The original poster just told me that the map file is 2.6 GB. Please don't
encourage him to attach it to a ccp4bb email!
-James Holton
MAD Scientist
On Tue, Jul 13, 2010 at 2:58 PM, <martyn.w...@stfc.ac.uk> wrote:
> Actually, zero spacegroup should be tolerated by the CCP4 library now.
>
> We were recently alerted to another problem, caused by non-zero origin in
> the EM map header. But I think this is different to the problem of the
> original poster.
>
> It's probably fair to say we haven't tested enough against real EM maps,
> and perhaps we should.
>
> Perhaps the original poster could make their problem maps available??
>
> Cheers
> Martyn
>
> -----Original Message-----
> From: CCP4 bulletin board on behalf of Christoph Best
> Sent: Tue 7/13/2010 10:20 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] conversion of cyroEM reconstruction from MRC to CCP4
> format
>
> Hello,
>
> we have found that there are some minor issues in MRC files using in Em
> that can make them unpalatable to the CCP4 map library. You can easily
> look at header fields in Python - here is a sample program to quickly
> check some of the more common problems.
>
> from struct import *
>
> header=file('your_file_name.map').read(1024)
> print 'dimensions=',unpack_from('iii',header,0)
> print 'mode=',unpack_from('i',header,3*4)[0],'should be 0, 1, or 2'
> print 'space group=',unpack_from('i',header,22*4)[0],'should be 1'
> print 'magic=',unpack_from('cccc',header,52*4),'should be (\'M\', \'A\',
> \'P\', \' \')'
> print 'machine stamp=','%x' % unpack_from('i',header,53*4),' should be
> 4144 or 4444'
> print 'nsymbt=',unpack_from('i',header,23*4)[0],' should be 0'
>
> The issues we typically encountered were bad space groups (zero), wrong
> machine stamps (they should be 0x4444 or 0x4144), missing the "magic
> bytes" that spell "MAP ", or a value of nsymbt that indicates the
> presence of additional symmetry information following the header, which
> is then missing.
>
> Chimera ignores most of these issues.
>
> -Christoph
>
> --
> | Christoph Best <b...@ebi.ac.uk>
> http://www.ebi.ac.uk/~best <http://www.ebi.ac.uk/%7Ebest>
> | European Bioinformatics Institute, Cambridge, UK
> +44-1223-492649
>
