Generating electron density from protein coordinate (PDB)
Dear phenix users, Although phenix in general is used to convert electron density into protein coordinates (PDB), I am interested in retrieving electron density of an optimized PDB, hopefully at a resolution of ~1-2A. Since there could be manipulation of the coordinate file upstream, some crystal structure information could be lost. I notice that phenix generates structure factor from coordinates (assuming P1 symmetry) by phenix.fmodel. However, the conversion from structure factor to electron density requires a normalization constant (sum of atomic form factors). I am still trying to identify the correct function to use to output a non-binary output format. phenix.maps might work but I am unsure about the map_type. If anyone is willing to provide some suggestions, that would be very helpful. Sincerely, Simon
Hi Simon,
Although phenix in general is used to convert electron density into protein coordinates (PDB), I am interested in retrieving electron density of an optimized PDB, hopefully at a resolution of ~1-2A. Since there could be manipulation of the coordinate file upstream, some crystal structure information could be lost.
I notice that phenix generates structure factor from coordinates (assuming P1 symmetry) by phenix.fmodel. However, the conversion from structure factor to electron density requires a normalization constant (sum of atomic form factors). I am still trying to identify the correct function to use to output a non-binary output format. phenix.maps might work but I am unsure about the map_type.
you can use phenix.fmodel to generate a Fourier image of model electron density distribution at specified resolution just like this (typing from memory, check syntax) phenix.fmodel model.pdb high_res=2.3 This will generate the exact map, then Fourier transform it and retain and output Fourier map coefficients up to specified (high_res) resolution. You can also cut it at low-res end: using low_res keyword. You can convert the output of the above command into real map using phenix.mtz2map map_coeffs.mtz Also, you can calculate exact density distribution using phenix.model_map model.pdb These are a few pointers for you to play with and see if you get what you want.. Let us know if you have any questions or need help. Good luck! Pavel
Dear Pavel,
Thanks for your prompt reply. I tried phoenix.model_map and it successfully
generates ccp4 and xplor files. However, I fail to understand the xplor
file format for further analysis. Is there any suggested documentation on
xplor (ccp4) format? Visualization on pymol also suggests that my electron
density was truncated by the box boundary. Is there any way to first
centralize the box at the core of the protein, then create a box with a
defined (sub)region of the PDB?
Regards,
Simon
On Thu, Mar 19, 2020 at 7:14 AM Pavel Afonine
Hi Simon,
Although phenix in general is used to convert electron density into protein coordinates (PDB), I am interested in retrieving electron density of an optimized PDB, hopefully at a resolution of ~1-2A. Since there could be manipulation of the coordinate file upstream, some crystal structure information could be lost.
I notice that phenix generates structure factor from coordinates (assuming P1 symmetry) by phenix.fmodel. However, the conversion from structure factor to electron density requires a normalization constant (sum of atomic form factors). I am still trying to identify the correct function to use to output a non-binary output format. phenix.maps might work but I am unsure about the map_type.
you can use phenix.fmodel to generate a Fourier image of model electron density distribution at specified resolution just like this (typing from memory, check syntax)
phenix.fmodel model.pdb high_res=2.3
This will generate the exact map, then Fourier transform it and retain and output Fourier map coefficients up to specified (high_res) resolution. You can also cut it at low-res end: using low_res keyword.
You can convert the output of the above command into real map using
phenix.mtz2map map_coeffs.mtz
Also, you can calculate exact density distribution using
phenix.model_map model.pdb
These are a few pointers for you to play with and see if you get what you want.. Let us know if you have any questions or need help.
Good luck! Pavel
Hi Simon,
I tried phoenix.model_map and it successfully generates ccp4 and xplor files.
note, this generates a model-calculated exact map (infinite resolution). I'm not sure this is what you want, thinking of practical applications. You can always FT this map to get an image of it at particular resolution, but this is a separate step. Just making sure you are aware of all of this.
However, I fail to understand the xplor file format for further analysis. Is there any suggested documentation on xplor (ccp4) format?
While X-plor is old format (yet much easier to understand and deal with at low-level than ccp4), ccp4 is pretty much the standard these days with most software being able to deal with it. So I'd say some web search should get you up to speed!
Visualization on pymol also suggests that my electron density was truncated by the box boundary. Is there any way to first centralize the box at the core of the protein, then create a box with a defined (sub)region of the PDB?
Perhaps you want to calculate the map in the entire unit cell and then choose how to crop it for your convenience. Does this answer your questions? Do you still have more? Please feel free to let us know and we will follow up! Pavel
Hi Simon,
Although phenix in general is used to convert electron density into protein coordinates (PDB), I am interested in retrieving electron density of an optimized PDB, hopefully at a resolution of ~1-2A. Since there could be manipulation of the coordinate file upstream, some crystal structure information could be lost.
I notice that phenix generates structure factor from coordinates (assuming P1 symmetry) by phenix.fmodel. However, the conversion from structure factor to electron density requires a normalization constant (sum of atomic form factors). I am still trying to identify the correct function to use to output a non-binary output format. phenix.maps might work but I am unsure about the map_type.
you can use phenix.fmodel to generate a Fourier image of model electron density distribution at specified resolution just like this (typing from memory, check syntax) phenix.fmodel model.pdb high_res=2.3 This will generate the exact map, then Fourier transform it and retain and output Fourier map coefficients up to specified (high_res) resolution. You can also cut it at low-res end: using low_res keyword. You can convert the output of the above command into real map using phenix.mtz2map map_coeffs.mtz Also, you can calculate exact density distribution using phenix.model_map model.pdb These are a few pointers for you to play with and see if you get what you want.. Let us know if you have any questions or need help. Good luck! Pavel
participants (2)
-
Kit Sang Chu -
Pavel Afonine