I am trying to open a SHARP map (ccp4 format, i.e. .map format), but it
does not open the map. According to the pymol users manual, it should open
ccp4 format maps. Has anyone had this problem before, and what can I do to
get around it?
From: Jacob Corn <jcorn@uc...> - 2006-02-08 17:47:32
This brings up an minor issue I have with the way PyMOL deals with maps. As
Sivaram has found out, file extension matters a lot in PyMOL. So if I have a
normal ccp4-format map with the extension '.ccp4', PyMOL is happy and will
display the map normally. However, if the extension is something else, PyMOL
will still read in the map without giving any errors, but is entirely incapable
of displaying that map. Neither the density wizard nor manual isomesh commands
have any effect. PyMOL apparently can do a sanity check, though, since an error
appears if one changes the extension to mismatch the map (eg, give a ccp4 map
the extension '.xplor').
It would find it very convenient if some sort of stupidity-rectifier were added
on to the sanity check. That is, if someone reads in a file with a wrong
extension, or a file with a non-descriptive extension ('.map'), PyMOL would try
to figure out what kind file it actually is. Perhaps chastize the user a bit for
being sloppy, but still let them use the map without deleting the object,
renaming the file, and reloading the map.
sivaram mylavarapu wrote:
> Hi all!
> I am trying to open a SHARP map (ccp4 format, i.e. .map format), but
> it does not open the map. According to the pymol users manual, it should
> open ccp4 format maps. Has anyone had this problem before, and what can
> I do to get around it?
> Sivaram Mylavarapu.
The Berger Lab
UC Berkeley - Molecular and Cell Biology
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