Dears,
I discovered HKL2MAP during a workshop in Grenoble which is maybe
interesting for you
http://schneider.group.ifom-ieo-campus.it/hkl2map/index.html#Reference
It works very straightforward (at least for me).
In another hand, have a look at the mtz2sca program.
I benefit from this opportunity to greet and thanks all organizers, teachers
and participants of this workshop.
Cheers,
Stefan Nicolet
-Message d'origine-
De : CCP4 bulletin board [mailto:[EMAIL PROTECTED] De la part de Ian
Tickle
Envoyé : jeudi, 1. mars 2007 19:18
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] MTZ to Shel-X?
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:
>> -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 = ...
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 SortMinMaxNum % Mean Mean Resolution
Type Column
num order Missing complete abs. LowHigh
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 NONE4.2 854.8 314 99.0182.2682.26 34.92 1.33
F F
5 NONE0.7 241.2 314 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 NONE0.5 5370.6 314 99.01 5.88 5.88 34.92 1.33
Q SIGIMEAN
8 NONE0.019.0 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:
>> -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'
