[Chimera-users] Chimera-Modeller interface, template selection

Julia Shifman jshifman at mail.huji.ac.il
Thu Nov 17 05:14:46 PST 2016


Dear Elaine,

I was able to get over the first bug and not to download the file form the pDB. However, I am experiencing another problem with modeling two chains. For some reason my models come out with one chain correctly folded and the second chain fused to the C-terminus of the first chain and unfolded.  I am sending you the output file together with the alignment file. Could you tell me what the problem is?  Thanks,

Julia

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Dr. Julia Shifman
Department of Biological Chemistry
Hebrew University of Jerusalem
Phone:   972-2-658-4078

WEB:      www.bio.huji.ac.il/shifman


> On Nov 16, 2016, at 10:25 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi Dina!
> It will work if your structure is associated with your sequence alignment.  Then in the dialog where you choose template, it will list the name of the associated sequence.  So pick that one.  Then, when you execute there may be a message “could not discern PDB ID” or something like that, but it will still run the calculation.  It is only trying to find the PDB ID to be able to show more information in the template-choosing area of the dialog.
> 
> I tried it just now on some structure that was not opened from the PDB, and it worked to produce a model from that template, so hopefully it will work for you too.  You can check that the job is running in the Task Panel (opened by clicking the small “i” button near the lower right corner of the Chiemra window).
> I hope this helps,
> Elaine
> -----
> 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 16, 2016, at 12:48 AM, Dina Schneidman <dina.schneidman at mail.huji.ac.il> wrote:
> 
>> Hi,
>> 
>> Currently it is only possible to select a template from PDB based on the PDB code.
>> Would it be possible to have an option to use one of the currently open PDB files in Chimera?
>> 
>> Thanks!
>> Dina
> 



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