Hi Eldon,
Here are some more fixes to be able to parse the BMRB model-free
entries. The problem here is that the correlation time units are not
specified. I have guessed that they should be ps. The diff is below.
Cheers,
Edward
[edau@localhost bmr2.1_files_mod2]$ cat diff
diff -ur ./bmr17010.str ../bmr2.1_files/bmr17010.str
--- ./bmr17010.str 2011-01-28 09:05:58.000000000 +0100
+++ ../bmr2.1_files/bmr17010.str 2011-02-03 14:44:39.000000000 +0100
@@ -1466,8 +1466,9 @@
_Sample_conditions_label $sample_conditions_1
_Mol_system_component_name 'Tryptophan apo-repressor, chain 1'
- _Tau_e_value_units .
- _Tau_s_value_units .
+ _Tau_e_value_units ps
+ _Tau_f_value_units ps
+ _Tau_s_value_units ps
_Text_data_format .
_Text_data .
diff -ur ./bmr17012.str ../bmr2.1_files/bmr17012.str
--- ./bmr17012.str 2011-01-28 09:06:04.000000000 +0100
+++ ../bmr2.1_files/bmr17012.str 2011-02-03 14:45:54.000000000 +0100
@@ -1045,8 +1045,9 @@
_Sample_conditions_label $sample_conditions_1
_Mol_system_component_name 'Tryptophan apo-repressor, chain 1'
- _Tau_e_value_units .
- _Tau_s_value_units .
+ _Tau_e_value_units ps
+ _Tau_f_value_units ps
+ _Tau_s_value_units ps
_Text_data_format .
_Text_data .
diff -ur ./bmr6470.str ../bmr2.1_files/bmr6470.str
--- ./bmr6470.str 2011-01-28 06:06:43.000000000 +0100
+++ ../bmr2.1_files/bmr6470.str 2011-02-03 14:27:52.000000000 +0100
@@ -969,6 +969,7 @@
stop_
_Sample_conditions_label $condition_1
+ _Tau_e_value_units ps
_Mol_system_component_name Ubiquitin
loop_
On 2 February 2011 14:35, Edward d'Auvergne <edward@xxxxxxxxxxxxx> wrote:
Hi Eldon,
I don't know if this is the best channel for this information. Is
there a BMRB mailing list where it would be better for this
information?
Ok, this is how I have found these inconsistencies. I have used relax
to read in the BMRB NMR-STAR formatted files. This uses bmrblib which
I wrote (http://gna.org/projects/bmrblib/). This library is pretty
close to complete for relaxation data and model-free data, and would
be very easy to extend to handle the entirety of the NMR-STAR
dictionary. It can both read and write valid NMR-STAR formatted files
in versions 2.1, 3.0, and 3.1 (a little debugging might be still
required, and expansion to different revisions such as 2.1.1 is also
possible). This Python library is an abstraction of the underlying
file format. The very low level reading and writing of the STAR
format is handled by Jurgen F. Doreleijers' pystarlib (jurgenfd att
gmail dott com, http://code.google.com/p/pystarlib/).
For reading the entire BMRB model-free data content, I have performed
the following. I have downloaded all of the files from
http://www.bmrb.wisc.edu/search/query_grid/query_1_46.html using the
link http://www.bmrb.wisc.edu/ftp/pub/bmrb/compress/query_1_46.tar.gz.
These are all in the version 2.1 or 2.1.1 format. Then using the
file names, I have downloaded all of the corresponding v3.1 files from
http://www.bmrb.wisc.edu/ftp/pub/bmrb/entry_lists/nmr-star3.1/. It
looks like maybe 30% of the old formatted files have been converted to
the newer format so far. I will write 2 subsequent emails with
explanations of the problems with the version 2.1 files and the 3.1
files separately.
In this mail, I would like to describe general problems. The first is
that pystarlib cannot handle the semi-colon notation in non-free
looping tag categories, e.g.:
loop_
_Vendor.Name
_Vendor.Address
_Vendor.Electronic_address
_Vendor.Entry_ID
_Vendor.Software_ID
'J. Patrick Loria' .
;
http://xbeams.chem.yale.edu/~loria/
patrick.loria@xxxxxxxx
; 15097 1
This is in the v3.1 file bmr15097.str. The basic pystarlib
functionality probably needs to be fixed, assuming this construct is a
valid STAR format. The second is that the bmr4970.str entry is not
parsable. This file has multiple 15N S2_parameters saveframes:
save_S2_parameters_15N_22C
save_S2_parameters_15N_35C
save_S2_parameters_15N_47C
save_S2_parameters_15N_60C
save_S2_parameters_15N_73C
But these all have:
loop_
_Sample_label
$sample_one
stop_
_Sample_conditions_label $sample_conditions_one
They might be the same sample, but the sample conditions are different
as the temperature is changing. By eye, this is obvious, but for the
automatic parsing of this data, the file has to be blacklisted and
skipped.
Cheers,
Edward
Re: Inconsistencies in the v2.1 (or v2.1.1) BMRB model-free entries.