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
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: [email protected] [[email protected]] on behalf of Guenter Fritz [[email protected]] Sent: Monday, May 06, 2013 4:30 AM To: [email protected] 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 [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
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
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: [email protected] [[email protected]] on behalf of Guenter Fritz [[email protected]] Sent: Monday, May 06, 2013 4:30 AM To: [email protected] 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 [email protected] http://phenix-online.org/mailman/listinfo/phenixbb _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
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: [email protected] [[email protected]] on behalf of Guenter Fritz [[email protected]] 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
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: [email protected] [[email protected]] on behalf of Guenter Fritz [[email protected]] Sent: Monday, May 06, 2013 4:30 AM To: [email protected] 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 [email protected] http://phenix-online.org/mailman/listinfo/phenixbb _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
participants (2)
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Guenter Fritz -
Terwilliger, Thomas C