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<div>Hi Maike,</div>
<div><br>
</div>
<div>What you are doing looks like it should work, however you might want to use this value for keep_pdb_atoms:</div>
<div><br>
</div>
<div> keep_pdb_atoms=False #keep the ligand atoms if model (pdb) and ligand overlap</div>
<div><br>
</div>
<div>because as it is you will take the atoms from the model that autobuild builds if</div>
<div>they overlap with the ones from your input model. Note that autobuild will</div>
<div>try to build everything...and then in places where your input model is present, it</div>
<div>should be used. If that isn't happening, please let me know and I'll try to </div>
<div>figure out why.</div>
<div>All the best,</div>
<div>Tom T</div>
<div>
<div style="font-family: Times New Roman; color: #000000; font-size: 16px">
<hr tabindex="-1">
<div id="divRpF668898" style="direction: ltr; "><font face="Tahoma" size="2" color="#000000"><b>From:</b> phenixbb-bounces@phenix-online.org [phenixbb-bounces@phenix-online.org] on behalf of Maike Bublitz [mbu@mb.au.dk]<br>
<b>Sent:</b> Friday, March 23, 2012 7:35 AM<br>
<b>To:</b> phenixbb@phenix-online.org<br>
<b>Subject:</b> Re: [phenixbb] phenix_automr error and autobuild question<br>
</font><br>
</div>
<div></div>
<div>Thank you Nat,<br>
<br>
Phaser-MR (from the GUI) worked fine with the fixed ensemble.<br>
<br>
But for the autobuild problem - it does run if I provide an mtz file with phases derived from the known part of the model for the initial map, but it seems to ignore the pdb file which I define as ligand and obviously tries to build the whole thing - which
fails.<br>
Here are some of the parameters I have defined in the .eff file. Am I missing something?<br>
<br>
autobuild {<br>
data = mydata_phased_with_partial_model_in_sigmaa.mtz<br>
model = None<br>
seq_file = component_to_build.fasta<br>
map_file = mydata_phased_with_partial_model_in_sigmaa.mtz<br>
refinement_file =mydata_phased_with_partial_model_in_sigmaa.mtz<br>
hires_file = Auto<br>
input_files {<br>
input_labels = FP SIGFP PHIC WCMB None None None None FreeRflag<br>
input_map_labels = FP PHIC WCMB<br>
input_refinement_labels =FP SIGFP FreeRflag<br>
input_lig_file_list = refined_known_component.pdb<br>
keep_input_ligands = True<br>
keep_input_waters = False<br>
keep_pdb_atoms = True<br>
refine_eff_file_list = None<br>
map_file_is_density_modified = False<br>
map_file_fom = None<br>
use_map_file_as_hklstart = False<br>
use_map_in_resolve_with_model = False<br>
}<br>
model_building {<br>
build_type = *RESOLVE RESOLVE_AND_BUCCANEER<br>
include_input_model = False<br>
refine = True<br>
two_fofc_in_rebuild = False<br>
refine_map_coeff_labels = "2FOFCWT PH2FOFCWT"<br>
filled_2fofc_maps = True<br>
map_phasing = False<br>
}<br>
rebuild_in_place {<br>
rebuild_in_place = Auto True *False<br>
}<br>
<br>
Best regards,<br>
Maike <br>
<br>
On 22.03.2012 14:33, Nathaniel Echols wrote:
<blockquote type="cite">On Thu, Mar 22, 2012 at 6:23 AM, Maike Bublitz <span dir="ltr">
<<a href="mailto:mbu@mb.au.dk" target="_blank">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">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" target="_blank">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>
<br>
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