Re: [ccp4bb] VERY old mtz file..

[Zhijie Li]

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 
<270165b9f4cf-dmarc-requ...@jiscmail.ac.uk>
 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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Re: [ccp4bb] VERY old mtz file..

[James Holton]

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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Re: [ccp4bb] VERY old mtz file..

[graeme.win...@diamond.ac.uk]

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 more impressed that Eleanor has files from ’92 - quite 
possibly older than many who will read this message!

All the best, Graeme


On 9 Nov 2018, at 13:53, Pavel Afonine 
mailto:pafon...@gmail.com>> wrote:

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 
mailto:vonrh...@globalphasing.com>> wrote:
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 require an
SGI or Dec/Alpha machine ;-)

If that doesn't help I would first check that it is actually a correct
MTZ file: does the ASCII header (trailer) show up with

  strings your.mtz

towards the end?

Cheers

Clemens

On Fri, Nov 09, 2018 at 12:47:09PM +, 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)
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

--

*--
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
* Global Phasing Ltd., Sheraton House, Castle Park
* Cambridge CB3 0AX, UK   
www.globalphasing.com
*--



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Re: [ccp4bb] VERY old mtz file..

[Susan Lea]

bring back the lcf format reflection file ;-)

Prof. Susan M. Lea,  FMedSci  tel: +44 1865 275181
--
Director of the Central Oxford Structural Microscopy and Imaging Centre & 
Professor 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 file..


PS if you're interested in software archaeology and you have the CCP4 library 
source code handy, check out these routines that I wrote for VAX/VMS.  Yes, we 
kept it in the source distribution all these years!

ccp4-7.0-src/checkout/libccp4/fortran/vmsdiskio.for

Subroutines QFIEEE & QTIEEE illustrate the horrible data mangling you had to do 
just to convert between Vax floating-point and IEEE (on top of the 
byte-swapping!).

Those were the days!

Cheers

-- Ian


On Fri, 9 Nov 2018 at 19:17, Ian Tickle 
mailto:ianj...@gmail.com>> wrote:

All MTZ (and map) files from the very beginning had an architecture-dependent 
'machine-stamp' in the header which *should* cause the read routines to do the 
necessary conversions if needed (i.e. where the writing & reading machine 
formats differ).  This was absolutely necessary in the days when we had a 
goodly mix of formats (VAX, Convex, Cray, SGI, IBM mainframe, IBM PC, Mac ...). 
 Now pretty well everything is Intel or compatible, i.e. little-endian IEEE 
format, so this functionality hasn't been real-world tested for aeons and it's 
possible in the meantime that it's fallen into disrepair.

Cheers

-- Ian


On Fri, 9 Nov 2018 at 18:57, Ethan A Merritt 
mailto:merr...@u.washington.edu>> wrote:
On Friday, November 9, 2018 9:12:36 AM PST Robert Esnouf wrote:
>
> Without checking further, there is a "dd" option for swapping big-endian to 
> little-endian... swab. This may simply be the issue...

DEC computers used a different floating point format.
Swapping endian-ness would be sufficient, although it might be required in 
addition.

Ethan


>
> The output of od -x may help decode the header of the file...
>
> Regards,
> Robert
>
> --
>
> Dr Robert Esnouf
>
> University Research Lecturer,
> Director of Research Computing BDI,
> 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
>
> Emails:
> rob...@strubi.ox.ac.uk / 
> rob...@well.ox.ac.uk / 
> robert.esn...@bdi.ox.ac.uk
>
> Tel:   (+44)-1865-287783 (WHG); (+44)-1865-743689 (BDI)
>
>
> -Original Message-
> From: "Pavel Afonine" mailto:pafon...@gmail.com>>
> 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 Shelx 
> or X-plor formats, for example) -;)
>
>
>  readable files.>
>
> On Fri, Nov 9, 2018 at 9:47 PM Clemens Vonrhein 
> mailto:vonrh...@globalphasing.com>> wrote:
>
> 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 require an
> SGI or Dec/Alpha machine ;-)
>
> If that doesn't help I would first check that it is actually a correct
> MTZ file: does the ASCII header (trailer) show up with
>
>   strings your.mtz
>
> towards the end?
>
> Cheers
>
> Clemens
>
> On Fri, Nov 09, 2018 at 12:47:09PM +, 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)
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
> --
>
> *--
> * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
> * Global Phasing Ltd., Sheraton House, Castle Park
> * Cambridge CB3 0AX, UK   
> www.globalphasing.com
> *--
>
> 
>
> To unsubscribe from the CCP4BB list, click the 

Re: [ccp4bb] VERY old mtz file..

[Ian Tickle]

PS if you're interested in software archaeology and you have the CCP4
library source code handy, check out these routines that I wrote for
VAX/VMS.  Yes, we kept it in the source distribution all these years!

ccp4-7.0-src/checkout/libccp4/fortran/vmsdiskio.for

Subroutines QFIEEE & QTIEEE illustrate the horrible data mangling you had
to do just to convert between Vax floating-point and IEEE (on top of the
byte-swapping!).

Those were the days!

Cheers

-- Ian


On Fri, 9 Nov 2018 at 19:17, Ian Tickle  wrote:

>
> All MTZ (and map) files from the very beginning had an
> architecture-dependent 'machine-stamp' in the header which *should* cause
> the read routines to do the necessary conversions if needed (i.e. where the
> writing & reading machine formats differ).  This was absolutely necessary
> in the days when we had a goodly mix of formats (VAX, Convex, Cray, SGI,
> IBM mainframe, IBM PC, Mac ...).  Now pretty well everything is Intel or
> compatible, i.e. little-endian IEEE format, so this functionality hasn't
> been real-world tested for aeons and it's possible in the meantime that
> it's fallen into disrepair.
>
> Cheers
>
> -- Ian
>
>
> On Fri, 9 Nov 2018 at 18:57, Ethan A Merritt 
> wrote:
>
>> On Friday, November 9, 2018 9:12:36 AM PST Robert Esnouf wrote:
>> >
>> > Without checking further, there is a "dd" option for swapping
>> big-endian to little-endian... swab. This may simply be the issue...
>>
>> DEC computers used a different floating point format.
>> Swapping endian-ness would be sufficient, although it might be required
>> in addition.
>>
>> Ethan
>>
>>
>> >
>> > The output of od -x may help decode the header of the file...
>> >
>> > Regards,
>> > Robert
>> >
>> > --
>> >
>> > Dr Robert Esnouf
>> >
>> > University Research Lecturer,
>> > Director of Research Computing BDI,
>> > 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
>> >
>> > Emails:
>> > rob...@strubi.ox.ac.uk / rob...@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..
>> >
>> > Now I see the value of storing data in plain text files even more (mind
>> Shelx or X-plor formats, for example) -;)
>> >
>> >
>> > > non-human readable files.>
>> >
>> > On Fri, Nov 9, 2018 at 9:47 PM Clemens Vonrhein <
>> vonrh...@globalphasing.com> wrote:
>> >
>> > 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 require an
>> > SGI or Dec/Alpha machine ;-)
>> >
>> > If that doesn't help I would first check that it is actually a correct
>> > MTZ file: does the ASCII header (trailer) show up with
>> >
>> >   strings your.mtz
>> >
>> > towards the end?
>> >
>> > Cheers
>> >
>> > Clemens
>> >
>> > On Fri, Nov 09, 2018 at 12:47:09PM +, 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)
>> > >
>> > >
>> 
>> > >
>> > > To unsubscribe from the CCP4BB list, click the following link:
>> > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>> >
>> > --
>> >
>> > *--
>> > * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
>> > * Global Phasing Ltd., Sheraton House, Castle Park
>> > * Cambridge CB3 0AX, UK   www.globalphasing.com
>> > *--
>> >
>> > 
>> >
>> > To unsubscribe from the CCP4BB list, click the following link:
>> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>> >
>> >
>> >
>> > To unsubscribe from the CCP4BB list, click the following link:
>> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>> >
>> >
>> >
>> > 
>> >
>> > To unsubscribe from the CCP4BB list, click the following link:
>> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
>>
>> --
>> Ethan A Merritt
>> Biomolecular Structure Center,  

Re: [ccp4bb] VERY old mtz file..

[Ian Tickle]

All MTZ (and map) files from the very beginning had an
architecture-dependent 'machine-stamp' in the header which *should* cause
the read routines to do the necessary conversions if needed (i.e. where the
writing & reading machine formats differ).  This was absolutely necessary
in the days when we had a goodly mix of formats (VAX, Convex, Cray, SGI,
IBM mainframe, IBM PC, Mac ...).  Now pretty well everything is Intel or
compatible, i.e. little-endian IEEE format, so this functionality hasn't
been real-world tested for aeons and it's possible in the meantime that
it's fallen into disrepair.

Cheers

-- Ian


On Fri, 9 Nov 2018 at 18:57, Ethan A Merritt 
wrote:

> On Friday, November 9, 2018 9:12:36 AM PST Robert Esnouf wrote:
> >
> > Without checking further, there is a "dd" option for swapping big-endian
> to little-endian... swab. This may simply be the issue...
>
> DEC computers used a different floating point format.
> Swapping endian-ness would be sufficient, although it might be required in
> addition.
>
> Ethan
>
>
> >
> > The output of od -x may help decode the header of the file...
> >
> > Regards,
> > Robert
> >
> > --
> >
> > Dr Robert Esnouf
> >
> > University Research Lecturer,
> > Director of Research Computing BDI,
> > 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
> >
> > Emails:
> > rob...@strubi.ox.ac.uk / rob...@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..
> >
> > Now I see the value of storing data in plain text files even more (mind
> Shelx or X-plor formats, for example) -;)
> >
> >
> >  non-human readable files.>
> >
> > On Fri, Nov 9, 2018 at 9:47 PM Clemens Vonrhein <
> vonrh...@globalphasing.com> wrote:
> >
> > 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 require an
> > SGI or Dec/Alpha machine ;-)
> >
> > If that doesn't help I would first check that it is actually a correct
> > MTZ file: does the ASCII header (trailer) show up with
> >
> >   strings your.mtz
> >
> > towards the end?
> >
> > Cheers
> >
> > Clemens
> >
> > On Fri, Nov 09, 2018 at 12:47:09PM +, 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)
> > >
> > >
> 
> > >
> > > To unsubscribe from the CCP4BB list, click the following link:
> > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> >
> > --
> >
> > *--
> > * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
> > * Global Phasing Ltd., Sheraton House, Castle Park
> > * Cambridge CB3 0AX, UK   www.globalphasing.com
> > *--
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> >
> >
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> >
> >
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
>
> --
> Ethan A Merritt
> Biomolecular Structure Center,  K-428 Health Sciences Bldg
> MS 357742,   University of Washington, Seattle 98195-7742
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] VERY old mtz file..

[Ethan A Merritt]

On Friday, November 9, 2018 9:12:36 AM PST Robert Esnouf wrote:
> 
> Without checking further, there is a "dd" option for swapping big-endian to 
> little-endian... swab. This may simply be the issue... 

DEC computers used a different floating point format.
Swapping endian-ness would be sufficient, although it might be required in 
addition.

Ethan


> 
> The output of od -x may help decode the header of the file...
> 
> Regards,
> Robert
> 
> --
> 
> Dr Robert Esnouf 
> 
> University Research Lecturer, 
> Director of Research Computing BDI, 
> 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 
> 
> Emails: 
> rob...@strubi.ox.ac.uk / rob...@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..
> 
> Now I see the value of storing data in plain text files even more (mind Shelx 
> or X-plor formats, for example) -;)
> 
> 
>  readable files.>
> 
> 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 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 require an
> SGI or Dec/Alpha machine ;-)
> 
> If that doesn't help I would first check that it is actually a correct
> MTZ file: does the ASCII header (trailer) show up with
> 
>   strings your.mtz
> 
> towards the end?
> 
> Cheers
> 
> Clemens
> 
> On Fri, Nov 09, 2018 at 12:47:09PM +, 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)
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> 
> --
> 
> *--
> * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
> * Global Phasing Ltd., Sheraton House, Castle Park
> * Cambridge CB3 0AX, UK   www.globalphasing.com
> *--
> 
> 
> 
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> 
> 
> 
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> 
> 
> 
> 
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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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Re: [ccp4bb] VERY old mtz file..

[Robert Esnouf]

Without checking further, there is a "dd" option for swapping big-endian to 
little-endian... swab. This may simply be the issue... 

The output of od -x may help decode the header of the file...

Regards,
Robert

--

Dr Robert Esnouf 

University Research Lecturer, 
Director of Research Computing BDI, 
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 

Emails: 
rob...@strubi.ox.ac.uk / rob...@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..

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 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 require an
SGI or Dec/Alpha machine ;-)

If that doesn't help I would first check that it is actually a correct
MTZ file: does the ASCII header (trailer) show up with

  strings your.mtz

towards the end?

Cheers

Clemens

On Fri, Nov 09, 2018 at 12:47:09PM +, 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)
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

--

*--
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
* Global Phasing Ltd., Sheraton House, Castle Park
* Cambridge CB3 0AX, UK   www.globalphasing.com
*--



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Re: [ccp4bb] VERY old mtz file..

[Pavel Afonine]

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 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 require an
> SGI or Dec/Alpha machine ;-)
>
> If that doesn't help I would first check that it is actually a correct
> MTZ file: does the ASCII header (trailer) show up with
>
>   strings your.mtz
>
> towards the end?
>
> Cheers
>
> Clemens
>
> On Fri, Nov 09, 2018 at 12:47:09PM +, 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)
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
> --
>
> *--
> * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
> * Global Phasing Ltd., Sheraton House, Castle Park
> * Cambridge CB3 0AX, UK   www.globalphasing.com
> *--
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] VERY old mtz file..

[Clemens Vonrhein]

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 require an
SGI or Dec/Alpha machine ;-)

If that doesn't help I would first check that it is actually a correct
MTZ file: does the ASCII header (trailer) show up with

  strings your.mtz

towards the end?

Cheers

Clemens

On Fri, Nov 09, 2018 at 12:47:09PM +, 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)
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

-- 

*--
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
* Global Phasing Ltd., Sheraton House, Castle Park 
* Cambridge CB3 0AX, UK   www.globalphasing.com
*--



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[ccp4bb] VERY old mtz file..

[Eleanor Dodson]

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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Re: [ccp4bb] CC work / free

[Clement Degut]

Did not knew about that trick !
But I second that a well made script (i.e. not my homemade one) included in
software for paired refinement would be a great addition.

On Thu, 8 Nov 2018 at 20:13, Georg Mlynek  wrote:

> Dear Frank,
>
> pdb_redo webserver does. However you have to cheat to provoke it: The
> resolution remark in the PDB has to be 0.10A beyond what it was used
> before. You can use also use the command line version of pdb-redo to tweak
> settings for your calculation (the expert option).
>
> However it would be nice to have the option also in ccp4 and phenix. Doing
> this without a script is painful.
>
> Br, Georg.
>
> Am 11/8/2018 um 17:52 schrieb Frank von Delft:
>
> Does any refinement software automatically do the CC* resolution
> exploration ("paired refinement") that Kay did in the original paper?  Now
> that *would* be fantastically useful.
>
>
> On 08/11/2018 12:44, Pavel Afonine wrote:
>
> Clément,
> I'm guessing this is because it isn't clear what CCwork/CCfree can tell
> you that Rwork/Rfree can not. Needless to say we all more or less have a
> good idea about what the ok values for Rwork, Rfree and Rfree-Rwork (as
> function of resolution) while it is much less clear (to me at least) when
> it comes to CCwork/CCfree.
> I think phenix.refine used to report CCwork/CCfree in some releases but I
> removed it as useless.
> All the best,
> Pavel
>
> On Thu, Nov 8, 2018 at 8:16 PM Clement Degut <
> 26de0a160250-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> Hi all,
>>
>> This probably have already be discussed, but can't find trace of it :
>> Is there any reason I am not aware of that refinement software (thinking
>> of both phenix and refmac) do not output CC work / free ?
>> We all accepted CC 1/2 for resolution cut (whether it's 30 or 10 %) which
>> tend to lead to high Rfree ( last shells having very poor phases), at least
>> high overall R free in regard to the majority same resolution structures as
>> they been refined with I/sig > 3.
>> Which in return push people to cut resolution AFTER refinement which
>> obviously drastically decrease the R free and catapult your structure from
>> worst of the PDB to best of the PDB. It should never be done but it is
>> nonetheless.
>> How to blame a "non expert"  to do that when changing the resolution from
>> 1.49 to 1.5 change your Rfree by 2% (yes it exaggerated but you get the
>> idea).
>> Now it seems to me -but I may be very wrong as I am far from expert in
>> the arcane math of these- that CC work and free would be more agnostic to
>> this resolution cut off problem, as we compare it to the CC* value anyway ?
>> thought it will never start to be used if refinement software don't output
>> it as a standard (not talking about completely replacing Rfree here as it
>> is obviously useful).
>> Would CC work/free be a bad appreciation of the refinement process ?
>>
>> Thanks
>>
>> Clément
>>
>> --
>>
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>>
>
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>
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[ccp4bb] MoRDa update

[Alexey Vagin]

Dear All

MoRDa is a pipeline for molecular replacement structure solution.

A new update to the package is now available. The structure solution program is 
improved and database is extended .

Both update and installation instructions are available from Morda homepage 
.

The update is also available for existing local Morda installations and can be 
installed from command line: change to installation directory (by default 
MoRDa_DB) and type ./update_morda.

Also Morda at ccp4online  has been updated. 

Best regards
Alexey




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