On Sun, Jan 1, 2012 at 5:11 PM, Dialing Pretty
Attached is a part of electronic density pap I assigned to Pro. After Phenix refinement, we can see under the Pro ring there is a rather large green, above the Pro ring there is a part of red.
Do you think whether I assign the Pro correctly?
My guess is no, but it's difficult to be certain from a single image. If you're certain that the sequence assignment of the rest of the chain is correct (not out of register), the Pro might be a mistake (in which case you would need to have the expression construct or gene re-sequenced). I should repeat what Tim Springer told you a week or two ago: it would be wise to find a more experienced crystallographer in your department/institution (hopefully there is one available!), and have him or her go through the structure with you interactively in Coot. The bulletin boards are great resources if you need a second opinion, or require help figuring out how to use the software - however, they are not a substitute for direct assistance when you're learning out how to build a model manually. We're always happy to try to answer questions like this, of course, but I think you'll find this a much slower and less effective way to learn than talking to someone personally. -Nat