Re: [modeller_usage] Modeling magnesium ion: Segmentation fault

[Modeller Caretaker <modeller-care@ucsf.edu>]

On 5/28/10 6:31 AM, Renuka Robert wrote:
> I want to model ONLY magnesium ion (from protein B) on an already
> crystallized structure (protein A). So the sequence of my target and
> template is exactly the same. My alignment file is

Can you send me (not the list) your structure files too, please? I can't 
reproduce your problem (and thus fix the bug) without them. It is 
definitely a Modeller bug though (not something wrong with your inputs): 
Modeller should never crash with a segfault, regardless of what you feed it.

I think the surface area calculation is getting confused since you have 
no amino acid resides in one structure (but I'll need to check with your 
inputs). As a workaround, you can use the BLK residue '.' rather than 
'$'. Since MG is just a point anyway, your modeling results should be 
almost identical.

	Ben Webb, Modeller Caretaker
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