Morphing only a part of the model?
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Dear all, I am working on a multisubunit protein complex (ca. 2000 residues). I would like to morph only a part or one subunit into the experimental electron density without morphing the rest of the protein. iIs there a way to select a subunit or a part of the model? Best regards, Guenter
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Hi Guenter, Thanks for the question, I can see how this would be useful. Right now no, you can't do this but I'll see if I can put i in. If you are comfortable with scripts, you can try this: phenix_regression.wizards.test_command_line_resolve_memory test_morph_model_in_memory This will create a directory test_morph_model_in_memory and run a quick single morphing with no refinement of a small structure. You can edit the file "morph.py" and run it as in the example "test_morph_model_in_memory.com" supplying map coefficients for your map and a PDB file for just your one domain. You can then take the result, refine it if you like, then run the morph.py script again on the new model.... All the best, Tom T ________________________________________ From: phenixbb-bounces@phenix-online.org [phenixbb-bounces@phenix-online.org] on behalf of Guenter Fritz [guenter.fritz@uniklinik-freiburg.de] Sent: Monday, May 06, 2013 4:30 AM To: phenixbb@phenix-online.org Subject: [phenixbb] Morphing only a part of the model? Dear all, I am working on a multisubunit protein complex (ca. 2000 residues). I would like to morph only a part or one subunit into the experimental electron density without morphing the rest of the protein. iIs there a way to select a subunit or a part of the model? Best regards, Guenter _______________________________________________ phenixbb mailing list phenixbb@phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb
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Hi Tom, thanks a lot for the workaround! Just one more question: If I use just a part of the model for morphing it into the density, won't it "move" to other parts of the density which are then not occupied by the rest of the model? Or does the morphing procedure just allow small local changes? Thanks again and best wishes, Guenter
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Hi Guenter, Yes, something could move into density belonging to something else. However also yes, the movements will always be small (set by your value of rad_morph=6 in morph.py; the allowed movement in 1 cycle is rad_morph/3). All the best, Tom T ________________________________________ From: phenixbb-bounces@phenix-online.org [phenixbb-bounces@phenix-online.org] on behalf of Guenter Fritz [guenter.fritz@uniklinik-freiburg.de] Sent: Monday, May 06, 2013 9:50 AM To: PHENIX user mailing list Subject: Re: [phenixbb] Morphing only a part of the model? Hi Tom, thanks a lot for the workaround! Just one more question: If I use just a part of the model for morphing it into the density, won't it "move" to other parts of the density which are then not occupied by the rest of the model? Or does the morphing procedure just allow small local changes? Thanks again and best wishes, Guenter
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participants (2)
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Guenter Fritz
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Terwilliger, Thomas C