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This paper
http://journals.iucr.org/d/issues/2015/01/00/ba5226/index.html should be useful for use of Refmac. Possibly 5.5A is a bit low - Refmac has been used for reconstructions better than
4.0 A. Also it will depend how the local resolution varies over the map. You can restrain to an external reference structure, and certainly you would have to be very careful of overfitting.
Refmac refines in reciprocal space, so it does need to generate structure factors (i.e. produce .mtz file from .map/.mrc file). But the latest version of Refmac
will do this for you, see
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/refmac_keywords.html#id.seab0879x62k
The latest CCP4 release 6.5 has a version of Refmac which includes the latest set of EM-related keywords.
HTH
Martyn
From: Collaborative Computational Project in Electron cryo-Microscopy
[mailto:[log in to unmask]] On Behalf Of #AHMED TOFAYEL#
Sent: 16 March 2015 09:56
To: [log in to unmask]
Subject: [ccpem] Fitting and refining atomic coordinates into 5.5 Ang cryo EM map
Dear all,
I have fitted atomic coordinates of complete ribosome into a 5.5 Ang cryo map using "Fit in map" tool in Chimera. Now, at many positions the pdb seems to be not fitting
and completely out of density. I would like to know if we have any software/server which could read a pdb/mmcif structure so big as ribosome and refine it according to the map. It looks like Refmac could be used to do it but I guess it only wants the input
in .mtz format and I could not find a tool for converting .mrc to .mtz.
Any help will be highly appreciated.
Best
Tofayel