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From: "Ian Tickle" <[log in to unmask]>
To: <[log in to unmask]>
Cc: <[log in to unmask]>
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X-OriginalArrivalTime: 02 Mar 2007 11:50:40.0074 (UTC)
FILETIME=[FFEFF2A0:01C75CC0]
Thanks Eleanor, sorry I wasn't trying to get at you!
To grep for -1 at end of line:
grep -e -1$ file
(to find out what the '-e' flag is for, see the man page for grep!).
... and to everyone else, thanks for the offers, but I now have a
working jiffy to read h,k,l,I,SIGI,Rflag and write same in Shel-X format
(code available on request of course).
Cheers
-- Ian
> -----Original Message-----
> From: Eleanor Dodson [mailto:[log in to unmask]]
> Sent: 02 March 2007 10:11
> To: Ian Tickle
> Subject: Re: [ccp4bb] MTZ to Shel-X?
>
> 1) apologies for documentation
> 2) Thanks for detecting error - when I can find some test data I will
> pursue it..
> 3) Sorry about the FREE flag on the FREE line
>
> At one point SHELX ignored extra information in the
> reflection list,
> so I found it convenient to output the INS information as a
> header, and
> to flag the FREE reflections so that you could grep them out of the
> file. ( A flag of -1 is not greppable of course.. ) Maybe this is no
> longer necessary but some programs - was it XPLOR? ) required the
> working and test set of reflections to be in different files.
>
>
>
> However in the newer compilations of SHELX these flags are
> generating
> errors, and the only acceptable *hkl now has nothing except
> the indices
> and data.
>
> Thaat means one either has to persuade George to ignore these
> flags or
> edit them out. (or remove them but they had a use..)
>
>
> Eleanor
>
> Ian Tickle wrote:
> >
> > All, I thought this would be a simple task, but for the life of me I
> > can't see how to do it! All I want to do is convert an MTZ file to
> > Shel-X format for refinement. I thought it would take me 2
> secs, but
> > it's taken me at least 5 attempts, and it's still not right!
> >
> >
> > First I tried mtz2various with this command line:
> >
> > echo 'labi FP=F SIGFP=SIGF FREE=FreeR_flag\noutp shelx' |
> mtz2various
> > hklin 16294 hklout 16294.hkl
> >
> > with 'HKLF 3' in my .ins file. This works fine, but then shelxl
> > complains with:
> >
> > 11112222333344444444555555556666
> > >> -48 0 27 37.49 19.74 -1<< ??
> >
> > ** REFLECTION 30 HAS WRONG FORMAT **
> >
> >
> > OK fair enough I should have read the Shel-X manual first,
> because it
> > appears that 'HKLF 3' doesn't accept free R flags, it has
> to be 'HKLF 4'
> > (i.e. I's not F's). So when all else fails read the mtz2various
> > documentation (at least read it more thoroughly):
> >
> > * If only FP SIGFP or IP SIGIP are assigned on LABIN, then h k l FP
> > SIGFP or h k l IP SIGIP is output.
> >
> >
> > Great, precisely what I want! So for my second try let's go with:
> >
> > echo 'labi IP=IMEAN SIGIP=SIGIMEAN FREE=FreeR_flag\noutp shelx' |
> > mtz2various hklin 16294 hklout 16294.hkl
> >
> > but no:
> >
> > Data line--- labi IP=IMEAN SIGIP=SIGIMEAN FREE=FreeR_flag
> > MtzParseLabin: neither label recognised: IP IMEAN
> > MTZ2VARIOUS: Error in label assignments in LABIN
> >
> > Yet the output also says:
> >
> > LABIN <program label>=<file label> ...
> > Valid program labels are: FP, SIGFP
> > and optionally FPH, SIGFPH, IP, SIGIP, FC, PHIC, W, FPART, PHIPART,
> > PHIB, FOM, HLA HLB HLC HLD FREE
> >
> >
> > My first thought was "I've got the IMEAN/SIGIMEAN label
> wrong", but no,
> > mtzdump says:
> >
> > Col Sort Min Max Num % Mean Mean Resolution
> > Type Column
> > num order Missing complete abs.
> Low High
> > label
> >
> > 1 ASC -49 43 0 100.00 -8.7 18.6
> 48.75 1.33
> > H H
> > 2 NONE 0 32 0 100.00 12.0 12.0
> 48.75 1.33
> > H K
> > 3 NONE 0 41 0 100.00 15.7 15.7
> 48.75 1.33
> > H L
> > 4 NONE 4.2 854.8 314 99.01 82.26 82.26
> 34.92 1.33
> > F F
> > 5 NONE 0.7 241.2 314 99.01 3.38 3.38
> 34.92 1.33
> > Q SIGF
> > 6 NONE -58.6 8600.6 314 99.01 146.23 146.25
> 34.92 1.33
> > J IMEAN
> > 7 NONE 0.5 5370.6 314 99.01 5.88 5.88
> 34.92 1.33
> > Q SIGIMEAN
> > 8 NONE 0.0 19.0 0 100.00 9.48 9.48
> 48.75 1.33
> > I FreeR_flag
> >
> >
> > Then I look further down in mtz2various.doc:
> >
> > Input labels accepted are:
> >
> > H, K, L Indices
> > FP, SIGFP F and Sigma for native
> > FPH, SIGFPH F and Sigma for derivative
> > FC, PHIC F and Phase from model
> > FPART, PHIPART F and Phase from partial structure
> > DP, SIGDP Anomalous difference and Sigma
> > I, SIGI I and Sigma
> >
> >
> > So OK, fair enough IP, SIGIP was a typo (happens all the
> time in CCP4
> > documentation!), so problem solved, for my third go let's try:
> >
> > echo 'labi I=IMEAN SIGI=SIGIMEAN FREE=FreeR_flag\noutp shelx' |
> > mtz2various hklin 16294 hklout 16294.hkl
> >
> > Yes it worked!!! or did it??? I see that the output file
> has "HKLF 3"
> > in the header, and when I read the log file I see: ****NB Amplitude
> > Output , flagged with HKLF 3 ***. No good, Shel-X won't take free R
> > flags with HKLF 3 - and I thought mtz2various.doc said that
> if I/SIGI
> > are assigned then I/SIGI are output? (which would make a
> lot of sense!).
> >
> > Then I read in mtz2various.doc:
> >
> > FSQUARED
> >
> > If this flag is set, the program expects F and SIGF and
> will output
> > I
> > and SIGI: I = F*F, SIGI = 2*SIGF*F + SIGF*SIGF. These
> intensities
> > are
> > not necessarily the same as the measured intensities
> > (pre-TRUNCATE);
> > it is better to use the measured values if you have them.
> >
> > I completely agree with the last sentence! - but how to
> make it read I's
> > and write I's?
> >
> >
> > So in desperation to get something working, my fourth go is with:
> >
> > echo 'labi FP=F SIGFP=SIGF FREE=FreeR_flag\nfsqu\noutp shelx' |
> > mtz2various hklin 16294 hklout 16294.hkl
> >
> > This works: a file in HKLF 4 format containing apparently I
> & SIGI is
> > produced, but again Shel-X complains:
> >
> > 11112222333344444444555555556666
> > >> -48 0 27 37.49 19.74 -1<< ??
> >
> > ** REFLECTION 30 HAS WRONG FORMAT **
> >
> > Aaaargh - back to step 1!
> >
> >
> > So next I seek advice from a Shel-X user who says they've
> never seen the
> > "FREE" text at the end of the test reflection lines, e.g.:
> >
> > -48 0 27 114.07 151.73 -1 FREE
> >
> > and I say something along the lines of "don't be silly
> there's no way
> > the program would write it out like that if Shel-X didn't
> accept it" -
> > and just to prove to them how dumb their suggestion is I do a global
> > edit of the file, and of course it turns out they're quite
> right, and
> > technically it works - except of course that I is not the
> same as F^2 if
> > F has come from truncate (good thing I read the documentation!).
> >
> > I see that mtz2various.doc says "You may still have trouble getting
> > exactly the output you want.". Maybe that's the answer I've been
> > seeking! - or I've missed something very obvious. I could of course
> > have knocked up a jiffy Fortran program in 5 mins to read
> h, k ,l, I,
> > SIGI, Rflag in one format and write out h, k, l, I, SIGI, Rflag in
> > another format (and I'll probably end up doing just that!), but pity
> > those users who are not programmers!
> >
> > So what have I missed - any ideas?
> >
> > -- Ian
> >
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