Which is why I said "make available" rather than "post it" or "email
me" :)
And he has done just that .... will go have a look ....
m
On Tue, 2010-07-13 at 18:42 -0700, James Holton wrote:
>
> 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, <[log in to unmask]> 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: [log in to unmask]
> 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 <[log in to unmask]>
> http://www.ebi.ac.uk/~best
> | European Bioinformatics Institute, Cambridge, UK
> +44-1223-492649
>
>
--
***********************************************************************
* *
* Dr. Martyn Winn *
* *
* STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. *
* Tel: +44 1925 603455 E-mail: [log in to unmask] *
* Fax: +44 1925 603634 Skype name: martyn.winn *
* URL: http://www.ccp4.ac.uk/martyn/ *
***********************************************************************
