On Thursday 01 March 2007 10:17, 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!
Do the conversion on the shelx side, rather than the CCP4 side. http://shelx.uni-ac.gwdg.de/~tg/mtz2sca/mtz2sca.html > > > 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 > > Disclaimer > > This communication is confidential and may contain privileged information > intended solely for the named addressee(s). It may not be used or disclosed > except for the purpose for which it has been sent. If you are not the > intended recipient you must not review, use, disclose, copy, distribute or > take any action in reliance upon it. If you have received this communication > in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] > and destroy all copies of the message and any attached documents. > > > > Astex Therapeutics Ltd monitors, controls and protects all its messaging > traffic in compliance with its corporate email policy. The Company accepts no > liability or responsibility for any onward transmission or use of emails and > attachments having left the Astex Therapeutics domain. Unless expressly > stated, opinions in this message are those of the individual sender and not > of Astex Therapeutics Ltd. The recipient should check this email and any > attachments for the presence of computer viruses. Astex Therapeutics Ltd > accepts no liability for damage caused by any virus transmitted by this > email. E-mail is susceptible to data corruption, interception, unauthorized > amendment, and tampering, Astex Therapeutics Ltd only send and receive > e-mails on the basis that the Company is not liable for any such alteration > or any consequences thereof. > -- Ethan A Merritt Courier Deliveries: 1959 NE Pacific Dept of Biochemistry Health Sciences Building University of Washington - Seattle WA 98195-7742
