on behalf of miyatake [[email protected]] Sent: Saturday, January 03, 2015 7:34 AM To: [email protected] 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 [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

Terwilliger, Thomas Charles

4 Jan 4 Jan

5:45 a.m.

New subject: Rosetta refinement and MR_Rosetta

Hi Miyatake, I notice that the Phenix web site I pointed you to at http://www.phenix-online.org/documentation/reference/rosetta_refine.html#ins... 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 [[email protected]] Sent: Saturday, January 03, 2015 9:17 PM To: Terwilliger, Thomas Charles Cc: miyatake; [email protected] 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" 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#ins...

Let me know if that doesn't do it! All the best, Tom T

________________________________________ From: [email protected] [[email protected]] on behalf of miyatake [[email protected]] Sent: Saturday, January 03, 2015 7:34 AM To: [email protected] 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 [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

miyatake

7:04 a.m.

New subject: Rosetta refinement and MR_Rosetta

Hello, Tom, Thank you so much for your reply. After I set the environment variables, the build command "rosetta.build_phenix_interface" did not work. The situation is like as following lines; % echo $PHENIX_ROSETTA_PHATH /Applications/rosetta_2014.35.57232_bundle echo $ROSETTA3_DB /Applications/rosetta_2014.35.57232_bundle/main/database % 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 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. May I ask you to give me an advice? Best regards, Hideyuki Miyatake On Sun, 4 Jan 2015 13:45:31 +0000 "Terwilliger, Thomas Charles" 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#ins...

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 [[email protected]] Sent: Saturday, January 03, 2015 9:17 PM To: Terwilliger, Thomas Charles Cc: miyatake; [email protected] 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" 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#ins...

Let me know if that doesn't do it! All the best, Tom T

________________________________________ From: [email protected] [[email protected]] on behalf of miyatake [[email protected]] Sent: Saturday, January 03, 2015 7:34 AM To: [email protected] 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 [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

miyatake

11:21 p.m.

New subject: 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" 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#ins...

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 [[email protected]] Sent: Saturday, January 03, 2015 9:17 PM To: Terwilliger, Thomas Charles Cc: miyatake; [email protected] 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" 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#ins...

Let me know if that doesn't do it! All the best, Tom T

________________________________________ From: [email protected] [[email protected]] on behalf of miyatake [[email protected]] Sent: Saturday, January 03, 2015 7:34 AM To: [email protected] 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 [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

Terwilliger, Thomas Charles

5 Jan 5 Jan

5:49 a.m.

New subject: Rosetta refinement and MR_Rosetta

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 [[email protected]] Sent: Monday, January 05, 2015 12:21 AM To: Terwilliger, Thomas Charles Cc: miyatake; [email protected]; [email protected]; 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" 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#ins...

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 [[email protected]] Sent: Saturday, January 03, 2015 9:17 PM To: Terwilliger, Thomas Charles Cc: miyatake; [email protected] 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" 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#ins...

Let me know if that doesn't do it! All the best, Tom T

________________________________________ From: [email protected] [[email protected]] on behalf of miyatake [[email protected]] Sent: Saturday, January 03, 2015 7:34 AM To: [email protected] 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 [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

miyatake

7:12 a.m.

New subject: Rosetta refinement and MR_Rosetta

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" 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 [[email protected]] Sent: Monday, January 05, 2015 12:21 AM To: Terwilliger, Thomas Charles Cc: miyatake; [email protected]; [email protected]; 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" 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#ins...

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 [[email protected]] Sent: Saturday, January 03, 2015 9:17 PM To: Terwilliger, Thomas Charles Cc: miyatake; [email protected] 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" 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#ins...

Let me know if that doesn't do it! All the best, Tom T

________________________________________ From: [email protected] [[email protected]] on behalf of miyatake [[email protected]] Sent: Saturday, January 03, 2015 7:34 AM To: [email protected] 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 [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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miyatake
Randy Read
Terwilliger, Thomas Charles
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