[phenixbb] Did I work on this part of electronic density correctly

Nathaniel Echols nechols at lbl.gov
Sun Jan 1 17:59:24 PST 2012

On Sun, Jan 1, 2012 at 5:11 PM, Dialing Pretty <hdc123hdc123 at yahoo.com> wrote:
> 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

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


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