1 to the left, with the binary point"
>
>0.1.
>
>
>
>
>From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> on
behalf of Zhijie Li mailto:zhijie...@utoronto.ca>>
>Sent: Tuesday, November 13, 2018 7:43 PM
>T
ndices that look normal.
Zhijie
*From:* Nicholas Devenish mailto:ndeven...@gmail.com>>
*Sent:* Wednesday, November 14, 2018 9:29 AM
*To:* Zhijie Li
*Cc:* CCP4BB@jiscmail.ac.uk <mailto:CCP4BB@jiscmail.ac.uk>
*Subject:
idea is to try all possibilities
until we can recover miller indices that look normal.
Zhijie
From: Nicholas Devenish mailto:ndeven...@gmail.com>>
Sent: Wednesday, November 14, 2018 9:29 AM
To: Zhijie Li
Cc: CCP4BB@jiscmail.ac.uk<mailto:CCP4BB@jiscma
es, the idea is to try all
> possibilities until we can recover miller indices that look normal.
>
> Zhijie
>
> --
> *From:* Nicholas Devenish
> *Sent:* Wednesday, November 14, 2018 9:29 AM
> *To:* Zhijie Li
> *Cc:* CCP4BB@jiscmail.ac.uk
> *Su
ijie Li
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] VERY old mtz file..
Hi Zhijie,
Thanks for the answer. I'd read http://www.ccp4.ac.uk/html/mtzformat.html "The
first 4 half-bytes represent the real, complex, integer and character formats,
and the last two bytes are currently unused" - and as
ret it as half bytes!
>
>
> Zhijie
>
>
>
>
> From: Nicholas Devenish
> Sent: Wednesday, November 14, 2018 8:54 AM
> To: Zhijie Li
> Cc: CCP4BB@jiscmail.ac.uk
> Subject: Re: [ccp4bb] VERY old mtz file..
>
> Hi Zhijie,
>
> Looks like we both had the
it as half bytes!
Zhijie
From: Nicholas Devenish
Sent: Wednesday, November 14, 2018 8:54 AM
To: Zhijie Li
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] VERY old mtz file..
Hi Zhijie,
Looks like we both had the same thoughts!
On Wed, Nov 14, 2018 at 1:19 PM
Hi Zhijie,
Looks like we both had the same thoughts!
On Wed, Nov 14, 2018 at 1:19 PM Zhijie Li wrote:
> The semiBE.mtz has the big endian stamp (0x11 11 00 00 at bytes 9-12 )
> put in the header of the original file; everything else is untouched
>
Is this correct? I thought machine stamp
gt;
>>> >It's also said here, at the end of file :
>>> >
>>> >https://www.cs.auckland.ac.nz/~patrice/210LN/DR4.pdf
>>> >
>>> >"add 1 to the left, with the binary point"
>>> >
>>> >0.1.
>>> >
>&
Hi Nick,
Our LE outputs are exactly the same. Rmerge=100.0%!
Zhijie
From: CCP4 bulletin board on behalf of Nicholas
Devenish
Sent: Wednesday, November 14, 2018 7:15 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] VERY old mtz file..
Hi
gt;
>>> HTH
>>> Kay
>>>
>>> On Wed, 14 Nov 2018 00:51:02 +, Zhijie Li
>>> wrote:
>>>
>>> >It's also said here, at the end of file :
>>> >
>>> >https://www.cs.auckland.ac.nz/~patrice/210LN/DR4.pdf
>>> &
's also said here, at the end of file :
>> >
>> >https://www.cs.auckland.ac.nz/~patrice/210LN/DR4.pdf
>> >
>> >"add 1 to the left, with the binary point"
>> >
>> >0.1.
>> >
>> >
>> >
>> >
d values, rearranging the VAX F-float bytes, reading as
> >IEEE, then dividing by 4 gives the correct value. (The C[0]-1 treatment in
> >the ccp4 lib is neat.)
> >
> >
> >In this link describing VAX floats, it is unfortunate that it only states
> >that
gt;
> >
> >
> >From: CCP4 bulletin board on behalf of Zhijie Li
>
> >Sent: Tuesday, November 13, 2018 7:43 PM
> >To: CCP4BB@JISCMAIL.AC.UK
> >Subject: Re: [ccp4bb] VERY old mtz file..
> >
> >
> >Hi all,
> &g
__
>> From: CCP4 bulletin board on behalf of Zhijie Li
>>
>> Sent: Tuesday, November 13, 2018 7:43 PM
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: Re: [ccp4bb] VERY old mtz file..
>>
>>
>> Hi all,
>>
>>
>
>From: CCP4 bulletin board on behalf of Zhijie Li
>
>Sent: Tuesday, November 13, 2018 7:43 PM
>To: CCP4BB@JISCMAIL.AC.UK
>Subject: Re: [ccp4bb] VERY old mtz file..
>
>
>Hi all,
>
>
>I think I know why it is a division of 4 instead of 2 is involved in
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] VERY old mtz file..
Hi all,
I think I know why it is a division of 4 instead of 2 is involved in conversion
from VAX to IEEE now. Short answer: a 2 is in the exponent bits (bias of 128
instead of 127, visible), another 2 is hidden in the scientifi
To: Zhijie Li
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] VERY old mtz file..
Hi Zhijie
It's definitely a factor 4. The code is in subroutine QTIEEE in the Fortran
source I mentioned previously at this line:
See line:
A(I)=((A(I)+SIGN(2,A(I)))/4.AND..NOT.MNAN).OR.MDN2
If you prefer it in C
Hi Zhijie
It's definitely a factor 4. The code is in subroutine QTIEEE in the
Fortran source I mentioned previously at this line:
See line:
A(I)=((A(I)+SIGN(2,A(I)))/4.AND..NOT.MNAN).OR.MDN2
If you prefer it in C code it's in function vaxF2ieeeF in:
MTZ was always 32 bit floats for the main data, with ASCII headers at the end
Sent from my iPhone
> On 13 Nov 2018, at 21:29, Ethan A Merritt wrote:
>
>> On Tuesday, November 13, 2018 1:06:01 PM PST Zhijie Li wrote:
>> Hi Ethan,
>> Thanks for the information. My guess is that in MTZ only
On Tuesday, November 13, 2018 1:06:01 PM PST Zhijie Li wrote:
> Hi Ethan,
> Thanks for the information. My guess is that in MTZ only F-float is expected,
> because it is the only 32bit form?
I do not remember exactly what was used for mtz files at that time.
It might have been REAL*4 or it
Hi Ethan,
Thanks for the information. My guess is that in MTZ only F-float is expected,
because it is the only 32bit form?
Zhijie
> On Nov 13, 2018, at 3:44 PM, Ethan A Merritt wrote:
>
>> On Tuesday, November 13, 2018 11:51:55 AM PST Zhijie Li wrote:
>> If somebody is going to send these
>> ah, nostalgia
Ah, "mantissa!" Haven't heard "mantissa" in decades...
Is there such a thing as a "praying mantissa?" Seems like there could be a good
geek joke about it.
JPK
> However all procedures I have seen use a division of 4, which is quite
> puzzling to me. A real data file
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
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
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 wrote:
>
> Hi
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
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
Dear Pavol,
Reading text files without any software is a neat trick, if you can do it.
(no file on a computer is “human readable” - but many are encoded in a form
which allows a wide range of general tools to display it, not just specialist
crystallography software)
;-)
I have to say, I am
ssor of Microbiology
Sir William Dunn School of Pathology, Oxford OX1 3RE Professorial Fellow @
WadhamCollege
From: CCP4 bulletin board on behalf of Ian Tickle
Sent: 09 November 2018 19:32:50
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] VERY old mtz
t; > Head of Research Computing Core WHG,
>> > NDM Research Computing Strategy Officer
>> >
>> > Main office:
>> > Room 10/028, Wellcome Centre for Human Genetics,
>> > Old Road Campus, Roosevelt Drive, Oxford OX3 7BN, UK
>> >
>>
> Main office:
> > Room 10/028, Wellcome Centre for Human Genetics,
> > Old Road Campus, Roosevelt Drive, Oxford OX3 7BN, UK
> >
> > Emails:
> > rob...@strubi.ox.ac.uk / rob...@well.ox.ac.uk /
> robert.esn...@bdi.ox.ac.uk
> >
> > Tel: (+44)-1865-
...@well.ox.ac.uk / robert.esn...@bdi.ox.ac.uk
>
> Tel: (+44)-1865-287783 (WHG); (+44)-1865-743689 (BDI)
>
>
> -Original Message-
> From: "Pavel Afonine"
> To: CCP4BB@JISCMAIL.AC.UK
> Date: 09/11/18 13:54
> Subject: Re: [ccp4bb] VERY old mtz file
c.uk
Tel: (+44)-1865-287783 (WHG); (+44)-1865-743689 (BDI)
-Original Message-
From: "Pavel Afonine"
To: CCP4BB@JISCMAIL.AC.UK
Date: 09/11/18 13:54
Subject: Re: [ccp4bb] VERY old mtz file..
Now I see the value of storing data in plain text files even more (mind Shel
Now I see the value of storing data in plain text files even more (mind
Shelx or X-plor formats, for example) -;)
On Fri, Nov 9, 2018 at 9:47 PM Clemens Vonrhein
wrote:
> Hi Eleanor,
>
> You could try running the oldest MTZ2VARIOUS binary you can find -
> e.g.
>
> wget
Hi Eleanor,
You could try running the oldest MTZ2VARIOUS binary you can find -
e.g.
wget ftp://ftp.ccp4.ac.uk/ccp4/4.2/binaries/ccp4-4.2_Linux.tar.gz
tar -xvf ccp4-4.2_Linux.tar.gz bin/mtz2various
bin/mtz2various hklin ...
Any older binaries (ftp://ftp.ccp4.ac.uk/ccp4/4.0.1/) will
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