Re: [phenixbb] How do I gather the pieces after AutoBuild?
Hi Dale, If you run AutoBuild with "rebuild_in_place=Yes" then it will keep the pieces that you have, try to rebuild them (in nearby locations), and not reassemble the molecule. Rebuilding in place is supposed to be a way to finish off your structure, and that's why it doesn't move it around. In your case, you are rebuilding in place after Phaser molecular replacement. Usually Phaser will make a compact molecule during MR, so this should not normally be a problem. I gather that in this case it didn't do so, however. With rebuild_in_place=No then AutoBuild should try and make a compact molecule. If you have NCS then it will try to make a compact molecule with NCS. All the best, Tom T
Hi all,
I have finished my Autobuild but the resulting model has some residues that are scattered in distant asymmetric units. Coot shows their symmetry images where they belong, next to the rest of the protein. I could rebuild these residues by hand in the right place, or collecte together all the symmetry operators and write a script to gather them, but being lazy would like a more automated solution. Surely this happens to other people and there is a tool that solves this problem. I've read a bunch of the web pages for AutoBuild but didn't find a solution there.
My AutoBuild command was
phenix.autobuild model=AutoMR_run_4_/MR.1-protein.pdb data=1M50-2.mtz \ map_file=AutoMR_run_4_/MR.MAP_COEFFS.1.mtz \ seq_file=../fmo-ct.pir \ resolution=2.2 dmax=20 refinement_resolution=2.2 \ cif_def_file_list=/usr/users/dale/geometry/chromophores/bcl_tnt.cif \ input_lig_file_list=AutoMR_run_4_/MR.1-Bchl-a.pdb \ rebuild_in_place=Yes
Shouldn't AutoBuild build a compact model by default?
Dale Tronrud _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Dear Tom, I was about to write an answer to my own letter since I have a solution, but I don't understand it. I have a molecular replacement solution in which each molecule is compact and the two copies are right next to each other. AutoBuild is tearing pieces out and scattering them about symmetry space, although most of both molecules stay in the same place. My solution that fixes this problem and keeps the molecules together? Remove the methinone that the sequence file has as the first residue. The first 8 or 9 residues of this molecule are disordered in both the original crystal and this crystal. I was using the DNA sequence as the source for the amino acid sequence but I believe the Met is removed post-translationally. The first run had the Met and AutoBuild built molecules with some parts far removed from the majority of the two peptides. The second run had the Met removed from the sequence file, and as far as I recall nothing else changed, and this produced a proper model. Could this be a consequence of the sequence renumbering required by the differing alignments? I'm moving on with this model. Dale Thomas C. Terwilliger wrote:
Hi Dale,
If you run AutoBuild with "rebuild_in_place=Yes" then it will keep the pieces that you have, try to rebuild them (in nearby locations), and not reassemble the molecule. Rebuilding in place is supposed to be a way to finish off your structure, and that's why it doesn't move it around.
In your case, you are rebuilding in place after Phaser molecular replacement. Usually Phaser will make a compact molecule during MR, so this should not normally be a problem. I gather that in this case it didn't do so, however.
With rebuild_in_place=No then AutoBuild should try and make a compact molecule. If you have NCS then it will try to make a compact molecule with NCS.
All the best, Tom T
Hi all,
I have finished my Autobuild but the resulting model has some residues that are scattered in distant asymmetric units. Coot shows their symmetry images where they belong, next to the rest of the protein. I could rebuild these residues by hand in the right place, or collecte together all the symmetry operators and write a script to gather them, but being lazy would like a more automated solution. Surely this happens to other people and there is a tool that solves this problem. I've read a bunch of the web pages for AutoBuild but didn't find a solution there.
My AutoBuild command was
phenix.autobuild model=AutoMR_run_4_/MR.1-protein.pdb data=1M50-2.mtz \ map_file=AutoMR_run_4_/MR.MAP_COEFFS.1.mtz \ seq_file=../fmo-ct.pir \ resolution=2.2 dmax=20 refinement_resolution=2.2 \ cif_def_file_list=/usr/users/dale/geometry/chromophores/bcl_tnt.cif \ input_lig_file_list=AutoMR_run_4_/MR.1-Bchl-a.pdb \ rebuild_in_place=Yes
Shouldn't AutoBuild build a compact model by default?
Dale Tronrud _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
participants (2)
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Dale Tronrud -
Thomas C. Terwilliger