[phenixbb] SA omit map for ligand

Nathaniel Echols nechols at lbl.gov
Fri May 27 07:21:05 PDT 2011

On Fri, May 27, 2011 at 6:36 AM, Thomas C. Terwilliger <terwilliger at lanl.gov
> 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,

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.

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