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

Elaine Meng meng at cgl.ucsf.edu
Thu Nov 17 10:58:03 PST 2016


Hi Julia,
You cannot model multichain structures using the simple Modeller interface in Chimera.  To do that you would have to run Modeller “manually” outside of Chimera.  Even though the template may have additional chains, they will be ignored in the modeling process. This is described in the documentation:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html#comparative>

The “/“ character in the sequence alignment to mean chain break is notation specific to Modeller, and not understood by Chimera (or other programs as far as I know, since it is not in the official alignment format definitions). Chimera interprets each sequence as only a single chain, which is why when you use  this interface, you get additional residues stuck on the end of the other chain.

So, none of these things are bugs, just limitations of what you can do with the simple Modeller interface in Chimera.  Sorry, you may need to use Modeller the “hard way.”
Regards,
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 17, 2016, at 5:14 AM, Julia Shifman <jshifman at mail.huji.ac.il> wrote:
> 
> 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
> 
> <5C7_model.pdb><5C7Jcut.pdb><5C7Jchainc-fill.ali>
> 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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