new feature: conversion of atomic coordinates to electron density map
Hi, I am not quite sure, whether this is possible with Chimera ... but it would be great if there is a feature that would allow to convert a .pdb structure (atomic coordinates) into a map usually obtained by electron microscopy (sections) - for example into mrc/ccp4 format. Even filtering this map then to different resolutions (including storing entire maps) would be an interesting feature. Thanks, -Thomas __________________________________________ Thomas C Marlovits, PhD, M.A.S IMP - Institute of Molecular Pathology IMBA - Institute of Molecular Biotechnology, Austrian Academy of Sciences Dr. Bohr-Gasse 3 A-1030 Vienna AUSTRIA marlovits@imp.univie.ac.at Tel (+ 43) 1 79044 4630
Hi Thomas, There is a Chimera extension that produces an MRC density map from a PDB file. It is part of the Analysis of Intermediate Resolution Structures (AIRS) toolkit that is distributed with the EM single article reconstruction package EMAN1. http://ncmi.bcm.tmc.edu/software/AIRS http://blake.bcm.tmc.edu/eman If you install EMAN and configure Chimera to find the EMAN / Chimera extensions as described here http://ncmi.bcm.tmc.edu/software/AIRS/doc_html then there will be a Chimera menu entry Tools / AIRS / PDB to MRC. It allows you to specify a resolution and number of angstroms per pixel for the map. This is a good bit of work to setup and I plan on including the ability to make a density map from a PDB model directly in Chimera distributions in the future. It will use a Gaussian for each atom. I'll add this to my list of requested Chimera features. http://www.cgl.ucsf.edu/chimera/plans.html Thanks for the suggestion. Tom
Dear all, I am using chimera to read two small molecules in pdb format, align them and save their coordinates. I would like to know if there is a way to save the coordinates in a pdb file keeping the atom order of the original pdb file I have read. Thanks for your help. Laura
Hi Laura, Chimera's PDB support was written with macromolecules in mind and adheres as closely as possible to the PDB standard. This means that it outputs amino and nucleic acid atoms within a residue in the same order that the PDB uses, regardless of original input order. Not much thought was given to the order of "other" residue atoms, and they basically come out in random order -- which is obviously bad in your case. I'm going to open a bug report on this, with you on the recipient so that you will know when the behavior is fixed. Until then, the only way to preserve ordering is to output in some other format, e.g. Mol2, which may or may not be acceptable for what you're doing. --Eric Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu
participants (4)
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Eric Pettersen -
Laura Masgrau -
Thomas C Marlovits -
Tom Goddard