[phenixbb] AutoBuild after resolve

Thomas C. Terwilliger terwilliger at lanl.gov
Sat Feb 28 08:58:15 PST 2009

Hi Mo,

Yes, you're right you want to use "Optional map coefficient file name" to
input your density-modified phases.  I'm sorry about the bug in reading
the labels. I think that if you download the current development version
from the website at www.phenix-online.org then this will go away. (If not,
please let me know!)

Also note that the temporary.com file running density modification won't
actually say "phases_from_resolve". It should however say
"hklstart"....something.mtz which sets that flag inside resolve.

All the best,
Tom T

Thanks for the e-mail!

I think I've figured out the problem. I had been using the GUI to set
"input_map_file" and "input_map_labels" rather than using "Optional map
coefficient file name". It wasn't reading in the solvent flattened data
correctly (and thus not setting "phases_from_resolve").

In addition there seems to be a bug in how the optional map file labels
read, since:
temporary.com:LABIN FP=PHIdm PHIB=FOMdm FOM=Fdm

Is there a fix for this (version 1.3), as I've flipped them round and
get them mis-assigned?


On Fri, Feb 27, 2009 at 7:49 PM, Thomas C. Terwilliger
<terwilliger at lanl.gov
> wrote:

> Hi Mo,
> There isn't any place in the AutoBuild GUI specifically for
> "phases_from_resolve".  If you really want to set this parameter you can
> go to the "uncommon inputs" window and set "resolve_command" to
> "phases_from_resolve".
> I think that you don't want to do this, however.  I am assuming that
> this
> means that you are using a density-modified map as input to AutoBuild
> with
> data=my_density_modified_map.mtz.
> What you want to do instead is say (or set in the GUI):
> data=my_experimental_fobs_and_phases.mtz \
> input_map_file=my_density_modified_map.mtz
> and then AutoBuild will start from your density modified map, but it
> will
> use experimental phase information as the prior phase information. It
> will
> also automatically set the parameter "phases_from_resolve" so that that
> you do not have to.
> I hope that helps!
> -Tom T
> Hi all,
> Can someone tell me where in the AutoBuild GUI I can set
> "phases_from_resolve"? I've looked for it in the "set variable" section,
> but
> it's not listed.
> Thanks!
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