On 08/19/2013 01:19 PM, Rolf Huehne wrote:
> On 08/19/2013 02:10 AM, Robert Hanson wrote:
>> For example, your database shows structures. What's the best default
>> orientation to show such that the longest side of the box is along X and
>> the shortest depth is toward the user?
>>
>> rotate BEST
>>
> I thought that this might be an intended usage. But I didn't understand
> it from the description.
>
> Have you compared the results with the much faster (and atom number
> independent) approximation using the boundbox plane sizes, like we are
> using it in the Jena3D viewer (jena3d.jenage.de)?
>
> Although it doesn't work perfectly for all PDB entries it works overall
> quite well. And if you have to precalculate about 300.000 images for all
> PDB structures it makes quite a difference if the selection of the
> orientation takes milliseconds or in the range of seconds.
>
I did a little comparison between
"http://chemapps.stolaf.edu/jmol/jsmol/simple.htm"; and our predefined
images.
It was hard to find an example that would need improvement, looking
quickly at the thumbnails of the first 10000 protein structures in a
customized JenaLib entry list
("http://jenalib.fli-leibniz.de/cgi-bin/entry_list.pl?TYPE=customized&TABLE=&STATISTICS=&DATABASE_FILTER=pdb&DATABASE_FILTER=ndb&METHOD_FILTER=x-ray_neutron_methods&METHOD_FILTER=nmr_methods&METHOD_FILTER=electron_methods&METHOD_FILTER=other_methods&METHOD_FILTER=theoretical_models&MOLECULE_TYPE_FILTER=protein&SORT1=pdb_expdata_type&SORT2=idb_id&SORT3=default&LIST_INFO=serial_number&LIST_INFO=image&LIST_INFO=pdb_expdata_type&LIST_INFO=pdb_entry_type_list&LIST_INFO=pdb_release_date&LIST_INFO=pdb_header&DATE=any&DAY1=&MONTH1=&YEAR1=&DAY2=&MONTH2=&YEAR2=&OUTPUT_FORMAT=pre&WIDTH=200&LIMIT=limit&ENTRY_LIMIT=10000&SEARCH_TERMS=&CODE_LIST=&VIEW=build+entry+list";).
The only one I found this way was 1PFD, although it looks not so bad.
But in my opinion the "rotate best" result looks even a little bit worse.
So I just picked some test candidates looking good in Jena3D/JenaLib and
tried "rotate best":
- 1AZN and 1B4M look good
- 3J0Q looks not quite as good
- 1AW0 and 1CRP look worse but still better than default
- 108L and 1A23 look not good
Regards,
Rolf
--
Rolf Huehne
Postdoc
Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI)
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