On Thu, Mar 22, 2012 at 6:23 AM, Maike Bublitz <span dir="ltr"><<a href="mailto:mbu@mb.au.dk">mbu@mb.au.dk</a>></span> wrote:<br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">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):<br>
<br>
****************************************<br>
AutoMR Input failed<br>
Python argument types in<br>
��� SOLU.addSOLU_6DIM_ENSE(InputMR_AUTO, str, list, bool, list,
float, bool, bool, bool)<br>
did not match C++ signature:<br>
��� addSOLU_6DIM_ENSE(phaser::SOLU {lvalue}, std::string,
scitbx::vec3<double>, bool, scitbx::vec3<double>,
double, bool, bool, bool, bool, scitbx::vec3<double>, double)<br>
****************************************<br>
*************ERROR ENDING *******************<br>
<br>
I can't figure out what I'm doing wrong. Any suggestions?<br></div></blockquote><div><br></div><div>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.</div>
<div><br></div><div>>�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?</div><div><br></div><div>I think you need to define the existing component as ligands, as described here:</div><div><br></div><div><a href="https://www.phenix-online.org/version_docs/dev-1012/autobuild.htm#anch103">https://www.phenix-online.org/version_docs/dev-1012/autobuild.htm#anch103</a><br>
</div><div><br></div><div>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.</div>
<div><br></div><div>-Nat</div></div>