[phenixbb] phenix_automr error and autobuild question

[Nathaniel Echols]

On Thu, Mar 22, 2012 at 6:23 AM, Maike Bublitz <mbu at mb.au.dk> wrote:

> 1) I have trouble getting a molecular replacement job to run (Phenix
> Version 1.7.3-928), where I want to keep one ensemble fixed in its known
> orientation, only looking for a second ensemble. I keep on getting the
> following error message, both from the GUI and from command line (using a
> 'mymr.eff' parameter file):
>
> ****************************************
> AutoMR Input failed
> Python argument types in
>     SOLU.addSOLU_6DIM_ENSE(InputMR_AUTO, str, list, bool, list, float,
> bool, bool, bool)
> did not match C++ signature:
>     addSOLU_6DIM_ENSE(phaser::SOLU {lvalue}, std::string,
> scitbx::vec3<double>, bool, scitbx::vec3<double>, double, bool, bool, bool,
> bool, scitbx::vec3<double>, double)
> ****************************************
> *************ERROR ENDING *******************
>
> I can't figure out what I'm doing wrong. Any suggestions?
>

This is definitely a bug.  Two suggestions: a) try the Phaser-MR GUI
instead, it may not have this problem, or b) update to the latest nightly
build and see if it's fixed there.  I will see if we can add a regression
test for specifying a fixed ensemble.

> 2) Which parameters would I need to specify to let phenix.autobuild build
a model for one protein of a 2-component complex from scratch, while
keeping the other component unchanged (and using it to calculate the
phases)? Is that possible?

I think you need to define the existing component as ligands, as described
here:

https://www.phenix-online.org/version_docs/dev-1012/autobuild.htm#anch103

I suspect this means that you'll need to supply an initial map for phases,
rather than having it calculate them from the "ligands", but I've never
actually tried this myself.

-Nat
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