Hi Brian,
> 1/ "Select experiment for peak list" dialog offers only existing _3D_
> experiments in the "Existing 3D experiment" list making it impossible to
> select an existing 2D experiment. Since ANSIG 3D crosspeak files contain
> both 2D & 3D, this is a pain. This is probably due to the litter left by
> ANSIG in the 3rd dim since some of the 2Ds come up with a list of
> "Existing 2D experiment"s to select from.
Well it should display only relevant experiments, but as you say this is a
problem with ANSIG where the litter in the third ppm column makes it
difficult to distinguish between 2D and 3D. Anyway for ANSIG (only!) all
experiments are now listed.
>2/ Experiment type "tocsy_HCCH" (3D) seems to actually be a 2D prototype
> so one of the three dimensions can't be assigned.
A mistake in the spectrum reference data (this is currently still derived
from strings but will be better (data modelled) in the future). This is
fixed in the new version - if you want to change it in an existing project
you'll have to edit the top project XML file yourself. Search for
'tocsy_HCCH.hc', and replace it by 'tocsy_HcCh.hc'.
> 3/ Assumption of dimension ordering for ANSIG format crosspeaks is always
> the reverse of the usual situation. i.e. you assume 0 = acqu, 1 = indirect
> 1, 2 = indirect 2 whereas ANSIG is usually 0 = indirect 2, 1 = indirect 1,
> 2 = acqu for a 3D. Could there be at least a toggle to handle
> this?
The 'preferred' dimension order is now set automatically to 'reversed' for
ANSIG. I also set 'reversed' order for XEASY, all other formats are
currently 'normal' order. If anyone wants to see the default order changed
for a format, let me know!
> 4/ The "Do not load" button when selecting which experiments to import
> from a crosspeak file still doesn't work. (I assume it's meant to allow
> you to deselect experiments from the list - instead it just seems to do
> the same as hitting "OK"). This would be a really useful feature.
'Do not load' now cancels the whole import - you have to positively select
the experiments you want to import.
> More generally, I find it painfully slow when deleting imported objects
> e.g. the duff tocsy_HCCH spectra imported in the wrong prototype, or
> deleting a (~130 aa) molecule - even on a speedy machine.
Are you deleting from the general editor or Analysis? Deleting already not
fast as pure API code, but when you do it from a program that uses
'notifiers' to update all windows then it will become a real drag. We'll
discuss what we can do about this... .
All the above format converter changes (plus others, mainly in the
sequence import handling - we hope those will make you happy Brian!) will
be available in the almost-available next release... watch this space!
Have a nice weekend everyone,
Wim.
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Wim Vranken [log in to unmask]
Macromolecular Structure Database (MSD) group
European Bioinformatics Institute (EMBL outstation)
Wellcome Trust Genome Campus
Cambridge CB10 1SD, UK
Tel: +44-1223-494682 Fax: +44-1223-494487
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