Hi, No, if you run AutoMR from the command line you'll run into the same bug, and I don't think there's a command-line equivalent to Phaser-MR. You could run it from a keyword script, as explained on one of our tutorial pages (http://www.phaser.cimr.cam.ac.uk/index.php/MR_using_keyword_input). In this case, you could specify the fixed partial solution as an ensemble, then provide SOLU commands to say that it's already in the right orientation, e.g. ENSEMBLE fixed PDBFILE fixed.pdb IDENTITY 45 SOLU SET SOLU ORIGIN ENSEMBLE fixed However, unless the job that got you the partial solution was very slow, the easiest approach might be just to start over, specifying more than one search component in the AutoMR command and doing the whole search for multiple components in one job. Note that, if you use a keyword script, you should replace "phaser" with "phenix.phaser" to get the Phenix version of Phaser if you don't want an older version installed as part of CCP4. Best wishes, Randy On 16 Feb 2012, at 13:33, Alexander Batyuk wrote:
Dear Randy,
Thank you! Is there any way to do it from the command line?
Best wishes,
Alex
On 16 Feb 2012, at 14:26, Randy Read wrote:
Dear Alexander,
Thanks for reporting this. It turns out that the addSOLU_6DIM_ENSE function was updated in Phaser, to add some new arguments necessary to handle translational NCS, without the code in AutoMR being changed at the same time. Either this option to provide a fixed ensemble in AutoMR is used very rarely, or (more worryingly) people who have run into the problem have been silently frustrated, because these changes were introduced some time ago.
We'll sort out the best way to fix this, probably in time for the next nightly build. In the meantime, you should be able to achieve the same goal through the Phaser-MR interface. When you define the ensemble for the fixed partial solution in that interface, just check the box labelled "Ensemble is fixed partial solution". Under the "Search procedure" tab, you don't want to check the ensemble for the fixed partial solution, just the one(s) for anything left to place.
Best wishes,
Randy Read
On 16 Feb 2012, at 11:21, Alexander Batyuk wrote:
Dear all,
I have the following error while trying to put fixed ensemble into AutoMR:
Adding Ensemble c1 as fixed solution with: Euler angles: [359.98, 0.0, 0.0] Coords (orthogonal A): [-1.0, 0.476, -1.001] *************ERROR ENDING *******************
**************************************** 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 *******************
What could be the reason for that? I'm running dev-986 on OS X 10.6.8. Stable 1.7.3 gives the same error.
Best wishes,
Alex
-- Alex Batyuk The Plueckthun Lab www.bioc.uzh.ch/plueckthun
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------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: [email protected] Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
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-- Alex Batyuk The Plueckthun Lab www.bioc.uzh.ch/plueckthun
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: [email protected] Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk