cif parser & ccp4 mon_lib incompatibility

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Re: [cctbxbb] [ccp4bb] CCP4 Update...

James Stroud

10 Apr 2013 10 Apr '13

10:05 p.m.

Hi All, It's a fresh install of the latest-greatest cctbx and of ccp4. Any ideas? % cctbx.python ./tst_sa.py CifParserError: /Applications/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif(line 1) : error 4 : Unexpected token, at offset -1 near global : unexpected input... expected one of : Actually dude, we didn't seem to be expecting anything here, or at least I could not work out what I was expecting, like so many of us these days! Here's the top of the cif file: global _lib_name mon_lib _lib_version 5.36 _lib_update 03/05/12 --------------------------------- # # --- LIST OF MONOMERS --- # data_comp_list loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group James

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Nathaniel Echols

10 Apr 10 Apr

10:20 p.m.

On Wed, Apr 10, 2013 at 3:05 PM, James Stroud wrote:

...

=% cctbx.python ./tst_sa.py CifParserError: /Applications/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif(line 1) : error 4 : Unexpected token, at offset -1 near global : unexpected input... expected one of : Actually dude, we didn't seem to be expecting anything here, or at least I could not work out what I was expecting, like so many of us these days!

The monomer library does indeed contain many files that don't conform to the official CIF standard, but that usually isn't a problem because the strict parsing is supposed to be disabled. Is the script you're running mmtbx/dynamics/tst_sa.py? Try setting the environment variable LIBTBX_DISABLE_TRACEBACKLIMIT and re-run, and send us the traceback. -Nat

James Stroud

10:28 p.m.

Hi Nat, On Apr 10, 2013, at 4:20 PM, Nathaniel Echols wrote:

...

The monomer library does indeed contain many files that don't conform to the official CIF standard, but that usually isn't a problem because the strict parsing is supposed to be disabled. Is the script you're running mmtbx/dynamics/tst_sa.py?

Yes, that is the script I'm running.

...

Try setting the environment variable LIBTBX_DISABLE_TRACEBACKLIMIT and re-run, and send us the traceback.

Here's the results: % setenv LIBTBX_DISABLE_TRACEBACKLIMIT 1 % cctbx.python ./tst_sa.py Traceback (most recent call last): File "./tst_sa.py", line 267, in <module> exercise_1() File "./tst_sa.py", line 122, in exercise_1 pi = get_pdb_inputs(pdb_str=pdb_str_1) File "./tst_sa.py", line 108, in get_pdb_inputs rama_potential=None, log = None) File "/usr/local/cctbx/cctbx_sources/mmtbx/command_line/real_space_refine.py", line 37, in get_processed_pdb_object mon_lib_srv = mmtbx.monomer_library.server.server() File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 223, in __init__ list_cif = mon_lib_list_cif() File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 63, in mon_lib_list_cif strict=strict) File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 57, in __init__ self.cif = read_cif(file_name=self.path) File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 92, in read_cif return iotbx.cif.reader(file_path=file_name, strict=False).model() File "/usr/local/cctbx/cctbx_sources/iotbx/cif/__init__.py", line 71, in __init__ raise CifParserError(self.parser.parser_errors()[0]) CifParserError: /Applications/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif(line 1) : error 4 : Unexpected token, at offset -1 near global : unexpected input... expected one of : Actually dude, we didn't seem to be expecting anything here, or at least I could not work out what I was expecting, like so many of us these days! James

Nathaniel Echols

10:38 p.m.

Actually, I think there may be a problem with your CCP4 installation - the exact same file on my computer starts with "global_", while yours lacks the trailing underscore, and editing mine to match reproduces the crash. With the underscore in place it should work (assuming nothing else has changed). On Wed, Apr 10, 2013 at 3:28 PM, James Stroud wrote:

...

Hi Nat,

On Apr 10, 2013, at 4:20 PM, Nathaniel Echols wrote:

The monomer library does indeed contain many files that don't conform to the official CIF standard, but that usually isn't a problem because the strict parsing is supposed to be disabled. Is the script you're running mmtbx/dynamics/tst_sa.py?

Yes, that is the script I'm running.

Try setting the environment variable LIBTBX_DISABLE_TRACEBACKLIMIT and re-run, and send us the traceback.

Here's the results:

% setenv LIBTBX_DISABLE_TRACEBACKLIMIT 1 % cctbx.python ./tst_sa.py Traceback (most recent call last): File "./tst_sa.py", line 267, in <module> exercise_1() File "./tst_sa.py", line 122, in exercise_1 pi = get_pdb_inputs(pdb_str=pdb_str_1) File "./tst_sa.py", line 108, in get_pdb_inputs rama_potential=None, log = None) File "/usr/local/cctbx/cctbx_sources/mmtbx/command_line/real_space_refine.py", line 37, in get_processed_pdb_object mon_lib_srv = mmtbx.monomer_library.server.server() File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 223, in __init__ list_cif = mon_lib_list_cif() File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 63, in mon_lib_list_cif strict=strict) File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 57, in __init__ self.cif = read_cif(file_name=self.path) File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 92, in read_cif return iotbx.cif.reader(file_path=file_name, strict=False).model() File "/usr/local/cctbx/cctbx_sources/iotbx/cif/__init__.py", line 71, in __init__ raise CifParserError(self.parser.parser_errors()[0]) CifParserError: /Applications/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif(line 1) : error 4 : Unexpected token, at offset -1 near global : unexpected input... expected one of : Actually dude, we didn't seem to be expecting anything here, or at least I could not work out what I was expecting, like so many of us these days!

James

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Nathaniel Echols

10:44 p.m.

PS. Actually, there are other differences: global_ _lib_name mon_lib _lib_version 5.39 _lib_update 06/11/12 So it's three months newer than the one you're using. Have you run the CCP4 updater? On Wed, Apr 10, 2013 at 3:38 PM, Nathaniel Echols wrote:

...

Actually, I think there may be a problem with your CCP4 installation - the exact same file on my computer starts with "global_", while yours lacks the trailing underscore, and editing mine to match reproduces the crash. With the underscore in place it should work (assuming nothing else has changed).

On Wed, Apr 10, 2013 at 3:28 PM, James Stroud wrote:

...
Hi Nat,

On Apr 10, 2013, at 4:20 PM, Nathaniel Echols wrote:

The monomer library does indeed contain many files that don't conform to the official CIF standard, but that usually isn't a problem because the strict parsing is supposed to be disabled. Is the script you're running mmtbx/dynamics/tst_sa.py?

Yes, that is the script I'm running.

Try setting the environment variable LIBTBX_DISABLE_TRACEBACKLIMIT and re-run, and send us the traceback.

Here's the results:

% setenv LIBTBX_DISABLE_TRACEBACKLIMIT 1 % cctbx.python ./tst_sa.py Traceback (most recent call last): File "./tst_sa.py", line 267, in <module> exercise_1() File "./tst_sa.py", line 122, in exercise_1 pi = get_pdb_inputs(pdb_str=pdb_str_1) File "./tst_sa.py", line 108, in get_pdb_inputs rama_potential=None, log = None) File "/usr/local/cctbx/cctbx_sources/mmtbx/command_line/real_space_refine.py", line 37, in get_processed_pdb_object mon_lib_srv = mmtbx.monomer_library.server.server() File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 223, in __init__ list_cif = mon_lib_list_cif() File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 63, in mon_lib_list_cif strict=strict) File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 57, in __init__ self.cif = read_cif(file_name=self.path) File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 92, in read_cif return iotbx.cif.reader(file_path=file_name, strict=False).model() File "/usr/local/cctbx/cctbx_sources/iotbx/cif/__init__.py", line 71, in __init__ raise CifParserError(self.parser.parser_errors()[0]) CifParserError: /Applications/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif(line 1) : error 4 : Unexpected token, at offset -1 near global : unexpected input... expected one of : Actually dude, we didn't seem to be expecting anything here, or at least I could not work out what I was expecting, like so many of us these days!

James

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James Stroud

10:58 p.m.

Hi Nat, On Apr 10, 2013, at 4:44 PM, Nathaniel Echols wrote:

...

PS. Actually, there are other differences:

global_ _lib_name mon_lib _lib_version 5.39 _lib_update 06/11/12

So it's three months newer than the one you're using. Have you run the CCP4 updater?

Thanks for tracking this down. The installer I used was double-clickable black-box "foolproof" no-thinking point-and-click: ccp4-6.3.0.2-arp.dmg I just ran the updater (bin/update) but it didn't touch mon_lib_list.cif even though it reported to complete successfully. If I have more cif problems, I'll download the latest ccp4 sources and see what happens when I build from scratch. James

...

On Wed, Apr 10, 2013 at 3:38 PM, Nathaniel Echols wrote: Actually, I think there may be a problem with your CCP4 installation - the exact same file on my computer starts with "global_", while yours lacks the trailing underscore, and editing mine to match reproduces the crash. With the underscore in place it should work (assuming nothing else has changed).

On Wed, Apr 10, 2013 at 3:28 PM, James Stroud wrote: Hi Nat,

On Apr 10, 2013, at 4:20 PM, Nathaniel Echols wrote:

...
The monomer library does indeed contain many files that don't conform to the official CIF standard, but that usually isn't a problem because the strict parsing is supposed to be disabled. Is the script you're running mmtbx/dynamics/tst_sa.py?

Yes, that is the script I'm running.

...
Try setting the environment variable LIBTBX_DISABLE_TRACEBACKLIMIT and re-run, and send us the traceback.

Here's the results:

% setenv LIBTBX_DISABLE_TRACEBACKLIMIT 1 % cctbx.python ./tst_sa.py Traceback (most recent call last): File "./tst_sa.py", line 267, in <module> exercise_1() File "./tst_sa.py", line 122, in exercise_1 pi = get_pdb_inputs(pdb_str=pdb_str_1) File "./tst_sa.py", line 108, in get_pdb_inputs rama_potential=None, log = None) File "/usr/local/cctbx/cctbx_sources/mmtbx/command_line/real_space_refine.py", line 37, in get_processed_pdb_object mon_lib_srv = mmtbx.monomer_library.server.server() File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 223, in __init__ list_cif = mon_lib_list_cif() File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 63, in mon_lib_list_cif strict=strict) File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 57, in __init__ self.cif = read_cif(file_name=self.path) File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 92, in read_cif return iotbx.cif.reader(file_path=file_name, strict=False).model() File "/usr/local/cctbx/cctbx_sources/iotbx/cif/__init__.py", line 71, in __init__ raise CifParserError(self.parser.parser_errors()[0]) CifParserError: /Applications/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif(line 1) : error 4 : Unexpected token, at offset -1 near global : unexpected input... expected one of : Actually dude, we didn't seem to be expecting anything here, or at least I could not work out what I was expecting, like so many of us these days!

James

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Oleg Dolomanov

11:12 p.m.

Hi, the CIF parser will report this error if any of the CIF items is outside data_ or save_ blocks. So you need to change 'global' to 'data_global' to prevent this error. Cheers, o From: [email protected] Date: Wed, 10 Apr 2013 16:58:40 -0600 To: [email protected] Subject: Re: [cctbxbb] cif parser & ccp4 mon_lib incompatibility Hi Nat, On Apr 10, 2013, at 4:44 PM, Nathaniel Echols wrote:PS. Actually, there are other differences: global__lib_name mon_lib_lib_version 5.39_lib_update 06/11/12 So it's three months newer than the one you're using. Have you run the CCP4 updater? Thanks for tracking this down. The installer I used was double-clickable black-box "foolproof" no-thinking point-and-click: ccp4-6.3.0.2-arp.dmg I just ran the updater (bin/update) but it didn't touch mon_lib_list.cif even though it reported to complete successfully. If I have more cif problems, I'll download the latest ccp4 sources and see what happens when I build from scratch. James On Wed, Apr 10, 2013 at 3:38 PM, Nathaniel Echols wrote: Actually, I think there may be a problem with your CCP4 installation - the exact same file on my computer starts with "global_", while yours lacks the trailing underscore, and editing mine to match reproduces the crash. With the underscore in place it should work (assuming nothing else has changed). On Wed, Apr 10, 2013 at 3:28 PM, James Stroud wrote: Hi Nat, On Apr 10, 2013, at 4:20 PM, Nathaniel Echols wrote: The monomer library does indeed contain many files that don't conform to the official CIF standard, but that usually isn't a problem because the strict parsing is supposed to be disabled. Is the script you're running mmtbx/dynamics/tst_sa.py? Yes, that is the script I'm running. Try setting the environment variable LIBTBX_DISABLE_TRACEBACKLIMIT and re-run, and send us the traceback. Here's the results: % setenv LIBTBX_DISABLE_TRACEBACKLIMIT 1% cctbx.python ./tst_sa.pyTraceback (most recent call last): File "./tst_sa.py", line 267, in <module> exercise_1() File "./tst_sa.py", line 122, in exercise_1 pi = get_pdb_inputs(pdb_str=pdb_str_1) File "./tst_sa.py", line 108, in get_pdb_inputs rama_potential=None, log = None) File "/usr/local/cctbx/cctbx_sources/mmtbx/command_line/real_space_refine.py", line 37, in get_processed_pdb_object mon_lib_srv = mmtbx.monomer_library.server.server() File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 223, in __init__ list_cif = mon_lib_list_cif() File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 63, in mon_lib_list_cif strict=strict) File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 57, in __init__ self.cif = read_cif(file_name=self.path) File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 92, in read_cif return iotbx.cif.reader(file_path=file_name, strict=False).model() File "/usr/local/cctbx/cctbx_sources/iotbx/cif/__init__.py", line 71, in __init__ raise CifParserError(self.parser.parser_errors()[0])CifParserError: /Applications/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif(line 1) : error 4 : Unexpected token, at offset -1 near global : unexpected input... expected one of : Actually dude, we didn't seem to be expecting anything here, or at leastI could not work out what I was expecting, like so many of us these days! James _______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb _______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb _______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

Nathaniel Echols

11:17 p.m.

On Wed, Apr 10, 2013 at 4:12 PM, Oleg Dolomanov wrote:

...

the CIF parser will report this error if any of the CIF items is outside data_ or save_ blocks. So you need to change 'global' to 'data_global' to prevent this error.

This would be true when using the CIF reader on its own, but for macromolecular apps (including the test script that's failing), we disable this error checking specifically for the CCP4 monomer library. In fact the version we distribute with Phenix ($PHENIX/chem_data/mon_lib/list/mon_lib_list.cif) starts like this: global_ _lib_name mon_lib _lib_version 4.11 _lib_update 15/04/05 It is very likely that we may start to distribute the entire chem_data tree from our web site as an optional add-on, which will greatly ease the use of CCTBX in other macromolecular applications (e.g. MolProbity). Of course the CCP4 version will be more complete and up-to-date, although a) some of those restraints are not especially well-validated, and b) we incorporate additional information in the restraints we distribute. -Nat

Oleg Dolomanov

11:24 p.m.

Sorry, yes,'global_' is also a special global data block and should work... From: [email protected] Date: Wed, 10 Apr 2013 16:17:53 -0700 To: [email protected] Subject: Re: [cctbxbb] cif parser & ccp4 mon_lib incompatibility On Wed, Apr 10, 2013 at 4:12 PM, Oleg Dolomanov wrote: the CIF parser will report this error if any of the CIF items is outside data_ or save_ blocks. So you need to change 'global' to 'data_global' to prevent this error. This would be true when using the CIF reader on its own, but for macromolecular apps (including the test script that's failing), we disable this error checking specifically for the CCP4 monomer library. In fact the version we distribute with Phenix ($PHENIX/chem_data/mon_lib/list/mon_lib_list.cif) starts like this: global__lib_name mon_lib_lib_version 4.11_lib_update 15/04/05 It is very likely that we may start to distribute the entire chem_data tree from our web site as an optional add-on, which will greatly ease the use of CCTBX in other macromolecular applications (e.g. MolProbity). Of course the CCP4 version will be more complete and up-to-date, although a) some of those restraints are not especially well-validated, and b) we incorporate additional information in the restraints we distribute. -Nat _______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

Richard Gildea

11 Apr 11 Apr

4:56 a.m.

The unquoted word 'global_' (with trailing underscore) is part of the STAR file syntax (upon which CIF is based), but is explicitly forbidden in the formal CIF syntax: http://www.iucr.org/resources/cif/spec/version1.1/cifsyntax#global However, for compatibility with the monomer library which is using the global_ keyword despite it being forbidden in the CIF syntax, we added support for a non-strict mode of the CIF parser in the iotbx which could support global_ data blocks. Of course, if the trailing underscore is lost, then it is a syntax error either way, as the parser is looking for the start of a data block, signified by a data block heading (starting with 'data_'). Cheers, Richard On 10 April 2013 16:24, Oleg Dolomanov wrote:

...

Sorry, yes,'global_' is also a special global data block and should work...

------------------------------ From: [email protected] Date: Wed, 10 Apr 2013 16:17:53 -0700

To: [email protected] Subject: Re: [cctbxbb] cif parser & ccp4 mon_lib incompatibility

On Wed, Apr 10, 2013 at 4:12 PM, Oleg Dolomanov wrote:

the CIF parser will report this error if any of the CIF items is outside data_ or save_ blocks. So you need to change 'global' to 'data_global' to prevent this error.

This would be true when using the CIF reader on its own, but for macromolecular apps (including the test script that's failing), we disable this error checking specifically for the CCP4 monomer library. In fact the version we distribute with Phenix ($PHENIX/chem_data/mon_lib/list/mon_lib_list.cif) starts like this:

global_ _lib_name mon_lib _lib_version 4.11 _lib_update 15/04/05

It is very likely that we may start to distribute the entire chem_data tree from our web site as an optional add-on, which will greatly ease the use of CCTBX in other macromolecular applications (e.g. MolProbity). Of course the CCP4 version will be more complete and up-to-date, although a) some of those restraints are not especially well-validated, and b) we incorporate additional information in the restraints we distribute.

-Nat

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Nathaniel Echols

5:46 a.m.

On Wed, Apr 10, 2013 at 3:58 PM, James Stroud wrote:

...

Thanks for tracking this down. The installer I used was double-clickable black-box "foolproof" no-thinking point-and-click: ccp4-6.3.0.2-arp.dmg

Well, for what it's worth, I just nuked my installation and downloaded the same thing minus ARP/wARP, and now I have the same header as you reported. Will continue digging tomorrow, but I suspect that either the updates will eventually fix the problem, or something has changed in the installer (although using an older version of the monomer library seems like a weird choice). Also note that you can download the monomer library as a separate package from Garib Murshudov's home page: http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/ [ click "software" --> "Refmac5" --> "Dictionary of ligands" ] and this looks like it is formatted correctly. -Nat

James Stroud

6:11 a.m.

On Apr 10, 2013, at 11:46 PM, Nathaniel Echols wrote:

...

On Wed, Apr 10, 2013 at 3:58 PM, James Stroud wrote: Thanks for tracking this down. The installer I used was double-clickable black-box "foolproof" no-thinking point-and-click: ccp4-6.3.0.2-arp.dmg

Well, for what it's worth, I just nuked my installation and downloaded the same thing minus ARP/wARP, and now I have the same header as you reported. Will continue digging tomorrow, but I suspect that either the updates will eventually fix the problem, or something has changed in the installer (although using an older version of the monomer library seems like a weird choice).

I actually iterated through updates until I there were no more. I think I over-shot the sweet spot, though: chernev 13% setenv MMTBX_CCP4_MONOMER_LIB /usr/local/ccp4-6.3.0/lib/data/monomers/ chernev 14% cctbx.python ./tst_sa.py Traceback (most recent call last): File "./tst_sa.py", line 267, in <module> exercise_1() File "./tst_sa.py", line 122, in exercise_1 pi = get_pdb_inputs(pdb_str=pdb_str_1) File "./tst_sa.py", line 108, in get_pdb_inputs rama_potential=None, log = None) File "/usr/local/cctbx/cctbx_sources/mmtbx/command_line/real_space_refine.py", line 37, in get_processed_pdb_object mon_lib_srv = mmtbx.monomer_library.server.server() File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 226, in __init__ geostd_list_cif_obj = geostd_list_cif() File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 69, in geostd_list_cif strict=strict) File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 56, in __init__ + ", ".join(mon_lib_env_vars)) mmtbx.monomer_library.server.MonomerLibraryServerError: Cannot find CCP4 monomer library. Please define one of these environment variables: MMTBX_CCP4_MONOMER_LIB, CLIBD_MON

...

Also note that you can download the monomer library as a separate package from Garib Murshudov's home page:

http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/ [ click "software" --> "Refmac5" --> "Dictionary of ligands" ]

and this looks like it is formatted correctly.

I'll give this one a try. James

...

-Nat

James Stroud

7:17 a.m.

Hi Nat, On Apr 10, 2013, at 11:46 PM, Nathaniel Echols wrote:

...

Also note that you can download the monomer library as a separate package from Garib Murshudov's home page:

http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/ [ click "software" --> "Refmac5" --> "Dictionary of ligands" ]

and this looks like it is formatted correctly.

I downloaded this library, but its failing. Do you know what I'm doing wrong? James chernev 50% cctbx.python ./tst_sa.py Traceback (most recent call last): File "./tst_sa.py", line 267, in <module> exercise_1() File "./tst_sa.py", line 122, in exercise_1 pi = get_pdb_inputs(pdb_str=pdb_str_1) File "./tst_sa.py", line 108, in get_pdb_inputs rama_potential=None, log = None) File "/usr/local/cctbx/cctbx_sources/mmtbx/command_line/real_space_refine.py", line 37, in get_processed_pdb_object mon_lib_srv = mmtbx.monomer_library.server.server() File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 226, in __init__ geostd_list_cif_obj = geostd_list_cif() File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 69, in geostd_list_cif strict=strict) File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 56, in __init__ + ", ".join(mon_lib_env_vars)) mmtbx.monomer_library.server.MonomerLibraryServerError: Cannot find CCP4 monomer library. Please define one of these environment variables: MMTBX_CCP4_MONOMER_LIB, CLIBD_MON chernev 51% ls $MMTBX_CCP4_MONOMER_LIB/ total 10248 0 0/ 8 COPYING 0 g/ 0 n/ 0 u/ 0 1/ 0 a/ 0 h/ 0 o/ 0 v/ 0 2/ 0 b/ 0 i/ 0 p/ 0 w/ 0 3/ 0 c/ 0 j/ 2436 pdb_alt_names.txt 0 x/ 0 4/ 0 d/ 0 k/ 8 pdb_v2to3.py 0 y/ 0 5/ 4 dnarna_basepairs.txt 0 l/ 0 q/ 0 z/ 0 6/ 4 dnarna_basepairs_2.txt 0 list/ 0 r/ 0 7/ 0 e/ 0 m/ 0 s/ 0 8/ 104 ener_lib.cif 1340 mon_lib_ind.cif 0 t/ 0 9/ 0 f/ 6340 mon_lib_ind2.cif 4 template_link.pdb chernev 52% echo $MMTBX_CCP4_MONOMER_LIB/ /usr/local/refmac-v5.39/monomers/

Nathaniel Echols

2:49 p.m.

On Thu, Apr 11, 2013 at 12:17 AM, James Stroud wrote:

...

I downloaded this library, but its failing. Do you know what I'm doing wrong?

File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 226, in __init__ geostd_list_cif_obj = geostd_list_cif() File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 69, in geostd_list_cif strict=strict) File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 56, in __init__ + ", ".join(mon_lib_env_vars)) mmtbx.monomer_library.server.MonomerLibraryServerError: Cannot find CCP4 monomer library. Please define one of these environment variables: MMTBX_CCP4_MONOMER_LIB, CLIBD_MON

Ah, this I think is genuinely our fault - it is requiring that you have a file which is not part of the CCP4 monomer library at all, but rather part of a separate curated library ("geostd") which we distribute. This is clearly a bug; I'll bug the relevant parties. I think you're doing everything else correctly, though. For now, there are a couple of things to try: 1) "touch $MMTBX_CCP4_MONOMER_LIB/list/geostd_list.cif" which may or may not work. 2) Just pull out the entire chem_data tree from a Phenix installation and dump it in /usr/local/cctbx. Since we want to make this freely redistributable anyway, this will be a viable long-term solution (and since it's actually causing problems that this isn't readily available, I will see if I can push this quickly). But we may have a fix for the crash soon - will post a follow-up if and when it's committed to SVN. -Nat

Nathaniel Echols

6:44 p.m.

Okay, this problem should be fixed in the latest SVN revision - James, could you please update and let us know if you're still seeing problems? -Nat On Thu, Apr 11, 2013 at 7:49 AM, Nathaniel Echols wrote:

...

On Thu, Apr 11, 2013 at 12:17 AM, James Stroud wrote:

...
I downloaded this library, but its failing. Do you know what I'm doing wrong?

File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 226, in __init__ geostd_list_cif_obj = geostd_list_cif() File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 69, in geostd_list_cif strict=strict) File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 56, in __init__ + ", ".join(mon_lib_env_vars)) mmtbx.monomer_library.server.MonomerLibraryServerError: Cannot find CCP4 monomer library. Please define one of these environment variables: MMTBX_CCP4_MONOMER_LIB, CLIBD_MON

Ah, this I think is genuinely our fault - it is requiring that you have a file which is not part of the CCP4 monomer library at all, but rather part of a separate curated library ("geostd") which we distribute. This is clearly a bug; I'll bug the relevant parties. I think you're doing everything else correctly, though. For now, there are a couple of things to try:

1) "touch $MMTBX_CCP4_MONOMER_LIB/list/geostd_list.cif" which may or may not work.

2) Just pull out the entire chem_data tree from a Phenix installation and dump it in /usr/local/cctbx. Since we want to make this freely redistributable anyway, this will be a viable long-term solution (and since it's actually causing problems that this isn't readily available, I will see if I can push this quickly).

But we may have a fix for the crash soon - will post a follow-up if and when it's committed to SVN.

-Nat

James Stroud

12 Apr 12 Apr

5:49 a.m.

Hi Nat, I'm not sure of the correct way to update with SVN. I compared cctbx_sources and the SVN trunk (which had a .gitignore, suggesting its a git repository). The cctbx_sources from the bundle had some extra directories. Should I do an "svn co" of the trunk and then add the extra directories from the cctbx_sources and then re-build in place? James On Apr 11, 2013, at 12:44 PM, Nathaniel Echols wrote:

...

Okay, this problem should be fixed in the latest SVN revision - James, could you please update and let us know if you're still seeing problems?

-Nat

On Thu, Apr 11, 2013 at 7:49 AM, Nathaniel Echols wrote:

...
On Thu, Apr 11, 2013 at 12:17 AM, James Stroud wrote:

...
I downloaded this library, but its failing. Do you know what I'm doing wrong?

File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 226, in __init__ geostd_list_cif_obj = geostd_list_cif() File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 69, in geostd_list_cif strict=strict) File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 56, in __init__ + ", ".join(mon_lib_env_vars)) mmtbx.monomer_library.server.MonomerLibraryServerError: Cannot find CCP4 monomer library. Please define one of these environment variables: MMTBX_CCP4_MONOMER_LIB, CLIBD_MON

Ah, this I think is genuinely our fault - it is requiring that you have a file which is not part of the CCP4 monomer library at all, but rather part of a separate curated library ("geostd") which we distribute. This is clearly a bug; I'll bug the relevant parties. I think you're doing everything else correctly, though. For now, there are a couple of things to try:

1) "touch $MMTBX_CCP4_MONOMER_LIB/list/geostd_list.cif" which may or may not work.

2) Just pull out the entire chem_data tree from a Phenix installation and dump it in /usr/local/cctbx. Since we want to make this freely redistributable anyway, this will be a viable long-term solution (and since it's actually causing problems that this isn't readily available, I will see if I can push this quickly).

But we may have a fix for the crash soon - will post a follow-up if and when it's committed to SVN.

-Nat

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

Graeme.Winter＠diamond.ac.uk

6:10 a.m.

Hi James, In an empty directory run cctbx_svn_getting_started.csh from libtbx/development in the cctbx sources - this downloads a source bundle, then moves much of it out of the way and checks out cctbx from svn over the top. I find taking the Python binary from the base of a cctbx binary build a helpful start. In a nutshell mkdir cctbx_from_svn cd cctbx_from_svn mkdir sources cd sources cctbx_svn_getting_started.csh cd .. mkdir build cd build /where/is/python/base/bin/python ../sources/cctbx_projects/libtbx/configure.py this_module that_module . setpaths.sh make (this is from memory: some of the details re: directories may be shonky and it's early…) It does work well though. Should also be on the wiki if not already… Best wishes, Graeme On 12 Apr 2013, at 06:49, James Stroud wrote:

...

Hi Nat,

I'm not sure of the correct way to update with SVN. I compared cctbx_sources and the SVN trunk (which had a .gitignore, suggesting its a git repository). The cctbx_sources from the bundle had some extra directories. Should I do an "svn co" of the trunk and then add the extra directories from the cctbx_sources and then re-build in place?

James

On Apr 11, 2013, at 12:44 PM, Nathaniel Echols wrote:

...
Okay, this problem should be fixed in the latest SVN revision - James, could you please update and let us know if you're still seeing problems?

-Nat

On Thu, Apr 11, 2013 at 7:49 AM, Nathaniel Echols wrote:

...
On Thu, Apr 11, 2013 at 12:17 AM, James Stroud wrote:

...
I downloaded this library, but its failing. Do you know what I'm doing wrong?

File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 226, in __init__ geostd_list_cif_obj = geostd_list_cif() File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 69, in geostd_list_cif strict=strict) File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 56, in __init__ + ", ".join(mon_lib_env_vars)) mmtbx.monomer_library.server.MonomerLibraryServerError: Cannot find CCP4 monomer library. Please define one of these environment variables: MMTBX_CCP4_MONOMER_LIB, CLIBD_MON

Ah, this I think is genuinely our fault - it is requiring that you have a file which is not part of the CCP4 monomer library at all, but rather part of a separate curated library ("geostd") which we distribute. This is clearly a bug; I'll bug the relevant parties. I think you're doing everything else correctly, though. For now, there are a couple of things to try:

1) "touch $MMTBX_CCP4_MONOMER_LIB/list/geostd_list.cif" which may or may not work.

2) Just pull out the entire chem_data tree from a Phenix installation and dump it in /usr/local/cctbx. Since we want to make this freely redistributable anyway, this will be a viable long-term solution (and since it's actually causing problems that this isn't readily available, I will see if I can push this quickly).

But we may have a fix for the crash soon - will post a follow-up if and when it's committed to SVN.

-Nat

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

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

-- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

James Stroud

7:21 a.m.

On Apr 12, 2013, at 12:10 AM, wrote:

...

It does work well though. Should also be on the wiki if not already…

Thanks to you and Richard for help with the svn build. It seems to be building happily right now. By the way, is this the this the wiki? http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Cctbx It seems a little sparse considering the epic scale of the cctbx code base. James

Graeme.Winter＠diamond.ac.uk

7:29 a.m.

This wiki: http://sourceforge.net/p/cctbx/wiki/Home/ which has only just been enabled so is probably even more sparse. Note to self I should start to add stuff to this: for the DIALS stuff we have some raw material... On 12 Apr 2013, at 08:21, James Stroud wrote: On Apr 12, 2013, at 12:10 AM, mailto:[email protected]> mailto:[email protected]> wrote: It does work well though. Should also be on the wiki if not already… Thanks to you and Richard for help with the svn build. It seems to be building happily right now. By the way, is this the this the wiki? http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Cctbx It seems a little sparse considering the epic scale of the cctbx code base. James _______________________________________________ cctbxbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/cctbxbb -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

Richard Gildea

7:33 a.m.

The wiki - practically empty at this point - is at http://sourceforge.net/p/cctbx/wiki/Home/. We only recently got the wiki when we upgraded our svn to the new sourceforge version, so it is still waiting for people to have time to contribute, etc. If you have anything to contribute to it, feel free - it will have to be a community effort. Cheers, Richard On Friday, April 12, 2013, James Stroud wrote:

...

On Apr 12, 2013, at 12:10 AM, > > wrote:

It does work well though. Should also be on the wiki if not already…

Thanks to you and Richard for help with the svn build. It seems to be building happily right now.

By the way, is this the this the wiki?

http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Cctbx

It seems a little sparse considering the epic scale of the cctbx code base.

James

James Stroud

8:04 a.m.

New subject: cctbx wiki

On Apr 12, 2013, at 1:33 AM, Richard Gildea wrote:

...

The wiki - practically empty at this point - is at http://sourceforge.net/p/cctbx/wiki/Home/. We only recently got the wiki when we upgraded our svn to the new sourceforge version, so it is still waiting for people to have time to contribute, etc. If you have anything to contribute to it, feel free - it will have to be a community effort.

I've been taking notes at http://cctbxwiki.bravais.net/ with the intent that it could be mirrored, ripped, shared, or whatever fate befalls wiki content. I'm not a wiki pro, so I don't know how these things propagate, nor do I have any idea right now how to manage contributors, etc. I do have lots of styling there and some add-ons. It's also mediawiki, so I don't know how it fits with the sourceforge wiki. I made it mediawiki because I thought the official wiki was the one I linked to below and that someone could copy-pase the source from my wiki. It's of course under construction. I'm still figuring how to do what I want to do with the cctbx API, so getting the notes for posterity have been more important than organization, so far. Also, I have made a parser that generates a skeleton wiki page for classes given an object. See http://cctbxwiki.bravais.net/Cctbx.miller.array for an example. It needs some refinement for boost classes (especially the return values), but does a pretty good job. It's mostly designed to provide stubs for the methods. See http://cctbxwiki.bravais.net/Class_Index for the list of classes I've run through it so far. James

Jan Marten Simons

15 Apr 15 Apr

noon

New subject: cctbx wiki

Am Freitag 12 April 2013 10:04:20 schrieb James Stroud:

...

Also, I have made a parser that generates a skeleton wiki page for classes given an object. See http://cctbxwiki.bravais.net/Cctbx.miller.array for an example. It needs some refinement for boost classes (especially the return values), but does a pretty good job. It's mostly designed to provide stubs for the methods. See http://cctbxwiki.bravais.net/Class_Index for the list of classes I've run through it so far.

Hi James, Be sure to check the dox.sphinx directory in the source tree. As I think quite a lot of that could also be done (or is already done) by sphinx. I think it would be very useful to have usage examples merged into the source code as sphinx compatible doc strings. With regards, Dipl. Phys. Jan M. Simons Institute of Crystallography RWTH Aachen University

Richard Gildea

12 Apr 12 Apr

6:12 a.m.

Hi James, svn checkout svn://svn.code.sf.net/p/cctbx/code/trunk cctbx_project Should do what you need, and then just use that copy of the sources to replace the cctbx_sources from the bundle. I would copy the extra directories that aren't in the svn trunk so they are alongside the cctbx_project directory (but not inside, just to keep them separate). The usual directory structure amongst the phenix developers is something like: build/ sources/ sources/cctbx_project/ sources/boost/ sources/scons/ Etc. Then cd build/ python ../sources/cctbx_project/libtbx/configure.py mmtbx (or whatever modules you wish to build) source setpaths.sh libtbx.scons -j 2 (number of processors) Luc added the .gitignore because a few of us are using git-svn as our interface to subversion. Hope that helps, Richard On Thursday, April 11, 2013, James Stroud wrote:

...

Hi Nat,

I'm not sure of the correct way to update with SVN. I compared cctbx_sources and the SVN trunk (which had a .gitignore, suggesting its a git repository). The cctbx_sources from the bundle had some extra directories. Should I do an "svn co" of the trunk and then add the extra directories from the cctbx_sources and then re-build in place?

James

On Apr 11, 2013, at 12:44 PM, Nathaniel Echols wrote:

...
Okay, this problem should be fixed in the latest SVN revision - James, could you please update and let us know if you're still seeing problems?

-Nat

On Thu, Apr 11, 2013 at 7:49 AM, Nathaniel Echols wrote:

...
On Thu, Apr 11, 2013 at 12:17 AM, James Stroud wrote:

...
I downloaded this library, but its failing. Do you know what I'm doing wrong?

File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 226, in __init__ geostd_list_cif_obj = geostd_list_cif() File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 69, in geostd_list_cif strict=strict) File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 56, in __init__ + ", ".join(mon_lib_env_vars)) mmtbx.monomer_library.server.MonomerLibraryServerError: Cannot find CCP4 monomer library. Please define one of these environment variables: MMTBX_CCP4_MONOMER_LIB, CLIBD_MON

Ah, this I think is genuinely our fault - it is requiring that you have a file which is not part of the CCP4 monomer library at all, but rather part of a separate curated library ("geostd") which we distribute. This is clearly a bug; I'll bug the relevant parties. I think you're doing everything else correctly, though. For now, there are a couple of things to try:

1) "touch $MMTBX_CCP4_MONOMER_LIB/list/geostd_list.cif" which may or may not work.

2) Just pull out the entire chem_data tree from a Phenix installation and dump it in /usr/local/cctbx. Since we want to make this freely redistributable anyway, this will be a viable long-term solution (and since it's actually causing problems that this isn't readily available, I will see if I can push this quickly).

But we may have a fix for the crash soon - will post a follow-up if and when it's committed to SVN.

-Nat

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

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

James Stroud

4:35 p.m.

Hi Nat, On Apr 11, 2013, at 12:44 PM, Nathaniel Echols wrote:

...

Okay, this problem should be fixed in the latest SVN revision - James, could you please update and let us know if you're still seeing problems?

I updated via svn and tst_sa.py worked perfectly. Thanks! James

...

On Thu, Apr 11, 2013 at 7:49 AM, Nathaniel Echols wrote:

...
On Thu, Apr 11, 2013 at 12:17 AM, James Stroud wrote:

...
I downloaded this library, but its failing. Do you know what I'm doing wrong?

File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 226, in __init__ geostd_list_cif_obj = geostd_list_cif() File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 69, in geostd_list_cif strict=strict) File "/usr/local/cctbx/cctbx_sources/mmtbx/monomer_library/server.py", line 56, in __init__ + ", ".join(mon_lib_env_vars)) mmtbx.monomer_library.server.MonomerLibraryServerError: Cannot find CCP4 monomer library. Please define one of these environment variables: MMTBX_CCP4_MONOMER_LIB, CLIBD_MON

Ah, this I think is genuinely our fault - it is requiring that you have a file which is not part of the CCP4 monomer library at all, but rather part of a separate curated library ("geostd") which we distribute. This is clearly a bug; I'll bug the relevant parties. I think you're doing everything else correctly, though. For now, there are a couple of things to try:

1) "touch $MMTBX_CCP4_MONOMER_LIB/list/geostd_list.cif" which may or may not work.

2) Just pull out the entire chem_data tree from a Phenix installation and dump it in /usr/local/cctbx. Since we want to make this freely redistributable anyway, this will be a viable long-term solution (and since it's actually causing problems that this isn't readily available, I will see if I can push this quickly).

But we may have a fix for the crash soon - will post a follow-up if and when it's committed to SVN.

-Nat

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

Marcin Wojdyr

11 Apr 11 Apr

10:53 a.m.

On 11 April 2013 06:46, Nathaniel Echols wrote:

...

Well, for what it's worth, I just nuked my installation and downloaded the same thing minus ARP/wARP, and now I have the same header as you reported. Will continue digging tomorrow, but I suspect that either the updates will eventually fix the problem, or something has changed in the installer (although using an older version of the monomer library seems like a weird choice).

Also note that you can download the monomer library as a separate package from Garib Murshudov's home page:

http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/ [ click "software" --> "Refmac5" --> "Dictionary of ligands" ]

and this looks like it is formatted correctly.

The problem with global is listed on Garib's website ("global did not have undescore"), fixed in 5.38: http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/Dictionary/bug... In CCP4, it was likely fixed in one of the updates. Cheers Marcin

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Graeme.Winter＠diamond.ac.uk
James Stroud
Jan Marten Simons
Marcin Wojdyr
Nathaniel Echols
Oleg Dolomanov
Richard Gildea