[Chimera-users] Automatic setting of suggested contour level

[Hurt, Darrell (NIH/NIAID) [E]]

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
 
31 Center Drive, Room 3B62B, MSC 2135
Bethesda, MD 20892-2135
Office: 301-402-0095
Mobile: 301-758-3559Web: BCBB Home Page
<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/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.






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.
>> 
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>> 
>