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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.