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Hi Josh,
'Free format' simply means read the numbers in order, regardless of the
layout, as defined by the list of file labels on the LABOUT command,
with each reflection starting on a new line. It's the most appropriate
format for data typed in from a standard PC keyboard.
'Fixed format' is a hangover from the days of punched cards and like
them should be consigned to a museum (I haven't seen a punched card for
20 years & there must be plenty of people around who've never seen
one!). It was possible to program the card punching machine (using
another card) so that it automatically moved the current data card to
the next number field defined by the program card, so the numbers
appeared in neat columns, with an identical layout on each data card.
It was then necessary to specify the exact columns where the data
appeared on the card for the reading program.
You have defined 10 labels so it will read the first 10 numbers it finds
in order into the 10 columns for reflection 1, i.e.:
6 0 0 59.092 266.854 0.913
-0.332 -6.034 0.000
0.000
into the columns that you have labelled H K L FP SIGFP FOM HLA HLB HLC
HLD. Then it reads the next 10 numbers starting on the next line into
the same columns for reflection 2, i.e.:
9 0 0 67.240 267.679 0.936
-0.326 -8.038 0.000
0.000
and so on until it runs out of numbers. This is why you can't skip any
columns doing it this way.
I don't know why arp/warp doesn't recognise the column labels, I'm not
an arp/warp user so I can't help you there. You presumably have to tell
arp/warp what your data columns are called using a LABIN command,
something like LABIN FP=FP SIGFP=SIGFP etc. However it sounds like the
MTZ file has been created as intended (check using mtzdump), you just
need to figure out how to read it.
-- Ian
> -----Original Message-----
> From: xtal_bb [mailto:[EMAIL PROTECTED]
> Sent: Tuesday, April 25, 2006 3:14 AM
> To: Ian Tickle
> Subject: Re: [ccp4bb]: CNS hkl file to MTZ
>
> hi lan
> Thank you for your detail description. It really help me a lot.
> However I still have questions about format and columns.
>
> The hkl file has been convert by the perl script and the result showed
> as following:
> 6 0 0 59.092 266.854 0.913
> -0.332 -6.034 0.000
> 0.000
> 9 0 0 67.240 267.679 0.936
> -0.326 -8.038 0.000
> 0.000
> 12 0 0 153.690 4.798 0.991
> 54.169 4.547 0.000
> 0.000
> 15 0 0 170.460 167.125 0.991
> -54.749 12.514 0.000
> 0.000
> 18 0 0 28.990 288.227 0.937
> 2.578 -7.828 0.000
> 0.000
> 21 0 0 68.170 206.718 0.993
> -62.079 -31.247 0.000
> 0.000
> 24 0 0 23.810 130.262 0.960
> -8.222 9.708 0.000
> 0.000
> 27 0 0 97.360 48.581 0.996
> 79.117 89.680 0.000
> 0.000
> 30 0 0 77.770 326.100 0.996
> 94.111 -63.239 0.000
> 0.000
> 33 0 0 88.240 266.018 0.996
> .....
> Is it right? the file format is what you said free format?
>
> Then I used f2mtz with the script you suggested
> #############################################
> #!/bin/csh
> f2mtz hklin dm_cns.hkl hklout dm_cns.mtz << eof
> symmetry 146
> cell 158.294 158.294 97.387 90.0 90.0 120.0
> labout H K L FP SIGFP FOM HLA HLB HLC HLD
> ctypout H H H F Q W A A A A
> PNAME aroB_cns_dm
> DNAME nat
> XNAME aroB_Nat
> end
> eof
> ############################################
>
> and the converting process was very soon. So I got the
> converted mtz file.
>
> But when I would like to use arp/warp to perform model building, the
> program can't recognise any columns in it?
>
> I am confused that the file format converted by the perl script. The
> converted file is so call the free format, and how do we define the
> column in it? how does f2mtz can identify each column and convert all
> information correctly?
>
> above of all are confused me! Would you mind giving me some help?
>
> thanks in advance
>
> josh
>
>
> On 4/21/06, Ian Tickle <[EMAIL PROTECTED]> wrote:
> >
> > Hi Josh
> >
> > F2MTZ is the program you want. I would recommend using the
> 2-liner Perl
> > script that I made (and which is given in the program documentation
> > http://www.ccp4.ac.uk/dist/html/f2mtz.html#cns):
> >
> > #!/usr/bin/perl
> > until(($_=<>)=~/\binde/i){}
> > do{s/\b[a-z]\S*\s*//gi;print}while(<>);
> >
> > Usage: cut & paste it, save it (e.g. as 'cnshkl.pl'), make
> it executable
> > (chmod +x cnshkl.pl), then run it like so:
> >
> > cnshkl.pl in.hkl > out.hkl
> >
> > This strips out all the CNS-specific text and leaves you with a
> > completely numeric file that can easily be read by f2mtz in
> free format.
> > The bonus of this is that it relieves you completely of the
> headaches of
> > counting the no of header lines to skip, working out nasty Fortran
> > formats and other potential irritations such as E-format
> numbers which
> > will thwart attempts to use a fixed-format read.
> >
> > Then run f2mtz _without_ the SKIP or FORMAT options, e.g. something
> > like:
> >
> > f2mtz HKLIN out.hkl HKLOUT out.mtz <<EOF
> > CELL ...
> > SYMM ...
> > LABO H K L F ...
> > CTYP H H H F ...
> > NAME PROJECT ... CRYSTAL ... DATASET ...
> > TITL ...
> > EOF
> >
> > The only downside of using free format is that you must
> convert _all_
> > the data columns without exception in the input file: you can't be
> > selective as is possible with fixed format, but then it's
> trivial to use
> > MTZUTILS to remove any columns you don't want.
> >
> > HTH!
> >
> > -- Ian
> >
> > > -----Original Message-----
> > > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On
> > > Behalf Of xtal_bb
> > > Sent: Friday, April 21, 2006 8:49 AM
> > > To: [email protected]
> > > Subject: [ccp4bb]: CNS hkl file to MTZ
> > >
> > > *** For details on how to be removed from this list
> visit the ***
> > > *** CCP4 home page http://www.ccp4.ac.uk ***
> > >
> > >
> > > Hi, everyone
> > > I have a crytal solved by molecular replacement and
> performed density
> > > modification with CNS 1.1 and a new hkl file is created.
> Now I would
> > > like to convert this new hkl file to mtz file to perform model
> > > building by automatic program like arp/warp or resolve...
> > >
> > > However I have no idea how to convert them and transfer all column
> > > information into mtz. Could anyone give me suggestions?
> > >
> > > my hkl file looks like this:
> > > NREFlection= 35582
> > > ANOMalous=FALSe { equiv. to HERMitian=TRUE}
> > > DECLare NAME=FULL_MOD DOMAin=RECIprocal
> TYPE=COMP END
> > > DECLare NAME=FOM_MOD DOMAin=RECIprocal
> TYPE=REAL END
> > > DECLare NAME=HLAM DOMAin=RECIprocal
> TYPE=REAL END
> > > DECLare NAME=HLBM DOMAin=RECIprocal
> TYPE=REAL END
> > > DECLare NAME=HLCM DOMAin=RECIprocal
> TYPE=REAL END
> > > DECLare NAME=HLDM DOMAin=RECIprocal
> TYPE=REAL END
> > > GROUp TYPE=HL
> > > OBJEct=HLAM
> > > OBJEct=HLBM
> > > OBJEct=HLCM
> > > OBJEct=HLDM
> > > END
> > > INDE 6 0 0 FULL_MOD= 59.092 266.854
> FOM_MOD= 0.913
> > > HLAM= -0.332 HLBM= -6.034 HLCM= 0.000
> > > HLDM= 0.000
> > > INDE 9 0 0 FULL_MOD= 67.240 267.679
> FOM_MOD= 0.936
> > > HLAM= -0.326 HLBM= -8.038 HLCM= 0.000
> > > HLDM= 0.000
> > > INDE 12 0 0 FULL_MOD= 153.690 4.798
> FOM_MOD= 0.991
> > > HLAM= 54.169 HLBM= 4.547 HLCM= 0.000
> > > HLDM= 0.000
> > > INDE 15 0 0 FULL_MOD= 170.460 167.125
> FOM_MOD= 0.991
> > > HLAM= -54.749 HLBM= 12.514 HLCM= 0.000
> > > HLDM= 0.000
> > > INDE 18 0 0 FULL_MOD= 28.990 288.227
> FOM_MOD= 0.937
> > > HLAM= 2.578 HLBM= -7.828 HLCM= 0.000
> > > HLDM= 0.000
> > > INDE 21 0 0 FULL_MOD= 68.170 206.718
> FOM_MOD= 0.993
> > > HLAM= -62.079 HLBM= -31.247 HLCM= 0.000
> > > HLDM= 0.000
> > > .......
> > >
> > > any recommendation will be very appreciated
> > >
> > > josh
> > >
> > >
> > >
> >
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