Hi everyone, I am working on a series of crystals with overall same framework structure plus a different extra part which attaches to the framework. I want to compare the electron density maps of the crystals by overlapping the frameworks and see how the extra parts differ from each other. Is there a way I can do it? Thank you very much for your help! Sincerely, Xiang -- Li Xiang Department of chemistry, Purdue University Email：[email protected]
Hi Xiang, why not? You can arbitrarily choose one model and map as a reference and overlay the rest over it. Phenix tools such as "Structure comparison" or lower level ones such as phenix.superpose_maps and phenix.superpose_pdbs should help here. Nat spent time on this so I hope he offers more advice on this once he sees this email. If (and only if) nothing helps please feel free to get back to me and I may provide with a custom script to accomplish this task. Pavel On 8/24/14 8:35 PM, 李翔 wrote:
Hi everyone,
I am working on a series of crystals with overall same framework structure plus a different extra part which attaches to the framework. I want to compare the electron density maps of the crystals by overlapping the frameworks and see how the extra parts differ from each other. Is there a way I can do it?
Thank you very much for your help!
Sincerely, Xiang
-- Li Xiang Department of chemistry, Purdue University Email：[email protected] mailto:[email protected]
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On Sun, Aug 24, 2014 at 9:34 PM, Pavel Afonine
why not? You can arbitrarily choose one model and map as a reference and overlay the rest over it. Phenix tools such as "Structure comparison" or lower level ones such as phenix.superpose_maps and phenix.superpose_pdbs should help here. Nat spent time on this so I hope he offers more advice on this once he sees this email.
There isn't much to add to this, other than a more thorough description of what the programs do, which as usual, is not (yet) mentioned in our documentation: - phenix.superpose_maps: given two models and two MTZ files containing map coefficients, superposes the models (using user-provided selections if desired), moves them into a P1 box (where all sites > [0,0,0]), then transforms the selected maps to follow. Only works on one pair of map coefficients at a time, but allows any type of complex array to be used. - structure comparison: given M models containing N copies of chain X, and M corresponding MTZ files, extracts all copies of chain X, superposes in a P1 box, transforms the maps to follow. Works with any arbitrary number of models or chains, but limited to the most common map types (2mFo-DFc, mFo-DFc, anomalous). We can make these methods more flexible if necessary - this is probably another set of code that's overdue for refactoring and consolidation anyway. -Nat
participants (3)
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Nathaniel Echols -
Pavel Afonine -
李翔