Re: [ccp4bb] Using SFall for map conversion

[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 

+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

[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/

  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

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



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Re: [ccp4bb] Using SFall for map conversion

[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&A=1 
> 



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Re: [ccp4bb] Using SFall for map conversion

[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

--




To unsubscribe from the CCP4BB list, click the following link:
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[ccp4bb] Using SFall for map conversion

[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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[ccp4bb] Protein structures sought as targets for CASP modeling experiment

[Andriy Kryshtafovych]

CASP (Critical Assessment of protein Structure Prediction) is in search 
for targets for the upcoming CASP14 modeling experiment (starting next 
Monday, May 18, 2020).


CASP community experiments aim to advance the state of the art in 
protein structure modeling. Every other year since 1994, CASP collects 
information on soon-to-be released experimental structures, passes on 
sequence data to the structure modeling community, and collects blind 
predictions of structure for assessment. About 100 modeling groups from 
around the world participate in the unofficial 'Olympics in the protein 
structure modeling', as CASP is often dubbed. Results of CASP 
experiments are assessed by prominent specialists in the field 
(http://predictioncenter.org/index.cgi?page=assessors_list 
), and 
published in special issues of the journal PROTEINS (see 
https://onlinelibrary.wiley.com/doi/10.1002/prot.25823 
 for the latest 
issue).


The success of CASP depends on the generosity of the structure 
determination community, and over the years more than 150 structure 
determination groups provided targets for the challenge. We need 
modeling targets over a wide range of difficulty, for modeling with and 
without the aid of templates. X-ray, NMR and cryo-EM structures are 
welcome. We are particularly interested in membrane proteins, protein 
complexes, and cryo-EM structures. We have also extended CASP to include 
modeling assisted by sparse experimental data, in collaboration with 
experimental groups in NMR, SAXS, and crosslinking. For that, protein 
material is needed (of course this is not expected for most targets, but 
if available, it would be much appreciated!).


If you have anything suitable, we would appreciate if you get in touch 
with us by writing to c...@predictioncenter.org or suggest your protein 
directly through the CASP14 target entry page: 
http://www.predictioncenter.org/casp14/targets_submission.cgi. If your 
structure is ready for the PDB deposition, we encourage you to mark it 
as a "CASP target" in the PDB's submission system. For those of you who 
have not provided targets to CASP before, the procedure is simple and 
fast. We don’t need the structure in advance of its release by the PDB, 
and if we are notified early enough (a minimum of three weeks before 
release, more is better) there need be no delay in structure release. 
More details are available through the website provided above.


 CASP target providers are regularly invited to contribute to special 
issue papers, for example:


2019: Lepore R, Kryshtafovych A, Alahuhta M, Veraszto HA, Bomble YJ, 
Bufton JC, Bullock AN, Caba C, Cao H, Davies OR, Desfosses A, Dunne M, 
Fidelis K, Goulding CW, Gurusaran M, Gutsche I, Harding CJ, Hartmann MD, 
Hayes CS, Joachimiak A, Leiman PG, Loppnau P, Lovering AL, Lunin VV, 
Michalska K, Mir-Sanchis I, Mitra A, Moult J, Phillips GN Jr, Pinkas DM, 
Rice PA, Tong Y, Topf M, Walton JD, Schwede T. (2019). Target highlights 
in CASP13: experimental target structures through the eyes of their 
authors. Proteins 87 (12), 1037-1057. Published online: 2019 Aug 23. 
doi: 10.1002/prot.25805. PMID: 31442339


 2018: Kryshtafovych A, Albrecht R, Baslé A, Bule P, Caputo AT, 
Carvalho AL, Chao KL, Diskin R, Fidelis K, Fontes CMGA, Fredslund F, 
Gilbert HJ, Goulding CW, Hartmann MD, Hayes CS, Herzberg O, Hill JC, 
Joachimiak A, Kohring GW, Koning RI, Lo Leggio L, Mangiagalli M, 
Michalska K, Moult J, Najmudin S, Nardini M, Nardone V, Ndeh D, Nguyen 
TH, Pintacuda G, Postel S, van Raaij MJ, Roversi P, Shimon A, Singh AK, 
Sundberg EJ, Tars K, Zitzmann N, Schwede T. (2018). Target highlights 
from the first post-PSI CASP experiment (CASP12, May-August 2016). 
Proteins 86 (S1), 27-50. doi: 10.1002/prot.25392. PMID: 28960539


 2016: 
Kryshtafovych A, Moult J, Baslé A, Burgin A, Craig TK, Edwards 
RA, Fass D, Hartmann MD, Korycinski M, Lewis RJ, Lorimer D, Lupas AN, 
Newman J, Peat TS, Piepenbrink KH, Prahlad J, van Raaij MJ, Rohwer F, 
Segall AM, Seguritan V, Sundberg EJ, Singh AK, Wilson MA, Schwede T. 
(2016). Some of the most interesting CASP11 targets through the eyes of 
their authors. Proteins 84 (S1), 34-50. doi: 10.1002/prot.24942. PMID: 
26473983 



 2014: Kryshtafovych A, Moult J, Bales P, Bazan JF, Biasini M, Burgin 
A, Chen C, Cochran FV, Craig TK, Das R, Fass D, Garcia-Doval C, Herzberg 
O, Lorimer D, Luecke H, Ma X, Nelson DC, van Raaij MJ, Rohwer F, Segall 
A, Seguritan V, Zeth K, Schwede T. (2014). Challenging the 
state-of-the-art in protein structure prediction: Highlights of 
experimental target structures for the 10th critical assessment of 
techniques for protein structure prediction experiment CASP10. Proteins 
82 (S2), 26-42. doi: 10.1002/prot.24489. PMID: 24318984


 2011: Kryshtafovych A, Moult J, Bartual SG, Bazan JF, Berman H, 
Casteel DE, Christodoulou E, Everett JK, Hausmann J, He