Re: [modeller_usage] Heme out in space

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

On 6/14/14, 7:53 PM, Joel Tyndall wrote:
> I’ve been generating some models of some cytochrome proteins with heme.
> I have generated ~6 structures that are all fine but the next two have
> the heme placed out in space relative to the protein. I have seen this
> before but have put it down to user error.

This would be the case if there were no restraints on the heme, which 
will happen if you don't have any template protein within the cutoff 
distance:
http://salilab.org/modeller/9.13/manual/node70.html

You might sometimes get models that look OK because the heme is trapped 
purely by VDW interactions, or it just didn't have to wander off too far.

	Ben Webb, Modeller Caretaker
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