Re: [ccp4bb] Using SFall for map conversion

2020-05-15 Thread Soisson, Stephen M 
Sadly I am “well-seasoned” enough to remember the vax-Linux byte swaps.  Little 
endian vs big endian, and the whole thing.  I was not expecting the Convex 
reference here which brings back great memories of the Johns Hopkins Convex and 
the frigid room it resided in that sounded like you put your head in a jet 
turbine exhaust.  Good times.

Sent from my iPhone

On May 15, 2020, at 5:55 PM, Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:


EXTERNAL EMAIL – Use caution with any links or file attachments.
Hmmm

On Fri, 15 May 2020 at 22:53, Ian Tickle 
mailto:ianj...@gmail.com>> wrote:

It worked perfectly, no-one even noticed the bytes being swapped :)

I.


On Fri, 15 May 2020 at 22:37, Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
 wrote:
No no please no!!! How I hated the byte swap.. most people used VAXy things - 
York didn’t - our bytes were not your bytes  stuff of nightmares...

On Fri, 15 May 2020 at 22:25, Jonathan Cooper 
<0c2488af9525-dmarc-requ...@jiscmail.ac.uk>
 wrote:
Ian, I can, as a not very scientific footnote, confirm that Jim Austin still 
has your Convex on his farm and, it seems, most of the manuals:

http://u.cubeupload.com/jbcooper/smallIMGP0087.jpg
http://u.cubeupload.com/jbcooper/smallIMGP0086.jpg
http://u.cubeupload.com/jbcooper/smallIMGP0078.jpg
http://u.cubeupload.com/jbcooper/smallIMGP0077.jpg
http://u.cubeupload.com/jbcooper/smallIMGP0089.jpg
http://u.cubeupload.com/jbcooper/smallIMGP0084.jpg
http://u.cubeupload.com/jbcooper/smallIMGP0103.jpg
http://u.cubeupload.com/jbcooper/smallIMGP0110.jpg

He also has at least one of the ex-bbk Evans & Sutherland PS300's:

http://u.cubeupload.com/jbcooper/smallIMGP0091.jpg
http://u.cubeupload.com/jbcooper/smallIMGP0093.jpg

A few cobwebs, but pretty good going really for a 'former' pig-shed!! Not sure 
what happened to the 11/750, though... School of Pharmacy rings a bell??

None of this matters, but I just thought you might like to practice some 
'big-iron' byte-swapping again, and if so, York is the place to go, after 
covid-19, of course ;-0 ;-0
On Friday, 15 May 2020, 10:47:40 BST, Ian Tickle 
mailto:ianj...@gmail.com>> wrote:



Hi, that would have to be a very old map!  I remember implementing the 
auto-byte swap for VMS (necessary as we had both a Convex C220 running Unix and 
a VAX 11/750)!

In fact the Convex was rescued from scrap by Jim Austin and is still working: 
http://www.corestore.org/convex.htm

Cheers

-- Ian




Cheers

-- Ian


On Fri, 15 May 2020 at 09:24, Philippe BENAS 
<0d88e888355a-dmarc-requ...@jiscmail.ac.uk>
 wrote:
Dear Bernhard,

Is it an old map ?

Back to the old VAX times I had to dump CCP4 maps to ascii map files, then swap 
bytes from VAX-DOS to Unix before converting them again to a CCP4 map format (I 
think I was using mapman from USF) on a Unix workstation and be able to read 
them in Frodo-Strasbourg or O.

At least you could give it a shot and the ascii map file would help you 
figuring out the issue by a visual inspection of the header and sections.

All the best,
Philippe


Philippe BENAS, Ph.D.

ARN UPR 9002 CNRS
IBMC Strasbourg
2, Allée Konrad Röntgen
F-67084 STRASBOURG cedex
+33.3.8841.7109
E-mails: p.be...@ibmc-cnrs.unistra.fr, 
philippe_be...@yahoo.fr
URLs: http://www-ibmc.u-strasbg.fr/ , http://www-ibmc.u-strasbg.fr/spip-arn/




Le jeudi 14 mai 2020 à 22:45:09 UTC+2, Bernhard Rupp 
mailto:hofkristall...@gmail.com>> a écrit :



Hi Fellows,



I am failing on conversion of a ccp4 map to mtz using Sfall



I provide as a scale reference a mtz with FP SIGFP and R free



All cell constants and SG 20 and map headers seem to agree.



But I receive following warning:



*** WARNING - your map spacegroup is different to the program default one ***



and later



>> CCP4 library signal library_file:Cannot open file (Warning)

raised in tmpfile() failed, opening normal file instead. <<

INPUT X USED AS  X

INPUT Y USED AS  Z

INPUT Z USED AS  Y



Which then leads to the imho - given above- justified complaint:



Check map header agrees with fixed requirements for SFcalc for this spacegroup.

Check Nxyz 180 200 120180 200 120



Check map header agrees with fixed requirements for SFcalc for this  spacegroup.

Check Iuvw   3   2   1  3   1   2



SFALL:    Fatal disagreement between input info and map header



How do I fix this ?



In principle all the information is there to do the job…



Many thx, BR

--

Bernhard Rupp

Crystallographiae Vindicis Militum Ordo

http://www.hofkristallamt.org/

b...@hofkristallamt.org

+1

Re: [ccp4bb] Using SFall for map conversion

2020-05-15 Thread Ian Tickle 
I kept the Fortran and C language manuals, and still use them to this day.

I.


On Fri, 15 May 2020 at 22:25, Jonathan Cooper  wrote:

> Ian, I can, as a not very scientific footnote, confirm that Jim Austin
> still has your Convex on his farm and, it seems, most of the manuals:
>
> http://u.cubeupload.com/jbcooper/smallIMGP0087.jpg
> http://u.cubeupload.com/jbcooper/smallIMGP0086.jpg
> http://u.cubeupload.com/jbcooper/smallIMGP0078.jpg
> http://u.cubeupload.com/jbcooper/smallIMGP0077.jpg
> http://u.cubeupload.com/jbcooper/smallIMGP0089.jpg
> http://u.cubeupload.com/jbcooper/smallIMGP0084.jpg
> http://u.cubeupload.com/jbcooper/smallIMGP0103.jpg
> http://u.cubeupload.com/jbcooper/smallIMGP0110.jpg
>
> He also has at least one of the ex-bbk Evans & Sutherland PS300's:
>
> http://u.cubeupload.com/jbcooper/smallIMGP0091.jpg
> http://u.cubeupload.com/jbcooper/smallIMGP0093.jpg
>
> A few cobwebs, but pretty good going really for a 'former' pig-shed!! Not
> sure what happened to the 11/750, though... School of Pharmacy rings a
> bell??
>
> None of this matters, but I just thought you might like to practice some
> 'big-iron' byte-swapping again, and if so, York is the place to go, after
> covid-19, of course ;-0 ;-0
> On Friday, 15 May 2020, 10:47:40 BST, Ian Tickle 
> wrote:
>
>
>
> Hi, that would have to be a very old map!  I remember implementing the
> auto-byte swap for VMS (necessary as we had both a Convex C220 running Unix
> and a VAX 11/750)!
>
> In fact the Convex was rescued from scrap by Jim Austin and is still
> working: http://www.corestore.org/convex.htm
>
> Cheers
>
> -- Ian
>
>
>
>
> Cheers
>
> -- Ian
>
>
> On Fri, 15 May 2020 at 09:24, Philippe BENAS <
> 0d88e888355a-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> Dear Bernhard,
>
> Is it an old map ?
>
> Back to the old VAX times I had to dump CCP4 maps to ascii map files, then
> swap bytes from VAX-DOS to Unix before converting them again to a CCP4 map
> format (I think I was using mapman from USF) on a Unix workstation and be
> able to read them in Frodo-Strasbourg or O.
>
> At least you could give it a shot and the ascii map file would help you
> figuring out the issue by a visual inspection of the header and sections.
>
> All the best,
> Philippe
>
> --
> Philippe BENAS, Ph.D.
>
> ARN UPR 9002 CNRS
> IBMC Strasbourg
> 2, Allée Konrad Röntgen
> F-67084 STRASBOURG cedex
> +33.3.8841.7109
> E-mails: p.be...@ibmc-cnrs.unistra.fr, philippe_be...@yahoo.fr
> URLs: http://www-ibmc.u-strasbg.fr/ ,
> http://www-ibmc.u-strasbg.fr/spip-arn/
> --
>
>
>
> Le jeudi 14 mai 2020 à 22:45:09 UTC+2, Bernhard Rupp <
> hofkristall...@gmail.com> a écrit :
>
>
> Hi Fellows,
>
>
>
> I am failing on conversion of a ccp4 map to mtz using Sfall
>
>
>
> I provide as a scale reference a mtz with FP SIGFP and R free
>
>
>
> All cell constants and SG 20 and map headers seem to agree.
>
>
>
> But I receive following warning:
>
>
>
> *** WARNING - your map spacegroup is different to the program default one
> ***
>
>
>
> and later
>
>
>
> >> CCP4 library signal library_file:Cannot open file (Warning)
>
> raised in tmpfile() failed, opening normal file instead. <<
>
> INPUT X USED AS  X
>
> INPUT Y USED AS  Z
>
> INPUT Z USED AS  Y
>
>
>
> Which then leads to the imho - given above- justified complaint:
>
>
>
> Check map header agrees with fixed requirements for SFcalc for this
> spacegroup.
>
> Check Nxyz 180 200 120180 200 120
>
>
>
> Check map header agrees with fixed requirements for SFcalc for this
> spacegroup.
>
> Check Iuvw   3   2   1  3   1   2
>
> 
>
> SFALL:    Fatal disagreement between input info and map header
>
>
>
> How do I fix this ?
>
>
>
> In principle all the information is there to do the job…
>
>
>
> Many thx, BR
>
> --
>
> Bernhard Rupp
>
> Crystallographiae Vindicis Militum Ordo
>
> http://www.hofkristallamt.org/
>
> b...@hofkristallamt.org
>
> +1 925 209 7429
>
> +43 676 571 0536
>
> --
>
> Many plausible ideas vanish
>
> at the presence of thought
>
> --
>
>
>
> --
>
> 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
>



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] Using SFall for map conversion

2020-05-15 Thread Eleanor Dodson 
Hmmm

On Fri, 15 May 2020 at 22:53, Ian Tickle  wrote:

>
> It worked perfectly, no-one even noticed the bytes being swapped :)
>
> I.
>
>
> On Fri, 15 May 2020 at 22:37, Eleanor Dodson <
> 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> No no please no!!! How I hated the byte swap.. most people used VAXy
>> things - York didn’t - our bytes were not your bytes  stuff of
>> nightmares...
>>
>> On Fri, 15 May 2020 at 22:25, Jonathan Cooper <
>> 0c2488af9525-dmarc-requ...@jiscmail.ac.uk> wrote:
>>
>>> Ian, I can, as a not very scientific footnote, confirm that Jim Austin
>>> still has your Convex on his farm and, it seems, most of the manuals:
>>>
>>> http://u.cubeupload.com/jbcooper/smallIMGP0087.jpg
>>> http://u.cubeupload.com/jbcooper/smallIMGP0086.jpg
>>> http://u.cubeupload.com/jbcooper/smallIMGP0078.jpg
>>> http://u.cubeupload.com/jbcooper/smallIMGP0077.jpg
>>> http://u.cubeupload.com/jbcooper/smallIMGP0089.jpg
>>> http://u.cubeupload.com/jbcooper/smallIMGP0084.jpg
>>> http://u.cubeupload.com/jbcooper/smallIMGP0103.jpg
>>> http://u.cubeupload.com/jbcooper/smallIMGP0110.jpg
>>>
>>> He also has at least one of the ex-bbk Evans & Sutherland PS300's:
>>>
>>> http://u.cubeupload.com/jbcooper/smallIMGP0091.jpg
>>> http://u.cubeupload.com/jbcooper/smallIMGP0093.jpg
>>>
>>> A few cobwebs, but pretty good going really for a 'former' pig-shed!!
>>> Not sure what happened to the 11/750, though... School of Pharmacy rings a
>>> bell??
>>>
>>> None of this matters, but I just thought you might like to practice some
>>> 'big-iron' byte-swapping again, and if so, York is the place to go, after
>>> covid-19, of course ;-0 ;-0
>>> On Friday, 15 May 2020, 10:47:40 BST, Ian Tickle 
>>> wrote:
>>>
>>>
>>>
>>> Hi, that would have to be a very old map!  I remember implementing the
>>> auto-byte swap for VMS (necessary as we had both a Convex C220 running Unix
>>> and a VAX 11/750)!
>>>
>>> In fact the Convex was rescued from scrap by Jim Austin and is still
>>> working: http://www.corestore.org/convex.htm
>>>
>>> Cheers
>>>
>>> -- Ian
>>>
>>>
>>>
>>>
>>> Cheers
>>>
>>> -- Ian
>>>
>>>
>>> On Fri, 15 May 2020 at 09:24, Philippe BENAS <
>>> 0d88e888355a-dmarc-requ...@jiscmail.ac.uk> wrote:
>>>
>>> Dear Bernhard,
>>>
>>> Is it an old map ?
>>>
>>> Back to the old VAX times I had to dump CCP4 maps to ascii map files,
>>> then swap bytes from VAX-DOS to Unix before converting them again to a CCP4
>>> map format (I think I was using mapman from USF) on a Unix workstation and
>>> be able to read them in Frodo-Strasbourg or O.
>>>
>>> At least you could give it a shot and the ascii map file would help you
>>> figuring out the issue by a visual inspection of the header and sections.
>>>
>>> All the best,
>>> Philippe
>>>
>>> --
>>> Philippe BENAS, Ph.D.
>>>
>>> ARN UPR 9002 CNRS
>>> IBMC Strasbourg
>>> 2, Allée Konrad Röntgen
>>> F-67084 STRASBOURG cedex
>>> +33.3.8841.7109
>>> E-mails: p.be...@ibmc-cnrs.unistra.fr, philippe_be...@yahoo.fr
>>> URLs: http://www-ibmc.u-strasbg.fr/ ,
>>> http://www-ibmc.u-strasbg.fr/spip-arn/
>>> --
>>>
>>>
>>>
>>> Le jeudi 14 mai 2020 à 22:45:09 UTC+2, Bernhard Rupp <
>>> hofkristall...@gmail.com> a écrit :
>>>
>>>
>>> Hi Fellows,
>>>
>>>
>>>
>>> I am failing on conversion of a ccp4 map to mtz using Sfall
>>>
>>>
>>>
>>> I provide as a scale reference a mtz with FP SIGFP and R free
>>>
>>>
>>>
>>> All cell constants and SG 20 and map headers seem to agree.
>>>
>>>
>>>
>>> But I receive following warning:
>>>
>>>
>>>
>>> *** WARNING - your map spacegroup is different to the program default
>>> one ***
>>>
>>>
>>>
>>> and later
>>>
>>>
>>>
>>> >> CCP4 library signal library_file:Cannot open file (Warning)
>>>
>>> raised in tmpfile() failed, opening normal file instead. <<
>>>
>>> INPUT X USED AS  X
>>>
>>> INPUT Y USED AS  Z
>>>
>>> INPUT Z USED AS  Y
>>>
>>>
>>>
>>> Which then leads to the imho - given above- justified complaint:
>>>
>>>
>>>
>>> Check map header agrees with fixed requirements for SFcalc for this
>>> spacegroup.
>>>
>>> Check Nxyz 180 200 120180 200 120
>>>
>>>
>>>
>>> Check map header agrees with fixed requirements for SFcalc for this
>>> spacegroup.
>>>
>>> Check Iuvw   3   2   1  3   1   2
>>>
>>> 
>>>
>>> SFALL:    Fatal disagreement between input info and map header
>>>
>>>
>>>
>>> How do I fix this ?
>>>
>>>
>>>
>>> In principle all the information is there to do the job…
>>>
>>>
>>>
>>> Many thx, BR
>>>
>>> --
>>>
>>> Bernhard Rupp
>>>
>>> Crystallographiae Vindicis Militum Ordo
>>>
>>> http://www.hofkristallamt.org/
>>>
>>> b...@hofkristallamt.org
>>>
>>> +1 925 209 7429
>>>
>>> +43 676 571 0536
>>>
>>> --
>>>
>>> Many plausible ideas vanish
>>>
>>> at the presence of thought
>>>
>>> --
>>>
>>>
>>>
>>>

Re: [ccp4bb] Using SFall for map conversion

2020-05-15 Thread Ian Tickle 
It worked perfectly, no-one even noticed the bytes being swapped :)

I.


On Fri, 15 May 2020 at 22:37, Eleanor Dodson <
176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:

> No no please no!!! How I hated the byte swap.. most people used VAXy
> things - York didn’t - our bytes were not your bytes  stuff of
> nightmares...
>
> On Fri, 15 May 2020 at 22:25, Jonathan Cooper <
> 0c2488af9525-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> Ian, I can, as a not very scientific footnote, confirm that Jim Austin
>> still has your Convex on his farm and, it seems, most of the manuals:
>>
>> http://u.cubeupload.com/jbcooper/smallIMGP0087.jpg
>> http://u.cubeupload.com/jbcooper/smallIMGP0086.jpg
>> http://u.cubeupload.com/jbcooper/smallIMGP0078.jpg
>> http://u.cubeupload.com/jbcooper/smallIMGP0077.jpg
>> http://u.cubeupload.com/jbcooper/smallIMGP0089.jpg
>> http://u.cubeupload.com/jbcooper/smallIMGP0084.jpg
>> http://u.cubeupload.com/jbcooper/smallIMGP0103.jpg
>> http://u.cubeupload.com/jbcooper/smallIMGP0110.jpg
>>
>> He also has at least one of the ex-bbk Evans & Sutherland PS300's:
>>
>> http://u.cubeupload.com/jbcooper/smallIMGP0091.jpg
>> http://u.cubeupload.com/jbcooper/smallIMGP0093.jpg
>>
>> A few cobwebs, but pretty good going really for a 'former' pig-shed!! Not
>> sure what happened to the 11/750, though... School of Pharmacy rings a
>> bell??
>>
>> None of this matters, but I just thought you might like to practice some
>> 'big-iron' byte-swapping again, and if so, York is the place to go, after
>> covid-19, of course ;-0 ;-0
>> On Friday, 15 May 2020, 10:47:40 BST, Ian Tickle 
>> wrote:
>>
>>
>>
>> Hi, that would have to be a very old map!  I remember implementing the
>> auto-byte swap for VMS (necessary as we had both a Convex C220 running Unix
>> and a VAX 11/750)!
>>
>> In fact the Convex was rescued from scrap by Jim Austin and is still
>> working: http://www.corestore.org/convex.htm
>>
>> Cheers
>>
>> -- Ian
>>
>>
>>
>>
>> Cheers
>>
>> -- Ian
>>
>>
>> On Fri, 15 May 2020 at 09:24, Philippe BENAS <
>> 0d88e888355a-dmarc-requ...@jiscmail.ac.uk> wrote:
>>
>> Dear Bernhard,
>>
>> Is it an old map ?
>>
>> Back to the old VAX times I had to dump CCP4 maps to ascii map files,
>> then swap bytes from VAX-DOS to Unix before converting them again to a CCP4
>> map format (I think I was using mapman from USF) on a Unix workstation and
>> be able to read them in Frodo-Strasbourg or O.
>>
>> At least you could give it a shot and the ascii map file would help you
>> figuring out the issue by a visual inspection of the header and sections.
>>
>> All the best,
>> Philippe
>>
>> --
>> Philippe BENAS, Ph.D.
>>
>> ARN UPR 9002 CNRS
>> IBMC Strasbourg
>> 2, Allée Konrad Röntgen
>> F-67084 STRASBOURG cedex
>> +33.3.8841.7109
>> E-mails: p.be...@ibmc-cnrs.unistra.fr, philippe_be...@yahoo.fr
>> URLs: http://www-ibmc.u-strasbg.fr/ ,
>> http://www-ibmc.u-strasbg.fr/spip-arn/
>> --
>>
>>
>>
>> Le jeudi 14 mai 2020 à 22:45:09 UTC+2, Bernhard Rupp <
>> hofkristall...@gmail.com> a écrit :
>>
>>
>> Hi Fellows,
>>
>>
>>
>> I am failing on conversion of a ccp4 map to mtz using Sfall
>>
>>
>>
>> I provide as a scale reference a mtz with FP SIGFP and R free
>>
>>
>>
>> All cell constants and SG 20 and map headers seem to agree.
>>
>>
>>
>> But I receive following warning:
>>
>>
>>
>> *** WARNING - your map spacegroup is different to the program default one
>> ***
>>
>>
>>
>> and later
>>
>>
>>
>> >> CCP4 library signal library_file:Cannot open file (Warning)
>>
>> raised in tmpfile() failed, opening normal file instead. <<
>>
>> INPUT X USED AS  X
>>
>> INPUT Y USED AS  Z
>>
>> INPUT Z USED AS  Y
>>
>>
>>
>> Which then leads to the imho - given above- justified complaint:
>>
>>
>>
>> Check map header agrees with fixed requirements for SFcalc for this
>> spacegroup.
>>
>> Check Nxyz 180 200 120180 200 120
>>
>>
>>
>> Check map header agrees with fixed requirements for SFcalc for this
>> spacegroup.
>>
>> Check Iuvw   3   2   1  3   1   2
>>
>> 
>>
>> SFALL:    Fatal disagreement between input info and map header
>>
>>
>>
>> How do I fix this ?
>>
>>
>>
>> In principle all the information is there to do the job…
>>
>>
>>
>> Many thx, BR
>>
>> --
>>
>> Bernhard Rupp
>>
>> Crystallographiae Vindicis Militum Ordo
>>
>> http://www.hofkristallamt.org/
>>
>> b...@hofkristallamt.org
>>
>> +1 925 209 7429
>>
>> +43 676 571 0536
>>
>> --
>>
>> Many plausible ideas vanish
>>
>> at the presence of thought
>>
>> --
>>
>>
>>
>> --
>>
>> 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

Re: [ccp4bb] Using SFall for map conversion

2020-05-15 Thread Eleanor Dodson 
No no please no!!! How I hated the byte swap.. most people used VAXy things
- York didn’t - our bytes were not your bytes  stuff of nightmares...

On Fri, 15 May 2020 at 22:25, Jonathan Cooper <
0c2488af9525-dmarc-requ...@jiscmail.ac.uk> wrote:

> Ian, I can, as a not very scientific footnote, confirm that Jim Austin
> still has your Convex on his farm and, it seems, most of the manuals:
>
> http://u.cubeupload.com/jbcooper/smallIMGP0087.jpg
> http://u.cubeupload.com/jbcooper/smallIMGP0086.jpg
> http://u.cubeupload.com/jbcooper/smallIMGP0078.jpg
> http://u.cubeupload.com/jbcooper/smallIMGP0077.jpg
> http://u.cubeupload.com/jbcooper/smallIMGP0089.jpg
> http://u.cubeupload.com/jbcooper/smallIMGP0084.jpg
> http://u.cubeupload.com/jbcooper/smallIMGP0103.jpg
> http://u.cubeupload.com/jbcooper/smallIMGP0110.jpg
>
> He also has at least one of the ex-bbk Evans & Sutherland PS300's:
>
> http://u.cubeupload.com/jbcooper/smallIMGP0091.jpg
> http://u.cubeupload.com/jbcooper/smallIMGP0093.jpg
>
> A few cobwebs, but pretty good going really for a 'former' pig-shed!! Not
> sure what happened to the 11/750, though... School of Pharmacy rings a
> bell??
>
> None of this matters, but I just thought you might like to practice some
> 'big-iron' byte-swapping again, and if so, York is the place to go, after
> covid-19, of course ;-0 ;-0
> On Friday, 15 May 2020, 10:47:40 BST, Ian Tickle 
> wrote:
>
>
>
> Hi, that would have to be a very old map!  I remember implementing the
> auto-byte swap for VMS (necessary as we had both a Convex C220 running Unix
> and a VAX 11/750)!
>
> In fact the Convex was rescued from scrap by Jim Austin and is still
> working: http://www.corestore.org/convex.htm
>
> Cheers
>
> -- Ian
>
>
>
>
> Cheers
>
> -- Ian
>
>
> On Fri, 15 May 2020 at 09:24, Philippe BENAS <
> 0d88e888355a-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> Dear Bernhard,
>
> Is it an old map ?
>
> Back to the old VAX times I had to dump CCP4 maps to ascii map files, then
> swap bytes from VAX-DOS to Unix before converting them again to a CCP4 map
> format (I think I was using mapman from USF) on a Unix workstation and be
> able to read them in Frodo-Strasbourg or O.
>
> At least you could give it a shot and the ascii map file would help you
> figuring out the issue by a visual inspection of the header and sections.
>
> All the best,
> Philippe
>
> --
> Philippe BENAS, Ph.D.
>
> ARN UPR 9002 CNRS
> IBMC Strasbourg
> 2, Allée Konrad Röntgen
> F-67084 STRASBOURG cedex
> +33.3.8841.7109
> E-mails: p.be...@ibmc-cnrs.unistra.fr, philippe_be...@yahoo.fr
> URLs: http://www-ibmc.u-strasbg.fr/ ,
> http://www-ibmc.u-strasbg.fr/spip-arn/
> --
>
>
>
> Le jeudi 14 mai 2020 à 22:45:09 UTC+2, Bernhard Rupp <
> hofkristall...@gmail.com> a écrit :
>
>
> Hi Fellows,
>
>
>
> I am failing on conversion of a ccp4 map to mtz using Sfall
>
>
>
> I provide as a scale reference a mtz with FP SIGFP and R free
>
>
>
> All cell constants and SG 20 and map headers seem to agree.
>
>
>
> But I receive following warning:
>
>
>
> *** WARNING - your map spacegroup is different to the program default one
> ***
>
>
>
> and later
>
>
>
> >> CCP4 library signal library_file:Cannot open file (Warning)
>
> raised in tmpfile() failed, opening normal file instead. <<
>
> INPUT X USED AS  X
>
> INPUT Y USED AS  Z
>
> INPUT Z USED AS  Y
>
>
>
> Which then leads to the imho - given above- justified complaint:
>
>
>
> Check map header agrees with fixed requirements for SFcalc for this
> spacegroup.
>
> Check Nxyz 180 200 120180 200 120
>
>
>
> Check map header agrees with fixed requirements for SFcalc for this
> spacegroup.
>
> Check Iuvw   3   2   1  3   1   2
>
> 
>
> SFALL:    Fatal disagreement between input info and map header
>
>
>
> How do I fix this ?
>
>
>
> In principle all the information is there to do the job…
>
>
>
> Many thx, BR
>
> --
>
> Bernhard Rupp
>
> Crystallographiae Vindicis Militum Ordo
>
> http://www.hofkristallamt.org/
>
> b...@hofkristallamt.org
>
> +1 925 209 7429
>
> +43 676 571 0536
>
> --
>
> Many plausible ideas vanish
>
> at the presence of thought
>
> --
>
>
>
> --
>
> 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:
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>
> --
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>

Re: [ccp4bb] Using SFall for map conversion

2020-05-15 Thread Jonathan Cooper 
 Ian, I can, as a not very scientific footnote, confirm that Jim Austin still 
has your Convex on his farm and, it seems, most of the manuals: 
http://u.cubeupload.com/jbcooper/smallIMGP0087.jpg
http://u.cubeupload.com/jbcooper/smallIMGP0086.jpg
http://u.cubeupload.com/jbcooper/smallIMGP0078.jpg
http://u.cubeupload.com/jbcooper/smallIMGP0077.jpg
http://u.cubeupload.com/jbcooper/smallIMGP0089.jpg
http://u.cubeupload.com/jbcooper/smallIMGP0084.jpg
http://u.cubeupload.com/jbcooper/smallIMGP0103.jpg
http://u.cubeupload.com/jbcooper/smallIMGP0110.jpg

He also has at least one of the ex-bbk Evans & Sutherland PS300's:
http://u.cubeupload.com/jbcooper/smallIMGP0091.jpg
http://u.cubeupload.com/jbcooper/smallIMGP0093.jpg

A few cobwebs, but pretty good going really for a 'former' pig-shed!! Not sure 
what happened to the 11/750, though... School of Pharmacy rings a bell??
None of this matters, but I just thought you might like to practice some 
'big-iron' byte-swapping again, and if so, York is the place to go, after 
covid-19, of course ;-0 ;-0On Friday, 15 May 2020, 10:47:40 BST, Ian Tickle 
 wrote:  
 
 
Hi, that would have to be a very old map!  I remember implementing the 
auto-byte swap for VMS (necessary as we had both a Convex C220 running Unix and 
a VAX 11/750)!
In fact the Convex was rescued from scrap by Jim Austin and is still working: 
http://www.corestore.org/convex.htm
Cheers
-- Ian



Cheers
-- Ian

On Fri, 15 May 2020 at 09:24, Philippe BENAS 
<0d88e888355a-dmarc-requ...@jiscmail.ac.uk> wrote:

Dear Bernhard,

Is it an old map ?

Back to the old VAX times I had to dump CCP4 maps to ascii map files, then swap 
bytes from VAX-DOS to Unix before converting them again to a CCP4 map format (I 
think I was using mapman from USF) on a Unix workstation and be able to read 
them in Frodo-Strasbourg or O.

At least you could give it a shot and the ascii map file would help you 
figuring out the issue by a visual inspection of the header and sections.

All the best,
Philippe

Philippe BENAS, Ph.D.

ARN UPR 9002 CNRS
IBMC Strasbourg
2, Allée Konrad Röntgen
F-67084 STRASBOURG cedex
+33.3.8841.7109
E-mails: p.be...@ibmc-cnrs.unistra.fr, philippe_be...@yahoo.fr
URLs:   http://www-ibmc.u-strasbg.fr/ , http://www-ibmc.u-strasbg.fr/spip-arn/

 

Le jeudi 14 mai 2020 à 22:45:09 UTC+2, Bernhard Rupp 
 a écrit :  
 
 
Hi Fellows,

  

I am failing on conversion of a ccp4 map to mtz using Sfall

  

I provide as a scale reference a mtz with FP SIGFP and R free

  

All cell constants and SG 20 and map headers seem to agree.

  

But I receive following warning:

  

*** WARNING - your map spacegroup is different to the program default one ***

  

and later

  

>> CCP4 library signal library_file:Cannot open file (Warning)

    raised in tmpfile() failed, opening normal file instead. <<

    INPUT X USED AS  X

    INPUT Y USED AS  Z

    INPUT Z USED AS  Y

  

Which then leads to the imho - given above- justified complaint:

  

Check map header agrees with fixed requirements for SFcalc for this spacegroup.

Check Nxyz 180 200 120    180 200 120

  

Check map header agrees with fixed requirements for SFcalc for this  spacegroup.

Check Iuvw   3   2   1  3   1   2



SFALL:    Fatal disagreement between input info and map header

  

How do I fix this ? 

  

In principle all the information is there to do the job…

  

Many thx, BR

--

Bernhard Rupp

Crystallographiae Vindicis Militum Ordo

http://www.hofkristallamt.org/

b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

  
 

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https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
  

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Re: [ccp4bb] Using SFall for map conversion

2020-05-15 Thread Bernhard Rupp 
Thanks, I would not have the PDP 11 hardware anymore to read the 8” floppies  
No, the problem really was standard sequence of the grid axes sfall expects due 
to SG dependent FFT routines. 

Best, BR

 

From: Philippe BENAS  
Sent: Friday, May 15, 2020 01:23
To: ccp4bb@jiscmail.ac.uk; b...@hofkristallamt.org
Subject: Re: [ccp4bb] Using SFall for map conversion

 

Dear Bernhard,

 

Is it an old map ?

 

Back to the old VAX times I had to dump CCP4 maps to ascii map files, then swap 
bytes from VAX-DOS to Unix before converting them again to a CCP4 map format (I 
think I was using mapman from USF) on a Unix workstation and be able to read 
them in Frodo-Strasbourg or O.

 

At least you could give it a shot and the ascii map file would help you 
figuring out the issue by a visual inspection of the header and sections.

 

All the best,

Philippe

 

  _  

Philippe BENAS, Ph.D.

ARN UPR 9002 CNRS
IBMC Strasbourg
2, Allée Konrad Röntgen
F-67084 STRASBOURG cedex
+33.3.8841.7109

E-mails: p.be...@ibmc-cnrs.unistra.fr <mailto:p.be...@ibmc-cnrs.unistra.fr> , 
philippe_be...@yahoo.fr <mailto:philippe_be...@yahoo.fr> 
URLs: http://www-ibmc.u-strasbg.fr/ , http://www-ibmc.u-strasbg.fr/spip-arn/

  _  

 

 

 

Le jeudi 14 mai 2020 à 22:45:09 UTC+2, Bernhard Rupp mailto:hofkristall...@gmail.com> > a écrit : 

 

 

Hi Fellows,

 

I am failing on conversion of a ccp4 map to mtz using Sfall

 

I provide as a scale reference a mtz with FP SIGFP and R free

 

All cell constants and SG 20 and map headers seem to agree.

 

But I receive following warning:

 

*** WARNING - your map spacegroup is different to the program default one ***

 

and later

 

>>>>>> CCP4 library signal library_file:Cannot open file (Warning)

raised in tmpfile() failed, opening normal file instead. <<<<<<

INPUT X USED AS  X

INPUT Y USED AS  Z

INPUT Z USED AS  Y

 

Which then leads to the imho - given above- justified complaint:

 

Check map header agrees with fixed requirements for SFcalc for this spacegroup.

Check Nxyz 180 200 120180 200 120

 

Check map header agrees with fixed requirements for SFcalc for this  spacegroup.

Check Iuvw   3   2   1  3   1   2



SFALL:    Fatal disagreement between input info and map header

 

How do I fix this ? 

 

In principle all the information is there to do the job…

 

Many thx, BR

--

Bernhard Rupp

Crystallographiae Vindicis Militum Ordo

http://www.hofkristallamt.org/

b...@hofkristallamt.org <mailto:b...@hofkristallamt.org> 

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 

 

  _  

To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB 
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Re: [ccp4bb] Using SFall for map conversion

2020-05-15 Thread Bernhard Rupp 
Yes, as suggested, it works just fine with maprot and sfall out of the ccp4i 
interface, and the approximate scaling to refence Fo is enough for my hack.

Did not get the Refmac sfall option working but I am still troubleshooting this.

Will transition to clipper tools to avoid age discrimination.

 

Cheers, BR

 

From: CCP4 bulletin board  On Behalf Of Eleanor Dodson
Sent: Friday, May 15, 2020 02:46
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Using SFall for map conversion

 

maprot will rewrite your map with a changed axis order, as required for sfall.

And grateful as I am to see someone still loyal to sfall, 40+ years after it wa 
written!, there are more modern tools.

In the CCP4I interace go to 

Map & Mask faculities

Clipper Map tools, and there is a map to SFS utility.

 

Eleanor

 

 

 

On Fri, 15 May 2020 at 09:24, Philippe BENAS 
<0d88e888355a-dmarc-requ...@jiscmail.ac.uk 
<mailto:0d88e888355a-dmarc-requ...@jiscmail.ac.uk> > wrote:

Dear Bernhard,

 

Is it an old map ?

 

Back to the old VAX times I had to dump CCP4 maps to ascii map files, then swap 
bytes from VAX-DOS to Unix before converting them again to a CCP4 map format (I 
think I was using mapman from USF) on a Unix workstation and be able to read 
them in Frodo-Strasbourg or O.

 

At least you could give it a shot and the ascii map file would help you 
figuring out the issue by a visual inspection of the header and sections.

 

All the best,

Philippe

 


  _  


Philippe BENAS, Ph.D.

ARN UPR 9002 CNRS
IBMC Strasbourg
2, Allée Konrad Röntgen
F-67084 STRASBOURG cedex
+33.3.8841.7109

E-mails: p.be...@ibmc-cnrs.unistra.fr <mailto:p.be...@ibmc-cnrs.unistra.fr> , 
philippe_be...@yahoo.fr <mailto:philippe_be...@yahoo.fr> 
URLs: http://www-ibmc.u-strasbg.fr/ , http://www-ibmc.u-strasbg.fr/spip-arn/


  _  


 

 

 

Le jeudi 14 mai 2020 à 22:45:09 UTC+2, Bernhard Rupp mailto:hofkristall...@gmail.com> > a écrit : 

 

 

Hi Fellows,

 

I am failing on conversion of a ccp4 map to mtz using Sfall

 

I provide as a scale reference a mtz with FP SIGFP and R free

 

All cell constants and SG 20 and map headers seem to agree.

 

But I receive following warning:

 

*** WARNING - your map spacegroup is different to the program default one ***

 

and later

 

>>>>>> CCP4 library signal library_file:Cannot open file (Warning)

raised in tmpfile() failed, opening normal file instead. <<<<<<

INPUT X USED AS  X

INPUT Y USED AS  Z

INPUT Z USED AS  Y

 

Which then leads to the imho - given above- justified complaint:

 

Check map header agrees with fixed requirements for SFcalc for this spacegroup.

Check Nxyz 180 200 120180 200 120

 

Check map header agrees with fixed requirements for SFcalc for this  spacegroup.

Check Iuvw   3   2   1  3   1   2



SFALL:    Fatal disagreement between input info and map header

 

How do I fix this ? 

 

In principle all the information is there to do the job…

 

Many thx, BR

--

Bernhard Rupp

Crystallographiae Vindicis Militum Ordo

http://www.hofkristallamt.org/

b...@hofkristallamt.org <mailto:b...@hofkristallamt.org> 

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 

 


  _  


To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB 
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Re: [ccp4bb] Using SFall for map conversion

2020-05-15 Thread Eleanor Dodson 
Yes - but I meant too swap axes X Y Z yo X Z Y or whater the old inverse
FFT required to work in SG 20..


On Fri, 15 May 2020 at 10:47, Ian Tickle  wrote:

>
> Hi, that would have to be a very old map!  I remember implementing the
> auto-byte swap for VMS (necessary as we had both a Convex C220 running Unix
> and a VAX 11/750)!
>
> In fact the Convex was rescued from scrap by Jim Austin and is still
> working: http://www.corestore.org/convex.htm
>
> Cheers
>
> -- Ian
>
>
>
>
> Cheers
>
> -- Ian
>
>
> On Fri, 15 May 2020 at 09:24, Philippe BENAS <
> 0d88e888355a-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> Dear Bernhard,
>>
>> Is it an old map ?
>>
>> Back to the old VAX times I had to dump CCP4 maps to ascii map files,
>> then swap bytes from VAX-DOS to Unix before converting them again to a CCP4
>> map format (I think I was using mapman from USF) on a Unix workstation and
>> be able to read them in Frodo-Strasbourg or O.
>>
>> At least you could give it a shot and the ascii map file would help you
>> figuring out the issue by a visual inspection of the header and sections.
>>
>> All the best,
>> Philippe
>>
>> --
>> Philippe BENAS, Ph.D.
>>
>> ARN UPR 9002 CNRS
>> IBMC Strasbourg
>> 2, Allée Konrad Röntgen
>> F-67084 STRASBOURG cedex
>> +33.3.8841.7109
>> E-mails: p.be...@ibmc-cnrs.unistra.fr, philippe_be...@yahoo.fr
>> URLs: http://www-ibmc.u-strasbg.fr/ ,
>> http://www-ibmc.u-strasbg.fr/spip-arn/
>> --
>>
>>
>>
>> Le jeudi 14 mai 2020 à 22:45:09 UTC+2, Bernhard Rupp <
>> hofkristall...@gmail.com> a écrit :
>>
>>
>> Hi Fellows,
>>
>>
>>
>> I am failing on conversion of a ccp4 map to mtz using Sfall
>>
>>
>>
>> I provide as a scale reference a mtz with FP SIGFP and R free
>>
>>
>>
>> All cell constants and SG 20 and map headers seem to agree.
>>
>>
>>
>> But I receive following warning:
>>
>>
>>
>> *** WARNING - your map spacegroup is different to the program default one
>> ***
>>
>>
>>
>> and later
>>
>>
>>
>> >> CCP4 library signal library_file:Cannot open file (Warning)
>>
>> raised in tmpfile() failed, opening normal file instead. <<
>>
>> INPUT X USED AS  X
>>
>> INPUT Y USED AS  Z
>>
>> INPUT Z USED AS  Y
>>
>>
>>
>> Which then leads to the imho - given above- justified complaint:
>>
>>
>>
>> Check map header agrees with fixed requirements for SFcalc for this
>> spacegroup.
>>
>> Check Nxyz 180 200 120180 200 120
>>
>>
>>
>> Check map header agrees with fixed requirements for SFcalc for this
>> spacegroup.
>>
>> Check Iuvw   3   2   1  3   1   2
>>
>> 
>>
>> SFALL:    Fatal disagreement between input info and map header
>>
>>
>>
>> How do I fix this ?
>>
>>
>>
>> In principle all the information is there to do the job…
>>
>>
>>
>> Many thx, BR
>>
>> --
>>
>> Bernhard Rupp
>>
>> Crystallographiae Vindicis Militum Ordo
>>
>> http://www.hofkristallamt.org/
>>
>> b...@hofkristallamt.org
>>
>> +1 925 209 7429
>>
>> +43 676 571 0536
>>
>> --
>>
>> Many plausible ideas vanish
>>
>> at the presence of thought
>>
>> --
>>
>>
>>
>> --
>>
>> 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
>



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Re: [ccp4bb] Using SFall for map conversion

2020-05-15 Thread Ian Tickle 
Hi, that would have to be a very old map!  I remember implementing the
auto-byte swap for VMS (necessary as we had both a Convex C220 running Unix
and a VAX 11/750)!

In fact the Convex was rescued from scrap by Jim Austin and is still
working: http://www.corestore.org/convex.htm

Cheers

-- Ian




Cheers

-- Ian


On Fri, 15 May 2020 at 09:24, Philippe BENAS <
0d88e888355a-dmarc-requ...@jiscmail.ac.uk> wrote:

> Dear Bernhard,
>
> Is it an old map ?
>
> Back to the old VAX times I had to dump CCP4 maps to ascii map files, then
> swap bytes from VAX-DOS to Unix before converting them again to a CCP4 map
> format (I think I was using mapman from USF) on a Unix workstation and be
> able to read them in Frodo-Strasbourg or O.
>
> At least you could give it a shot and the ascii map file would help you
> figuring out the issue by a visual inspection of the header and sections.
>
> All the best,
> Philippe
>
> --
> Philippe BENAS, Ph.D.
>
> ARN UPR 9002 CNRS
> IBMC Strasbourg
> 2, Allée Konrad Röntgen
> F-67084 STRASBOURG cedex
> +33.3.8841.7109
> E-mails: p.be...@ibmc-cnrs.unistra.fr, philippe_be...@yahoo.fr
> URLs: http://www-ibmc.u-strasbg.fr/ ,
> http://www-ibmc.u-strasbg.fr/spip-arn/
> --
>
>
>
> Le jeudi 14 mai 2020 à 22:45:09 UTC+2, Bernhard Rupp <
> hofkristall...@gmail.com> a écrit :
>
>
> Hi Fellows,
>
>
>
> I am failing on conversion of a ccp4 map to mtz using Sfall
>
>
>
> I provide as a scale reference a mtz with FP SIGFP and R free
>
>
>
> All cell constants and SG 20 and map headers seem to agree.
>
>
>
> But I receive following warning:
>
>
>
> *** WARNING - your map spacegroup is different to the program default one
> ***
>
>
>
> and later
>
>
>
> >> CCP4 library signal library_file:Cannot open file (Warning)
>
> raised in tmpfile() failed, opening normal file instead. <<
>
> INPUT X USED AS  X
>
> INPUT Y USED AS  Z
>
> INPUT Z USED AS  Y
>
>
>
> Which then leads to the imho - given above- justified complaint:
>
>
>
> Check map header agrees with fixed requirements for SFcalc for this
> spacegroup.
>
> Check Nxyz 180 200 120180 200 120
>
>
>
> Check map header agrees with fixed requirements for SFcalc for this
> spacegroup.
>
> Check Iuvw   3   2   1  3   1   2
>
> 
>
> SFALL:    Fatal disagreement between input info and map header
>
>
>
> How do I fix this ?
>
>
>
> In principle all the information is there to do the job…
>
>
>
> Many thx, BR
>
> --
>
> Bernhard Rupp
>
> Crystallographiae Vindicis Militum Ordo
>
> http://www.hofkristallamt.org/
>
> b...@hofkristallamt.org
>
> +1 925 209 7429
>
> +43 676 571 0536
>
> --
>
> Many plausible ideas vanish
>
> at the presence of thought
>
> --
>
>
>
> --
>
> 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
>



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Re: [ccp4bb] Using SFall for map conversion

2020-05-15 Thread Eleanor Dodson 
maprot will rewrite your map with a changed axis order, as required for
sfall.
And grateful as I am to see someone still loyal to sfall, 40+ years after
it wa written!, there are more modern tools.
In the CCP4I interace go to
Map & Mask faculities
Clipper Map tools, and there is a map to SFS utility.

Eleanor



On Fri, 15 May 2020 at 09:24, Philippe BENAS <
0d88e888355a-dmarc-requ...@jiscmail.ac.uk> wrote:

> Dear Bernhard,
>
> Is it an old map ?
>
> Back to the old VAX times I had to dump CCP4 maps to ascii map files, then
> swap bytes from VAX-DOS to Unix before converting them again to a CCP4 map
> format (I think I was using mapman from USF) on a Unix workstation and be
> able to read them in Frodo-Strasbourg or O.
>
> At least you could give it a shot and the ascii map file would help you
> figuring out the issue by a visual inspection of the header and sections.
>
> All the best,
> Philippe
>
> --
> Philippe BENAS, Ph.D.
>
> ARN UPR 9002 CNRS
> IBMC Strasbourg
> 2, Allée Konrad Röntgen
> F-67084 STRASBOURG cedex
> +33.3.8841.7109
> E-mails: p.be...@ibmc-cnrs.unistra.fr, philippe_be...@yahoo.fr
> URLs: http://www-ibmc.u-strasbg.fr/ ,
> http://www-ibmc.u-strasbg.fr/spip-arn/
> --
>
>
>
> Le jeudi 14 mai 2020 à 22:45:09 UTC+2, Bernhard Rupp <
> hofkristall...@gmail.com> a écrit :
>
>
> Hi Fellows,
>
>
>
> I am failing on conversion of a ccp4 map to mtz using Sfall
>
>
>
> I provide as a scale reference a mtz with FP SIGFP and R free
>
>
>
> All cell constants and SG 20 and map headers seem to agree.
>
>
>
> But I receive following warning:
>
>
>
> *** WARNING - your map spacegroup is different to the program default one
> ***
>
>
>
> and later
>
>
>
> >> CCP4 library signal library_file:Cannot open file (Warning)
>
> raised in tmpfile() failed, opening normal file instead. <<
>
> INPUT X USED AS  X
>
> INPUT Y USED AS  Z
>
> INPUT Z USED AS  Y
>
>
>
> Which then leads to the imho - given above- justified complaint:
>
>
>
> Check map header agrees with fixed requirements for SFcalc for this
> spacegroup.
>
> Check Nxyz 180 200 120180 200 120
>
>
>
> Check map header agrees with fixed requirements for SFcalc for this
> spacegroup.
>
> Check Iuvw   3   2   1  3   1   2
>
> 
>
> SFALL:    Fatal disagreement between input info and map header
>
>
>
> How do I fix this ?
>
>
>
> In principle all the information is there to do the job…
>
>
>
> Many thx, BR
>
> --
>
> Bernhard Rupp
>
> Crystallographiae Vindicis Militum Ordo
>
> http://www.hofkristallamt.org/
>
> b...@hofkristallamt.org
>
> +1 925 209 7429
>
> +43 676 571 0536
>
> --
>
> Many plausible ideas vanish
>
> at the presence of thought
>
> --
>
>
>
> --
>
> 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
>



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Re: [ccp4bb] Using SFall for map conversion

2020-05-15 Thread Philippe BENAS 
Dear Bernhard,

Is it an old map ?

Back to the old VAX times I had to dump CCP4 maps to ascii map files, then swap 
bytes from VAX-DOS to Unix before converting them again to a CCP4 map format (I 
think I was using mapman from USF) on a Unix workstation and be able to read 
them in Frodo-Strasbourg or O.

At least you could give it a shot and the ascii map file would help you 
figuring out the issue by a visual inspection of the header and sections.

All the best,
Philippe

Philippe BENAS, Ph.D.

ARN UPR 9002 CNRS
IBMC Strasbourg
2, Allée Konrad Röntgen
F-67084 STRASBOURG cedex
+33.3.8841.7109
E-mails: p.be...@ibmc-cnrs.unistra.fr, philippe_be...@yahoo.fr
URLs:   http://www-ibmc.u-strasbg.fr/ , http://www-ibmc.u-strasbg.fr/spip-arn/

 

Le jeudi 14 mai 2020 à 22:45:09 UTC+2, Bernhard Rupp 
 a écrit :  
 
 
Hi Fellows,

  

I am failing on conversion of a ccp4 map to mtz using Sfall

  

I provide as a scale reference a mtz with FP SIGFP and R free

  

All cell constants and SG 20 and map headers seem to agree.

  

But I receive following warning:

  

*** WARNING - your map spacegroup is different to the program default one ***

  

and later

  

>> CCP4 library signal library_file:Cannot open file (Warning)

    raised in tmpfile() failed, opening normal file instead. <<

    INPUT X USED AS  X

    INPUT Y USED AS  Z

    INPUT Z USED AS  Y

  

Which then leads to the imho - given above- justified complaint:

  

Check map header agrees with fixed requirements for SFcalc for this spacegroup.

Check Nxyz 180 200 120    180 200 120

  

Check map header agrees with fixed requirements for SFcalc for this  spacegroup.

Check Iuvw   3   2   1  3   1   2



SFALL:    Fatal disagreement between input info and map header

  

How do I fix this ? 

  

In principle all the information is there to do the job…

  

Many thx, BR

--

Bernhard Rupp

Crystallographiae Vindicis Militum Ordo

http://www.hofkristallamt.org/

b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

  
 

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Re: [ccp4bb] Using SFall for map conversion

2020-05-14 Thread James Holton 

Yes, it's "mode sfcalc" in refmac:

echo mode sfcalc |\
refmac5 mapin density.map hklout density.mtz

As for automating sfall, I've found that using SFSG 1 makes it so all 
you need to do is make sure the map has the axis order for P1. I have a 
script that checks for this error and re-runs sfall with the right axis 
order in the event it comes up:

http://bl831.als.lbl.gov/~jamesh/pickup/ano_sfall.com

-James Holton
MAD Scientist

On 5/14/2020 3:28 PM, Bernhard Rupp wrote:


Thanks to all. Mapmask works. Yes the order to change to is ZXY. Map 
from coefficients indeed looks like the directly loaded map, jus the 
scale is different (I supplied no reference PDB)


The remaining issue is  - a pain to automate.

I tried Refmac- there is a mention of an sfall mode and I tried to 
input the map and a reference HKL .. In that case, refmac simply stops 
after reading the map.


If I add a XYZIN to scale the map, I get a mtz but not from the map, 
which is never read.


I am not even sure – this is from the EM part in the instructions – if 
this is intended to work in this fashion.


Has somebody tried that successfully with an Xray map?

Many thanks again, BR

*From:* CCP4 bulletin board  *On Behalf Of 
*Alejandro Buschiazzo

*Sent:* Thursday, May 14, 2020 15:10
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] Using SFall for map conversion

Oh…maybe I suggested the wrong order then (Y X Z  - for SG 20) ?

…I do realize YXZ is not an XYZ cyclic permutation (whereas ZXY is)…I 
dug it from an old script of mine, so now rechecked the FFT doc …but 
yes, FFT says that Y X Z is the std axis ordering for SGs higher-than 
18…I’m probably missing something silly here (any clue James?)


Best, ale



On May 14, 2020, at 6:45 PM, James Holton mailto:jmhol...@lbl.gov>> wrote:

Use mapmask first:

echo axis Z X Y |\
mapmask mapin1 old.map mapout new.map

For reasons I'm sure made sense at one time, sfall does not seem
to know how to automatically re-order the map axes.

Also, it is generally a good idea to expand to P1 first, and use
"SFSG 1" in sfall.  There are still some "gotcha" space groups in
the SFALL code for density near cell edges.  I can't remember
which ones now because years ago I started using SFSG 1 and the
problem went away.

-James Holton
MAD Scientist


On 5/14/2020 1:44 PM, Bernhard Rupp wrote:

Hi Fellows,

I am failing on conversion of a ccp4 map to mtz using Sfall

I provide as a scale reference a mtz with FP SIGFP and R free

All cell constants and SG 20 and map headers seem to agree.

But I receive following warning:

*** WARNING - your map spacegroup is different to the program
default one ***

and later

>>>>>> CCP4 library signal library_file:Cannot open
file (Warning)

raised in tmpfile() failed, opening normal file instead. <<<<<<

INPUT X USED AS  X

INPUT Y USED AS  Z

INPUT Z USED AS  Y

Which then leads to the imho - given above- justified complaint:

Check map header agrees with fixed requirements for SFcalc for
this spacegroup.

Check Nxyz 180 200 120    180 200 120

Check map header agrees with fixed requirements for SFcalc for
this  spacegroup.

Check Iuvw   3   2   1  3   1   2



SFALL:  Fatal disagreement between input info and map header

How do I fix this ?

In principle all the information is there to do the job…

Many thx, BR

--

Bernhard Rupp

Crystallographiae Vindicis Militum Ordo

http://www.hofkristallamt.org/

b...@hofkristallamt.org <mailto:b...@hofkristallamt.org>

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish

at the presence of thought

--



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Re: [ccp4bb] Using SFall for map conversion

2020-05-14 Thread Bernhard Rupp 
Thanks to all. Mapmask works. Yes the order to change to is ZXY. Map from 
coefficients indeed looks like the directly loaded map, jus the scale is 
different (I supplied no reference PDB)

The remaining issue is  - a pain to automate.

I tried Refmac- there is a mention of an sfall mode and I tried to input the 
map and a reference HKL .. In that case, refmac simply stops after reading the 
map.

If I add a XYZIN to scale the map, I get a mtz but not from the map, which is 
never read.

I am not even sure – this is from the EM part in the instructions – if this is 
intended to work in this fashion.

 

Has somebody tried that successfully with an Xray map?

 

Many thanks again, BR

 

From: CCP4 bulletin board  On Behalf Of Alejandro 
Buschiazzo
Sent: Thursday, May 14, 2020 15:10
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Using SFall for map conversion

 

Oh…maybe I suggested the wrong order then (Y X Z  - for SG 20) ?

 

…I do realize YXZ is not an XYZ cyclic permutation (whereas ZXY is)…I dug it 
from an old script of mine, so now rechecked the FFT doc …but yes, FFT says 
that Y X Z is the std axis ordering for SGs higher-than 18…I’m probably missing 
something silly here (any clue James?)

 

Best, ale





On May 14, 2020, at 6:45 PM, James Holton mailto:jmhol...@lbl.gov> > wrote:

 

Use mapmask first:

echo axis Z X Y |\
mapmask mapin1 old.map mapout new.map

For reasons I'm sure made sense at one time, sfall does not seem to know how to 
automatically re-order the map axes.

Also, it is generally a good idea to expand to P1 first, and use "SFSG 1" in 
sfall.  There are still some "gotcha" space groups in the SFALL code for 
density near cell edges.  I can't remember which ones now because years ago I 
started using SFSG 1 and the problem went away.

-James Holton
MAD Scientist




On 5/14/2020 1:44 PM, Bernhard Rupp wrote:

Hi Fellows,

 

I am failing on conversion of a ccp4 map to mtz using Sfall

 

I provide as a scale reference a mtz with FP SIGFP and R free

 

All cell constants and SG 20 and map headers seem to agree.

 

But I receive following warning:

 

*** WARNING - your map spacegroup is different to the program default one ***

 

and later

 

>>>>>> CCP4 library signal library_  file:Cannot open file 
>>>>>> (Warning)

raised in tmpfile() failed, opening normal file instead. <<<<<<

INPUT X USED AS  X

INPUT Y USED AS  Z

INPUT Z USED AS  Y

 

Which then leads to the imho - given above- justified complaint:

 

Check map header agrees with fixed requirements for SFcalc for this spacegroup.

Check Nxyz 180 200 120180 200 120

 

Check map header agrees with fixed requirements for SFcalc for this  spacegroup.

Check Iuvw   3   2   1  3   1   2



SFALL:    Fatal disagreement between input info and map header

 

How do I fix this ? 

 

In principle all the information is there to do the job…

 

Many thx, BR

--

Bernhard Rupp

Crystallographiae Vindicis Militum Ordo

 <http://www.hofkristallamt.org/> http://www.hofkristallamt.org/

 <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 

 


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Re: [ccp4bb] Using SFall for map conversion

2020-05-14 Thread Alejandro Buschiazzo 
Oh…maybe I suggested the wrong order then (Y X Z  - for SG 20) ?

…I do realize YXZ is not an XYZ cyclic permutation (whereas ZXY is)…I dug it 
from an old script of mine, so now rechecked the FFT doc …but yes, FFT says 
that Y X Z is the std axis ordering for SGs higher-than 18…I’m probably missing 
something silly here (any clue James?)

Best, ale

> On May 14, 2020, at 6:45 PM, James Holton  wrote:
> 
> Use mapmask first:
> 
> echo axis Z X Y |\
> mapmask mapin1 old.map mapout new.map
> 
> For reasons I'm sure made sense at one time, sfall does not seem to know how 
> to automatically re-order the map axes.
> 
> Also, it is generally a good idea to expand to P1 first, and use "SFSG 1" in 
> sfall.  There are still some "gotcha" space groups in the SFALL code for 
> density near cell edges.  I can't remember which ones now because years ago I 
> started using SFSG 1 and the problem went away.
> 
> -James Holton
> MAD Scientist
> 
> 
> On 5/14/2020 1:44 PM, Bernhard Rupp wrote:
>> Hi Fellows,
>>  
>> I am failing on conversion of a ccp4 map to mtz using Sfall
>>  
>> I provide as a scale reference a mtz with FP SIGFP and R free
>>  
>> All cell constants and SG 20 and map headers seem to agree.
>>  
>> But I receive following warning:
>>  
>> *** WARNING - your map spacegroup is different to the program default one ***
>>  
>> and later
>>  
>> >> CCP4 library signal library_file:Cannot  open file 
>> >> (Warning)
>> raised in tmpfile() failed, opening normal file instead. <<
>> INPUT X USED AS  X
>> INPUT Y USED AS  Z
>> INPUT Z USED AS  Y
>>  
>> Which then leads to the imho - given above- justified complaint:
>>  
>> Check map header agrees with fixed requirements for SFcalc for this 
>> spacegroup.
>> Check Nxyz 180 200 120180 200 120
>>  
>> Check map header agrees with fixed requirements for SFcalc for this  
>> spacegroup.
>> Check Iuvw   3   2   1  3   1   2
>> 
>> SFALL:    Fatal disagreement between input info and map header
>>  
>> How do I fix this ? 
>>  
>> In principle all the information is there to do the job…
>>  
>> Many thx, BR
>> --
>> Bernhard Rupp
>> Crystallographiae Vindicis Militum Ordo
>> http://www.hofkristallamt.org/ 
>> b...@hofkristallamt.org 
>> +1 925 209 7429
>> +43 676 571 0536
>> --
>> Many plausible ideas vanish 
>> at the presence of thought
>> --
>>  
>> 
>> 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:
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Re: [ccp4bb] Using SFall for map conversion

2020-05-14 Thread Alejandro Buschiazzo 
Hi Bernhard

I don’t know how you actually calculated your map. But it seems as thus it is 
not following the conventional requirement for the FFT calculation, with 
regards to the order of the map’s axes (, , , which must be 
some permutation of X Y Z). This shouldn’t normally happen, except if some 
non-standard axis choosing was made (even not on purpose).

mapdump mapin your.map 

will tell you which axis order your map file has, look for the line:
Fast, medium, slow axes .YXZ  (or whatever 
it says…should be Y X Z for C2221, if I recall correctly, double check)  


Option 1. 
In ccp4i map & mask utilities, go to the clipper utilities ("map to structure 
factors”), I believe clipper doesn’t care about axis order!

Option 2.
If for some reason you need to stick to sfall, you could try using mapmask for 
axis shifting. 
If I recall correctly (but please check if what you eventually get as output 
makes sense!) :

$mapmask MAPIN original.map MAPOUT shifted.map < On May 14, 2020, at 5:44 PM, Bernhard Rupp  wrote:
> 
> Hi Fellows,
>  
> I am failing on conversion of a ccp4 map to mtz using Sfall
>  
> I provide as a scale reference a mtz with FP SIGFP and R free
>  
> All cell constants and SG 20 and map headers seem to agree.
>  
> But I receive following warning:
>  
> *** WARNING - your map spacegroup is different to the program default one ***
>  
> and later
>  
> >> CCP4 library signal library_file:Cannot open file (Warning)
> raised in tmpfile() failed, opening normal file instead. <<
> INPUT X USED AS  X
> INPUT Y USED AS  Z
> INPUT Z USED AS  Y
>  
> Which then leads to the imho - given above- justified complaint:
>  
> Check map header agrees with fixed requirements for SFcalc for this 
> spacegroup.
> Check Nxyz 180 200 120180 200 120
>  
> Check map header agrees with fixed requirements for SFcalc for this  
> spacegroup.
> Check Iuvw   3   2   1  3   1   2
> 
> SFALL:    Fatal disagreement between input info and map header
>  
> How do I fix this ? 
>  
> In principle all the information is there to do the job…
>  
> Many thx, BR
> --
> Bernhard Rupp
> Crystallographiae Vindicis Militum Ordo
> http://www.hofkristallamt.org/ 
> b...@hofkristallamt.org 
> +1 925 209 7429
> +43 676 571 0536
> --
> Many plausible ideas vanish 
> at the presence of thought
> --
>  
> 
> 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] Using SFall for map conversion

2020-05-14 Thread James Holton 

Use mapmask first:

echo axis Z X Y |\
mapmask mapin1 old.map mapout new.map

For reasons I'm sure made sense at one time, sfall does not seem to know 
how to automatically re-order the map axes.


Also, it is generally a good idea to expand to P1 first, and use "SFSG 
1" in sfall.  There are still some "gotcha" space groups in the SFALL 
code for density near cell edges.  I can't remember which ones now 
because years ago I started using SFSG 1 and the problem went away.


-James Holton
MAD Scientist


On 5/14/2020 1:44 PM, Bernhard Rupp wrote:


Hi Fellows,

I am failing on conversion of a ccp4 map to mtz using Sfall

I provide as a scale reference a mtz with FP SIGFP and R free

All cell constants and SG 20 and map headers seem to agree.

But I receive following warning:

*** WARNING - your map spacegroup is different to the program default 
one ***


and later

>> CCP4 library signal library_file:Cannot open file (Warning)

raised in tmpfile() failed, opening normal file instead. <<

INPUT X USED AS  X

INPUT Y USED AS  Z

INPUT Z USED AS  Y

Which then leads to the imho - given above- justified complaint:

Check map header agrees with fixed requirements for SFcalc for this 
spacegroup.


Check Nxyz 180 200 120    180 200 120

Check map header agrees with fixed requirements for SFcalc for this  
spacegroup.


Check Iuvw   3   2   1  3   1   2



SFALL:  Fatal disagreement between input info and map header

How do I fix this ?

In principle all the information is there to do the job…

Many thx, BR

--

Bernhard Rupp

Crystallographiae Vindicis Militum Ordo

http://www.hofkristallamt.org/

b...@hofkristallamt.org 

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish

at the presence of thought

--




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[ccp4bb] Using SFall for map conversion

2020-05-14 Thread Bernhard Rupp 
Hi Fellows,

 

I am failing on conversion of a ccp4 map to mtz using Sfall

 

I provide as a scale reference a mtz with FP SIGFP and R free

 

All cell constants and SG 20 and map headers seem to agree.

 

But I receive following warning:

 

*** WARNING - your map spacegroup is different to the program default one
***

 

and later

 

>> CCP4 library signal library_file:Cannot open file (Warning)

raised in tmpfile() failed, opening normal file instead. <<

INPUT X USED AS  X

INPUT Y USED AS  Z

INPUT Z USED AS  Y

 

Which then leads to the imho - given above- justified complaint:

 

Check map header agrees with fixed requirements for SFcalc for this
spacegroup.

Check Nxyz 180 200 120180 200 120

 

Check map header agrees with fixed requirements for SFcalc for this
spacegroup.

Check Iuvw   3   2   1  3   1   2



SFALL:    Fatal disagreement between input info and map header

 

How do I fix this ? 

 

In principle all the information is there to do the job.

 

Many thx, BR

--

Bernhard Rupp

Crystallographiae Vindicis Militum Ordo

http://www.hofkristallamt.org/

b...@hofkristallamt.org  

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 




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