Seb, we should discuss and make a list of the necessary tags. We can
have relax ask the user to input the required data, this will be the
easiest for the user and BMRB input. Adding new tags appears to be
quite a lot easier with the BMRB than modifying existing designs, but
we should be certain of these tags and design the list to be the
highest quality possible.
How should we write this list ? By exchanging emails in a new thread ? Or by
svn ?
It would be best by email, as Eldon will need to add the tags and his
input will be needed.
* the number of different relaxation delays (including some
information on duplicates)
* the order with which the different relaxation delays were recorded
(and the use of interleaving)
This is a good idea, but is hard to implement as a strict definition.
Maybe a single tag with free-formatted text could be used. For
example:
_Auto_relaxation.Delay_interleaving
where the free text could be something like "300, 20, 1000, 10, 1500,
200". Eldon, is there another way of storing this info?
This is a good idea, although maybe free text could be replaced by, first, a
question on the number of delays, then tags for each delays (where the total
number would have been specified earlier). This would avoid having different
formatting in the free text list...
We can do this on the relax-side with one or two user functions.
Adding the number is not necessary as we can easily count the elements
of a list. In relax I would have 2 structures, a dictionary for
storing the delay times per experiment, and a list storing the order.
This will probably require 2 user functions.
Storing this data in the BMRB is a different question. The tags are
fixed, so you can't have one tag per delay. It might be possible to
create a new looping tag category, but this is not the best way to
store an ordered list. Maybe Eldon knows a better way. We can always
dump the information into the _Auto_relaxation_list.Details tag if we
have no interest in using it for automatic parsing of the BMRB, but I
think to make this type of information parsable would be a good idea.
What do you think?
* the number of samples used (if not a single one)
A single Auto_relaxation or Heteronuc_NOE saveframe should really come
from a single sample. If there are different samples for different
experiments, then _Auto_relaxation_list.Sample_condition_list_ID
should point to the different samples for each saveframe.
Currently, the name of the sample used for a single experiment is shown.
Although, for model-free analysis results, it would be nice to have, in
addition to the list of samples (as it is currently), the number of samples
directly written. This would make it easier for quick lookup of the data as
you could search for the tag and know directly if the analysis was made from
data with one or multiple samples. It would help judge consistency and
inconsistency issues...
This should be easy enough to see in the
_Order_parameter_experiment.Sample_ID tag. You just have to count the
number of different IDs. I think this information is already in the
model-free saveframes. I'm not sure how capable relax is of handling
this though.
Regards,
Edward
Re: Finished the reading of all the BMRB model-free data - necessary corrections to the database entries.