[Chimera-users] [Chimera-announce] new Chimera release (v1.10)

Elaine Meng meng at cgl.ucsf.edu
Mon Dec 1 15:06:54 PST 2014

Dear Debasish Banerjee,

There may have been changes in the  ModBase website, or maybe even the UniProt website -- you would need to ask those developers.   The ability of Chimera to show ModBase models did not change.

Today looking at the ModBase website, I'm having a problem  where it always says there are no models for some sequence, even when I know there are models.  I don't know if this is the same problem you were having.

I know there are models because I can fetch them using Chimera menu: File…Fetch by ID, choosing database: Modbase and entering a sequence ID (UniProt or other).  The same can be done with a command, for example: 

open modbase:P33533

So maybe you can use that approach instead.  Regards,

Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Nov 29, 2014, at 2:39 AM, "Debasish Banerjee" <dbanerjee at banerjee.net.in> wrote:

> To
> Elaine Meng,
> May be I didn't explain properly. Most UniprotKB database entries have used Modbase in the 3D structure database section. In any entry where Modbase is used, clicking on search button next to the  Modbase entry used to open that structure entry page using Chimera. With the current version that doesn't seem to happen (as it was happening with the earlier versions). Please advice.
> Thanking You,
> Debasish Banerjee
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Sent: Wed, 26 Nov 2014 23:02:40 
> To: Debasish Banerjee <dbanerjee at banerjee.net.in>
> Cc: Mailing List <chimera-users at cgl.ucsf.edu>
> Subject: Re: [Chimera-announce] new Chimera release (v1.10)
> On Nov 25, 2014, at 4:17 PM, Debasish Banerjee <dbanerjee at banerjee.net.in> wrote:
> > To,
> > Elaine Meng,
> > I had downloaded Chimara 1.10 but it doesn't seem to operate on other sites like UniprotKB. Can you please comment.
> > Debasish Banerjee
> Dear Debasish Banerjee,
> Not sure I understand your question.  UCSF Chimera is a molecular modeling/graphics program that you use on your own computer. 
> The only relationship to UniProtKB is that you can fetch sequences and annotations from that site while using Chimera.  Maybe you mean you had trouble fetching data from the web (Chimera menu: File… Fetch by ID)?  
> We haven’t heard reports of a problem.  For example, I can start UCSF Chimera 1.10, use menu: File… Fetch by ID, choose database “UniProt” and then get the sequence for NGF_HUMAN shown in Chimera.  Of course, you have to be connected to the internet.  Otherwise, if you have some specific problem you can use Chimera menu: Help… Report a Bug and give enough information about the steps you tried so that somebody else could reproduce it.
> Best,
> Elaine

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