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
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
_______________________________________________ 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
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
_______________________________________________ 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
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
-- Alex Batyuk The Plueckthun Lab www.bioc.uzh.ch/plueckthun
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
_______________________________________________ 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
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
-- 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
Hi All, I have a situation that I would appreciate any/all help from the community. Crystal appears to be C2221 with a complex of MolA:MolB. Diffraction to ~2.2A with 1 complex in the ASU. Rmerge 5.7% to 2.2A R/Rfree=18.9/23.5% However, MolB (a 6 helix-bundle protein) is only half visible and the space of the invisible helices is occupied by the same visible helices of a crystallographic 2-fold (along a-axis) related MolB. This, of course, cannot be physically true. Two alternative trials. 1) indexed in P21 (same unit cell) with the 21 of C2221 as the unique b axis. Solution has 4 complexes. The c2221 a direction 2-fold should be absent in P21. However, the 4 independent complexes pack exactly as in C2221. 2) indexed in P1. 8 molecules. Packing is again identical to that of C2221. In both cases, R/Rfree are about the same. When used the MolA/MolB (full molecule as search model), then no solutions were found by Phaser due to severe clashes. My guess is that the crystal is P21 with beta=90 and there is twinning (2-fold along a-axis). And the twin fraction is 50%. At the same time, the missing helices must also be disordered in each twin fraction. Does this sound plausible? Is there a way to incorporate the twin law in MR to break this ambiguity? Thanks a lot! Jeffrey
Hi Jeffrey, I would start this with phenix.xtriage. Is the twinning analysis (in particular the moments of the intensities) consistent with 50% twinning? It is not quite clear what you are describing with:
However, MolB (a 6 helix-bundle protein) is only half visible and the space of the invisible helices is occupied by the same visible helices
Perhaps a link to a picture would be helpful to visualize this. It would seem that you have a very low R/Rfree for having a significant part of the model still unmodelled. What happens if you leave out everything that is at all unclear. What is R/Rfree now? What does the map look like in the region in question? All the best, Tom T ________________________________________ From: [email protected] [[email protected]] on behalf of Luo, Jeffrey [JRDUS] [[email protected]] Sent: Tuesday, February 21, 2012 3:49 PM To: PHENIX user mailing list Subject: [phenixbb] Overlapping molecules Hi All, I have a situation that I would appreciate any/all help from the community. Crystal appears to be C2221 with a complex of MolA:MolB. Diffraction to ~2.2A with 1 complex in the ASU. Rmerge 5.7% to 2.2A R/Rfree=18.9/23.5% However, MolB (a 6 helix-bundle protein) is only half visible and the space of the invisible helices is occupied by the same visible helices of a crystallographic 2-fold (along a-axis) related MolB. This, of course, cannot be physically true. Two alternative trials. 1) indexed in P21 (same unit cell) with the 21 of C2221 as the unique b axis. Solution has 4 complexes. The c2221 a direction 2-fold should be absent in P21. However, the 4 independent complexes pack exactly as in C2221. 2) indexed in P1. 8 molecules. Packing is again identical to that of C2221. In both cases, R/Rfree are about the same. When used the MolA/MolB (full molecule as search model), then no solutions were found by Phaser due to severe clashes. My guess is that the crystal is P21 with beta=90 and there is twinning (2-fold along a-axis). And the twin fraction is 50%. At the same time, the missing helices must also be disordered in each twin fraction. Does this sound plausible? Is there a way to incorporate the twin law in MR to break this ambiguity? Thanks a lot! Jeffrey _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
participants (4)
-
Alexander Batyuk -
Luo, Jeffrey [JRDUS] -
Randy Read -
Terwilliger, Thomas C