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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