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.
