On Fri, May 27, 2011 at 6:36 AM, Thomas C. Terwilliger wrote: I am guessing that the specification of the chain as "chain B" rather than
as "B" might be the problem, but I am not certain of that. That's half of the problem - based on viewing the original email with screen
captures (which the list server rejected), the other problem is that the
full parameter input was this:
omit_chain_list chainB
I suspect there's some confusion with the command-line documentation. You
don't need to include the parameter name in the GUI, just the actual value,
i.e.
chain B
(without quotes)
But I agree with Tom, running phenix.refine on a modified PDB file will be
easier. I think Pavel plans to introduce an even easier way to do this in
phenix.maps at some point in the future.
-Nat