On 01/02/2017 17:11, Trevor Sewell wrote:
> I have a 3.4 A (enzyme – protein only) map that I have fitted manually using Coot and
> automatically with Rapper. It all looks very nice – I can fit all but 13 of the 330
> residues. I have the following questions:
> Is there a way of having Coot know that it is an electron map and not an x-ray map?
Yes, and/but it's not under user control.
> The main
> issue is that carboxyls seem to be invisible and Coot tries to fit them as though the map
> had them there
Well, if the atoms are part of the model, then Coot will try to fit them to the "data." I
routinely chop off GLU and ASP side-chain when modelling into cryo-EM maps (that's what the
K key is for).
Coot refines differently to Refmac.
> What is a reasonable starting weight for vdwrestraints ? Is there a rule of thumb for
> choosing this?
I don't typically adjust this. What make you think that you need to do so?
Paul.
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