It opens fine in Chimera and CCP4MG, but we have just noticed that the data
values in the map range from 0 to 0.48 – is this likely to cause a problem?
Chris
From: Robert Hanson [mailto:hans...@stolaf.edu]
Sent: 05 September 2014 15:49
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] Setting cutoff with some maps causes map to fail to
load
On Fri, Sep 5, 2014 at 8:46 AM,
<chris.w...@stfc.ac.uk<mailto:chris.w...@stfc.ac.uk>> wrote:
Hi Bob,
I should have probably said that this is an EM map, not a crystallography one!
doesn't matter. It's still messed up. Jmol reads EM maps just fine as far as I
know.
You sure it's OK?
- Is JMol able to set absolute cutoffs (as normally required for EM
maps), rather than using relative sigma values?
sure
isosurface cutoff x.x ....
- What is the default value of cutoff? The third object does display
1akeA_10A.mrc, so I’m not quite sure what you mean by saying that Jmol is
failing to read the file
I mean it read the header, indicating it was made by Chimera on Sept 7, 2009.
But all the numbers for the data values are just a lot of garbage. The right
amount of garbage, but still just random numbers. Obviously that's not true,
but I tried reading them little-endian and big-endian, and neither worked. So
it's something other than that.
Does Chimera open that? Does any other EM visualizer open it?
Bob
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