[Chimera-users] Automatic setting of suggested contour level

Hurt, Darrell (NIH/NIAID) [E] darrellh at niaid.nih.gov
Wed Nov 27 14:12:58 PST 2013


Hi Tom,

That certainly makes sense. I appreciate all your efforts in my behalf!

Happy Thanksgiving,
Darrell

-- 
Darrell Hurt, Ph.D.
Section Head, Computational Biology
Bioinformatics and Computational Biosciences Branch (BCBB)
OCICB/OSMO/OD/NIAID/NIH
 
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On 11/27/13 5:01 PM, "Tom Goddard" <goddard at sonic.net> wrote:

>Hi Darrell,
>
>  Chimera could fetch the EMDB XML metadata file and extract the
>suggested contour level and use it.  I have noticed that the suggested
>levels are sometimes very wrong, deep in the noise.  Some investigation
>will be needed to see if the levels are right often enough to be usable.
>I've made a Chimera feature request entry in our database.
>
>	http://plato.cgl.ucsf.edu/trac/chimera/ticket/12644
>
>It would be a good feature for Chimera 2 which we are working on but is
>probably a year or more away.  I'm spending most time on our next
>generation Chimera 2 rather than adding features to the current Chimera 1.
>
>	Tom
>
>
>On Nov 27, 2013, at 11:51 AM, "Hurt, Darrell (NIH/NIAID) [E]" wrote:
>
>> Hi Chimera team,
>> 
>> I love how Chimera seems to intelligently and automatically choose a
>>contour level for fetched EMDB files. However, I have noticed that most
>>EMDB files have a "suggested contour level" associated with them. It can
>>be obtained in the "header" XML files under the tag <contourLevel>. How
>>much more work would it be to automatically fetch this information when
>>fetching the map and then set the contour level to the recommended
>>setting? Would you consider doing it?
>> 
>> Thanks,
>> Darrell
>> 
>> --
>> Darrell Hurt, Ph.D.
>> Section Head, Computational Biology
>> Bioinformatics and Computational Biosciences Branch (BCBB)
>> OCICB/OSMO/OD/NIAID/NIH
>> 
>> 31 Center Drive, Room 3B62B, MSC 2135
>> Bethesda, MD 20892-2135
>> Office: 301-402-0095
>> Mobile: 301-758-3559
>> Web: BCBB Home 
>>Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Page
>>s/bcbb.aspx#niaid_inlineNav_Anchor>
>> Twitter: @niaidbioit<https://twitter.com/niaidbioit>
>> 
>> Disclaimer: The information in this e-mail and any of its attachments
>>is confidential and may contain sensitive information. It should not be
>>used by anyone who is not the original intended recipient. If you have
>>received this e-mail in error please inform the sender and delete it
>>from your mailbox or any other storage devices. National Institute of
>>Allergy and Infectious Diseases shall not accept liability for any
>>statements made that are sender's own and not expressly made on behalf
>>of the NIAID by one of its representatives.
>> 
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>




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