On Tuesday, November 13, 2018 11:51:55 AM PST Zhijie Li wrote:
> If somebody is going to send these files by email, please send one to me too.
> Thanks in advance. I actually prefer to get a MTZ file because the miller
> indices would serve as good clues for understanding the encodings. Even the
> first 1024 bytes of an MTZ would do (data array starts at byte 80 in MTZ).
>
> In my life I had only seen ieee754. According to what I can find, VAX has an
> exponent bias of 128 (ieee754 uses 127). Then it seems to me that when
> converting from vax to ieee a division of 2 is involved.
It's more complicated than that. VAXen supported multiple floating point
formats,
F-floating G-floating and H-floating.
They had differed by how many bits were used for the exponent, and hence how
many bits were left for the mantissa.
I can pull out the architecture manuals if necessary.
ah, nostalgia
Ethan
> However all procedures I have seen use a division of 4, which is quite
> puzzling to me. A real data file containing meaningful numbers (eg., HKL
> indices) would be very helpful. Thanks in advance.
>
> Zhijie
>
> > On Nov 13, 2018, at 2:21 PM, Johan Hattne <[email protected]> wrote:
> >
> > Related by not exactly on topic: would anybody on the list be able to share
> > old map files (not MTZ:s) with Convex, Cray, Fujitsu, or VAX reals/strings?
> > I’d be interested to see what those files actually look(ed) like.
> >
> > // Best wishes; Johan
> >
> >> On Nov 9, 2018, at 18:38, Zhijie Li <[email protected]> wrote:
> >>
> >> Hi all,
> >>
> >> On linux there are a few good GUI HEX editors. Here I’d like to recommend
> >> BLESS, which conveniently displays all possible numerical interpretations
> >> of the four bytes under cursor. It also allows the user to switch between
> >> big endian or little endian through a checkbox. Unfortunately all floats
> >> are assumed to be IEEE754, therefore VAX floats won’t be interpreted
> >> correctly. ( The simplest way to convert vax to ieee float would be to
> >> write a little program to do some bit operations. I’d be happy to take
> >> that as my weekend project)
> >>
> >>
> >> BTW, along the line of space efficiency, I can’t help noticing that the
> >> miller indices are saved as float32 in mtz, as all other numbers in mtz.
> >> This certainly have made mtz format a beautiful homogeneous data format
> >> ;). In this particular case, if we have doubts about the reliability of
> >> the machine stamp, trying to restore the miller indices would be a good
> >> way to test hypotheses.
> >>
> >> Zhijie
> >>
> >>> On Nov 9, 2018, at 9:04 PM, James Holton
> >>> <[email protected]> wrote:
> >>>
> >>> As a beamline scientist I must say I am glad that diffraction image data
> >>> is not usually stored as ASCII text. In fact, I am slowly warming to the
> >>> idea of storing it as not just binary, but compressed formats. Problem,
> >>> I'm sure will be that it won't be long before we forget how to
> >>> decompress them, as most of the algorithms we are using aren't all that
> >>> widespread. Probably around the same time future generations will curse
> >>> us for using ASCII instead of unicode, which is a 16-bit standard. I'm
> >>> sure we will be reviled for limiting ourselves so, just to save a factor
> >>> of two in disk space.
> >>> In situations like this I always use the unix "od" command. It makes
> >>> everything "human readable" by converting the bytes into strings you can
> >>> read. Then it is just a matter of figuring out what the bytes are.
> >>> Unfortunately, "od" only decodes floats on the native platform, so if the
> >>> mtz is from another platform (Windows vs Linux, for example), then you
> >>> might need to do some swapping. Thus far, I have encountered files that
> >>> require one of a few swapping strategies in order to make them work:
> >>>
> >>> 1 2 3 4 - no swapping
> >>>
> >>> 4 3 2 1 - reverse all bytes
> >>>
> >>> 3 4 1 2 - swap words and swap bytes within the words
> >>> 2 1 4 3 - reverse of previous
> >>>
> >>> 2-1 1 4 3 - same as last, but if not all zero, decrement byte #2 before
> >>> swapping
> >>> 3 4 1 2+1 - same as 3412, but if not all zero increment byte #2 before
> >>> swapping
> >>> I'm sure there are other combinations, but the oldest MTZ I have is only
> >>> from 1996.
> >>>
> >>> -James Holton
> >>> MAD Scientist
> >>>
> >>>
> >>>> On 11/9/2018 4:47 AM, Eleanor Dodson wrote:
> >>>> Anyone any idea what to do about this?? Created in 1992!!
> >>>> Seems unreadable..
> >>>>
> >>>> No CTYP lines input for file: 1
> >>>> Indices output even if all data items flagged "missing"
> >>>> Warning, NOT all LABOUT data lines given
> >>>> Warning: Machine stamp corrupted? Assuming native format.
> >>>>>>>>>> CCP4 library signal library_file:End of File (Error)
> >>>>
> >>>>
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> >>>
> >>>
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> >>>
> >>
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> >>
> >
> > Research Specialist @ Gonen Lab
> > ____________________________________________________
> > UCLA * 615 Charles E. Young Drive South
> > BSRB #347 * Los Angeles, CA 90095
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--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
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