Re: [ccp4bb] HKL to mtz

[SLAC]

You know, after f2mtz you can often have an mtz file with an unconventional ASU 
setting or unknown sort order. This breaks certain programs. So, I always run 
the result of f2mtz through a do-nothing run of the program called "CAD". Even 
if you don't tell it to do anything CAD always produces a "saeitized" output 
mtz. Have you tried that?

-James Holton
MAD Scientist

> On Oct 5, 2017, at 8:01 PM, ameya benz  wrote:
> 
> Hi,
> 
> I want to convert HKL file to mtz. I tried using F2mtz but somehow the output 
> mtz is not working. What parameters should I set during conversion. Or can 
> anyone suggest alternative to F2mtz?
> 
> regards,
> Ameya
> National chemical laboratory, Pune, India

Re: [ccp4bb] HKL to mtz

[Phil Evans]

Note that Combat and Scala are both obsolete

ccp4i2 has useful tasks for importing unmerged data (Data reduction) or merged 
data (Import merged data) from various formats

Phil


> On 6 Oct 2017, at 07:05, Ruud Hovius  wrote:
> 
> Hello, 
> 
> Using Combat followed by Scala in CCP4 works well with as input the .HKL from 
> XDS.
> or, Pointless-Aimless-Ctruncate with which it is also easy to exclude batches 
> .
> 
> best greetings, Ruud
> 
> On 6/10/17 05:01, ameya benz wrote:
>> Hi,
>> 
>> I want to convert HKL file to mtz. I tried using F2mtz but somehow the 
>> output mtz is not working. What parameters should I set during conversion. 
>> Or can anyone suggest alternative to F2mtz?
>> 
>> regards,
>> Ameya
>> National chemical laboratory, Pune, India
> 
> -- 
> 
> Ruud Hovius
> EPFL SB ISIC LIP
> BCH 4209
> CH-1015 Lausanne
> +41-21-693-9442
> 
> http://lip.epfl.ch

Re: [ccp4bb] HKL to mtz

[Graeme Winter]

pointless -c xdsin XDS_ASCII.HKL hklout xds_ascii.mtz
aimless hklin xds_ascii.mtz hklout merged.mtz << eof
scales unity
eof

should do it - is how I usually do this & it also gives a nice merging report...

Best wishes Graeme




From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of ameya benz 
[ameyab...@gmail.com]
Sent: 06 October 2017 04:01
To: ccp4bb
Subject: [ccp4bb] HKL to mtz

Hi,

I want to convert HKL file to mtz. I tried using F2mtz but somehow the output 
mtz is not working. What parameters should I set during conversion. Or can 
anyone suggest alternative to F2mtz?

regards,
Ameya
National chemical laboratory, Pune, India

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Re: [ccp4bb] HKL to mtz

[Eleanor Dodson]

Is your HKL file unmarked scaled data from XDS?
If so read it directly into the Data Reduction task (pointless / aimless
truncate) to produce a merged mtg file.

If the data is already merged, then f2mtz can convert it to an mtg

Eleanor

On 6 October 2017 at 07:05, Ruud Hovius  wrote:

> Hello,
>
> Using Combat followed by Scala in CCP4 works well with as input the .HKL
> from XDS.
> or, Pointless-Aimless-Ctruncate with which it is also easy to exclude
> batches .
>
> best greetings, Ruud
>
> On 6/10/17 05:01, ameya benz wrote:
>
> Hi,
>
> I want to convert HKL file to mtz. I tried using F2mtz but somehow the
> output mtz is not working. What parameters should I set during conversion.
> Or can anyone suggest alternative to F2mtz?
>
> regards,
> Ameya
> National chemical laboratory, Pune, India
>
>
> --
>
> Ruud Hovius
> EPFL SB ISIC LIP
> BCH 4209
> CH-1015 Lausanne+41-21-693-9442 <+41%2021%20693%2094%2042>http://lip.epfl.ch
>
>

Re: [ccp4bb] HKL to mtz

[Ruud Hovius]

Hello,

Using Combat followed by Scala in CCP4 works well with as input the .HKL 
from XDS.
or, Pointless-Aimless-Ctruncate with which it is also easy to exclude 
batches .


best greetings, Ruud

On 6/10/17 05:01, ameya benz wrote:

Hi,

I want to convert HKL file to mtz. I tried using F2mtz but somehow the 
output mtz is not working. What parameters should I set during 
conversion. Or can anyone suggest alternative to F2mtz?


regards,
Ameya
National chemical laboratory, Pune, India


--

Ruud Hovius
EPFL SB ISIC LIP
BCH 4209
CH-1015 Lausanne
+41-21-693-9442
http://lip.epfl.ch

Re: [ccp4bb] HKL to mtz

[Engin Özkan]

By HKL, I assume you mean an XDS output file. In that case, xdsconv from 
the XDS package works. Pick one of the CCP4 formats (like CCP4_I+F). 
Then, xdsconv essentially tells you to run f2mtz and cad (I think) with 
certain options. It does employ a French-Wilson scheme for converting 
negative intensities, if you like that.


I had been encountering (for a long time) one issue, though. The 
OUTPUT_FILE parameter seems to not take effect (at least in the CCP4_I+F 
format) and defaults to something like output_file.mtz within the 
commands xdsconv instructs you to type. Manually change it.


Engin

On 10/5/17 10:26 PM, Edward A. Berry wrote:

On 10/05/2017 11:01 PM, ameya benz wrote:

Hi,

I want to convert HKL file to mtz. I tried using F2mtz but somehow 
the output mtz is not working. What parameters should I set during 
conversion. Or can anyone suggest alternative to F2mtz?


regards,
Ameya
National chemical laboratory, Pune, India


Hi, Ameya,
F2mtz works.
In order for someone to help you you need to give more information.
What does your HKL file look like (show us the first 10-20 lines)?
Are you running f2mtz from one of the GUIs, or from a a script or 
commandline?
What parameters did you give (or what was your script)? (often the 
FORMAT statement is the problem).
And in what way the output mtz file is not working? maybe use mtzdump 
to show what you got.

Hope that will lead to a speedy resolution!


--
Engin Özkan, Ph.D.
Assistant Professor
Dept of Biochemistry and Molecular Biology
University of Chicago
Phone: (773) 834-5498
http://ozkan.uchicago.edu

Re: [ccp4bb] HKL to mtz

[Edward A. Berry]

On 10/05/2017 11:01 PM, ameya benz wrote:

Hi,

I want to convert HKL file to mtz. I tried using F2mtz but somehow the output 
mtz is not working. What parameters should I set during conversion. Or can 
anyone suggest alternative to F2mtz?

regards,
Ameya
National chemical laboratory, Pune, India


Hi, Ameya,
F2mtz works.
In order for someone to help you you need to give more information.
What does your HKL file look like (show us the first 10-20 lines)?
Are you running f2mtz from one of the GUIs, or from a a script or commandline?
What parameters did you give (or what was your script)? (often the FORMAT 
statement is the problem).
And in what way the output mtz file is not working? maybe use mtzdump to show 
what you got.
Hope that will lead to a speedy resolution!

Re: [ccp4bb] HKL to mtz

[Wojtas, Lukasz]

Use XPREP to convert HKL to SCA file  (options D and W) then CCP4 to get MTZ,


Lukasz Wojtas


From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of ameya benz 
<ameyab...@gmail.com>
Sent: Thursday, October 5, 2017 11:01:35 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] HKL to mtz

Hi,

I want to convert HKL file to mtz. I tried using F2mtz but somehow the output 
mtz is not working. What parameters should I set during conversion. Or can 
anyone suggest alternative to F2mtz?

regards,
Ameya
National chemical laboratory, Pune, India

[ccp4bb] HKL to mtz

[ameya benz]

Hi,

I want to convert HKL file to mtz. I tried using F2mtz but somehow the
output mtz is not working. What parameters should I set during conversion.
Or can anyone suggest alternative to F2mtz?

regards,
Ameya
National chemical laboratory, Pune, India

Re: [ccp4bb] hkl into mtz using f2mtz

[Eleanor Dodson]

I am no expert on CNS files, but do the entries for F_BULK and F_MODEL 
correspond to an amplitude and a phase - it certainly looks like that..


If so you can read both in:

I havent checked the format but your script would look like this

title [No title given]
format 
'(6X,3F5.0,6X,F10.0,6X,F10.0,6X,F10.0,/,25X,F10.0,6X,F10.0,7X,2F10.0,/,28X,F10.0,10X,F10.0,10X,F10.0,/,28X,F10.0,11X,F10.0,/,27X,2F10.0)'

skipline 5
labout H K L IP SIGIP FP SIGFP FreeRflag Fbulk PHIbulk HLA HLB HLC HLD 
FOM Fcalc PHIcalc

ctypout H H H J Q F Q X F P A A A A W F P
PNAME tony
DNAME z
XNAME x
end


Miriam Sharpe wrote:

Hi everyone,

I've been looking at ways to convert an old hkl file from a CNS refinement (see 
details below) into an mtz file.

F2mtz in ccp4 will do this once I have told it the fortran format of the hkl 
file (below), and specified the data type and label for the input fields.

However, I'm not sure how to define the F-MODEL and FBULK columns in terms of mtz column types. Both are two-part columns containing complex Fcalc with both amplitude and phase information. 


Any suggestions are most welcome!

Thanks,
Miriam Sharpe

Dr Miriam L Sharpe
Postdoctoral Fellow
Department of Biochemistry 
University of Otago

PO Box 56
710 Cumberland St
Dunedin 9054 , New Zealand
___
the list of columns in the hkl file:

IOBS=experimental intensity from .sca file
SIGI=sigma of IOBS
FOBS=square root of IOBS
SIGMA=sigma of FOBS
TEST=Rfree flag
FBULK=bulk solvent part of Fcalc
PA_MODEL = HL coeff.
PB_MODEL= HL coeff.
PC_MODEL = HL coeff.
PD_MODEL = HL coeff.
FOM_MODEL =figure of merit
F_MODEL  = complex Fcalc, includes both amplitude and phase

and the first two reflection entries:

 INDE38   214 IOBS=   771.500 SIGI=  1140.300 FOBS=27.780
   SIGMA=27.780 TEST= 0 FBULK= 0.33355.023
   PA_MODEL= 5.685 PB_MODEL= 5.558 PC_MODEL= 0.000
   PD_MODEL= 0.000 FOM_MODEL= 0.935
   F_MODEL=   135.59544.354
 INDE38   213 IOBS=18.500 SIGI=   861.100 FOBS= 4.300
   SIGMA= 4.300 TEST= 0 FBULK= 0.54282.489
   PA_MODEL= 1.334 PB_MODEL= 0.159 PC_MODEL= 0.000
   PD_MODEL= 0.000 FOM_MODEL= 0.555
   F_MODEL=   147.826 6.802

Corresponding Fortran format (I think):
(6X,3F5.0,6X,F10.0,6X,F10.0,6X,F10.0,/,25X,F10.0,6X,F10.0,7X,2F10.0,/,28X,F10.0,10X,F10.0,10X,F10.0,/,28X,F10.0,11X,F10.0,/,27X,2F10.0)


MTZ Column Types:
H
index h,k,l
F
structure amplitude, F
D
anomalous difference
Q
standard deviation of anything: J,F,D or other
P
phase angle in degrees
W
weight (of some sort)
A
phase probability coefficients (Hendrickson/Lattmann)
B
BATCH number
S
1/d**2 = 4 (sin theta/lambda)**2
J
intensity
Y
M/ISYM, packed partial/reject flag and symmetry number
I
any other integer
R
any other real
U
partial FC (see CAD)
V
partial PHIC (see CAD)

Re: [ccp4bb] hkl into mtz using f2mtz

[Kevin Cowtan]

This may also be a job for 'convert2mtz', which I think will pick up the 
complex columns automatically. Only available from the command line though.


Kevin

Eleanor Dodson wrote:
I am no expert on CNS files, but do the entries for F_BULK and F_MODEL 
correspond to an amplitude and a phase - it certainly looks like that..


If so you can read both in:

I havent checked the format but your script would look like this

title [No title given]
format 
'(6X,3F5.0,6X,F10.0,6X,F10.0,6X,F10.0,/,25X,F10.0,6X,F10.0,7X,2F10.0,/,28X,F10.0,10X,F10.0,10X,F10.0,/,28X,F10.0,11X,F10.0,/,27X,2F10.0)' 


skipline 5
labout H K L IP SIGIP FP SIGFP FreeRflag Fbulk PHIbulk HLA HLB HLC HLD 
FOM Fcalc PHIcalc

ctypout H H H J Q F Q X F P A A A A W F P
PNAME tony
DNAME z
XNAME x
end


Miriam Sharpe wrote:

Hi everyone,

I've been looking at ways to convert an old hkl file from a CNS 
refinement (see details  below) into an mtz file.


F2mtz in ccp4 will do this once I have told it the fortran format of 
the hkl file (below), and specified the data type and label for the 
input fields.


However, I'm not sure how to define the F-MODEL and FBULK columns in 
terms of mtz column types. Both are two-part columns containing 
complex Fcalc with both amplitude and phase information.

Any suggestions are most welcome!

Thanks,
Miriam Sharpe

Dr Miriam L Sharpe
Postdoctoral Fellow
Department of Biochemistry University of Otago
PO Box 56
710 Cumberland St
Dunedin 9054 , New Zealand
___
the list of columns in the hkl file:

IOBS=experimental intensity from .sca file
SIGI=sigma of IOBS
FOBS=square root of IOBS
SIGMA=sigma of FOBS
TEST=Rfree flag
FBULK=bulk solvent part of Fcalc
PA_MODEL = HL coeff.
PB_MODEL= HL coeff.
PC_MODEL = HL coeff.
PD_MODEL = HL coeff.
FOM_MODEL =figure of merit
F_MODEL  = complex Fcalc, includes both amplitude and phase

and the first two reflection entries:

 INDE38   214 IOBS=   771.500 SIGI=  1140.300 FOBS=27.780
   SIGMA=27.780 TEST= 0 FBULK= 
0.33355.023
   PA_MODEL= 5.685 PB_MODEL= 5.558 
PC_MODEL= 0.000

   PD_MODEL= 0.000 FOM_MODEL= 0.935
   F_MODEL=   135.59544.354
 INDE38   213 IOBS=18.500 SIGI=   861.100 FOBS= 4.300
   SIGMA= 4.300 TEST= 0 FBULK= 
0.54282.489
   PA_MODEL= 1.334 PB_MODEL= 0.159 
PC_MODEL= 0.000

   PD_MODEL= 0.000 FOM_MODEL= 0.555
   F_MODEL=   147.826 6.802

Corresponding Fortran format (I think):
(6X,3F5.0,6X,F10.0,6X,F10.0,6X,F10.0,/,25X,F10.0,6X,F10.0,7X,2F10.0,/,28X,F10.0,10X,F10.0,10X,F10.0,/,28X,F10.0,11X,F10.0,/,27X,2F10.0) 




MTZ Column Types:
H
index h,k,l
F
structure amplitude, F
D
anomalous difference
Q
standard deviation of anything: J,F,D or other
P
phase angle in degrees
W
weight (of some sort)
A
phase probability coefficients (Hendrickson/Lattmann)
B
BATCH number
S
1/d**2 = 4 (sin theta/lambda)**2
J
intensity
Y
M/ISYM, packed partial/reject flag and symmetry number
I
any other integer
R
any other real
U
partial FC (see CAD)
V
partial PHIC (see CAD)

[ccp4bb] hkl into mtz using f2mtz

[Miriam Sharpe]

Hi everyone,

I've been looking at ways to convert an old hkl file from a CNS refinement (see 
details below) into an mtz file.

F2mtz in ccp4 will do this once I have told it the fortran format of the hkl 
file (below), and specified the data type and label for the input fields.

However, I'm not sure how to define the F-MODEL and FBULK columns in terms of 
mtz column types. Both are two-part columns containing complex Fcalc with both 
amplitude and phase information. 

Any suggestions are most welcome!

Thanks,
Miriam Sharpe

Dr Miriam L Sharpe
Postdoctoral Fellow
Department of Biochemistry 
University of Otago
PO Box 56
710 Cumberland St
Dunedin 9054 , New Zealand
___
the list of columns in the hkl file:

IOBS=experimental intensity from .sca file
SIGI=sigma of IOBS
FOBS=square root of IOBS
SIGMA=sigma of FOBS
TEST=Rfree flag
FBULK=bulk solvent part of Fcalc
PA_MODEL = HL coeff.
PB_MODEL= HL coeff.
PC_MODEL = HL coeff.
PD_MODEL = HL coeff.
FOM_MODEL =figure of merit
F_MODEL  = complex Fcalc, includes both amplitude and phase

and the first two reflection entries:

 INDE38   214 IOBS=   771.500 SIGI=  1140.300 FOBS=27.780
   SIGMA=27.780 TEST= 0 FBULK= 0.33355.023
   PA_MODEL= 5.685 PB_MODEL= 5.558 PC_MODEL= 0.000
   PD_MODEL= 0.000 FOM_MODEL= 0.935
   F_MODEL=   135.59544.354
 INDE38   213 IOBS=18.500 SIGI=   861.100 FOBS= 4.300
   SIGMA= 4.300 TEST= 0 FBULK= 0.54282.489
   PA_MODEL= 1.334 PB_MODEL= 0.159 PC_MODEL= 0.000
   PD_MODEL= 0.000 FOM_MODEL= 0.555
   F_MODEL=   147.826 6.802

Corresponding Fortran format (I think):
(6X,3F5.0,6X,F10.0,6X,F10.0,6X,F10.0,/,25X,F10.0,6X,F10.0,7X,2F10.0,/,28X,F10.0,10X,F10.0,10X,F10.0,/,28X,F10.0,11X,F10.0,/,27X,2F10.0)


MTZ Column Types:
H
index h,k,l
F
structure amplitude, F
D
anomalous difference
Q
standard deviation of anything: J,F,D or other
P
phase angle in degrees
W
weight (of some sort)
A
phase probability coefficients (Hendrickson/Lattmann)
B
BATCH number
S
1/d**2 = 4 (sin theta/lambda)**2
J
intensity
Y
M/ISYM, packed partial/reject flag and symmetry number
I
any other integer
R
any other real
U
partial FC (see CAD)
V
partial PHIC (see CAD)

Re: [ccp4bb] hkl to mtz with anomalous data

[PhilEvans]

Tim

I think you could import it using COMBAT (with the user-define  
option), making a file which could be merged with Scala.


Scala can also write a scaled but unmerged mtz file, but I don't  
whether other programs can use this


It would easy for me to make POINTLESS read unmerged hkl files if this  
was useful. Does the file just contain h k l I sigma? It would need  
the cell dimensions as well


Best wishes
Phil Evans

On 29 May 2008, at 20:32, Tim Gruene wrote:


-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Hello everyone,

we have been trying to convert an unmerged hkl-file to mtz such that  
the labels F+/F- or F/DANO (or I+/- etc respectively) are  
calculated, and failed so far.


We would appreciate a hint towards the correct program/ options to  
use.


Cheers, Tim


- --
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

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Version: GnuPG v1.4.6 (GNU/Linux)

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iVQ+htqUa6tbyo4PXYMPEYg=
=CKRB
-END PGP SIGNATURE-

[ccp4bb] hkl to mtz with anomalous data

[Tim Gruene]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Hello everyone,

we have been trying to convert an unmerged hkl-file to mtz such that the 
labels F+/F- or F/DANO (or I+/- etc respectively) are calculated, and 
failed so far.


We would appreciate a hint towards the correct program/ options to use.

Cheers, Tim


- --
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

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Version: GnuPG v1.4.6 (GNU/Linux)

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iVQ+htqUa6tbyo4PXYMPEYg=
=CKRB
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