Hi Eleanor, thanks for the response. I have sent a series of working and nonworking mtz files to Paul so hopefully he can straighten it out.
the flag type for the dano column is correct and even though that error message from the terminal window complains about it, this does not appear to be the problem because the same error message pops up with the mtz file that works??? As for using phwt vs phic/fom - I used to look at anom maps created with both sets of phases but never noticed much of a difference so got lazy and just started going with phwt (it is one less click of the mouse afterall:-). But this is not the problem either because coot is able to produce anomalous maps using the dano/phwt combination in most cases. That being said, however, I went back to the problematic mtz and added phic/fom and now coot is able to create an anomalous map with phic/fom but still not with phwt. An fft anomalous map created with either phase set is still able to be read just fine into coot though. And here is some more information on the issue - this problem is now seen on two machines (1 running Mandriva 2009.1 and the other Mandriva 2010.0) and two coot versions (Coot 0.6.1 2740 and Coot 0.6.2-pre-1 3144 - both are the coot-Linux-i686-ubuntu-8.04.4-gtk2-python builds). With the new version, we get a new error message when trying to read in one of the "bad" DANO mtz files: Error in proc: wrong-type-arg args: (#f Wrong type (expecting ~A): ~S (real number #<primitive-procedure nan>) (#<primitive-procedure nan>))) thanks again, Eric On Wed, 1 Sep 2010, Eleanor Dodson wrote: > It is hard to diagnose this without the mtz file. > > A bit of theory - a DANO map musdt have the input phases advanced by 90 > degrees from the input phase. To indicate that should be done a Dano column > is flagges type D. You need to check that this is so in the input mtz. I > presume COOT then recognises this and sets up the correct type of map. > > The phases/weights you should select for use from the refmac output in cad > are PHIC and FOM, not PHWT. This can eqwual PHIC but in some cases where > mFo-DFc is negative it equals PHIC+180. > > but there is probably some other problem - Paul Emsley needs to comment.. > Eleanor > > Eric Larson wrote: >> Hello, >> >> I am experiencing strange behavior in coot when trying to create anomalous >> difference maps from ccp4-produced mtz files. It appears to be a bug in >> coot but it is possible that it is caused by a ccp4 program. It seems to be >> the same problem as was reported a year ago >> (http://www.mail-archive.com/coot@jiscmail.ac.uk/msg01122.html) but does >> not appear to have been resolved. In this case I have 2 mtz files that >> have been created through identical paths (as far as I can tell!) and one >> works and one doesn't in the same version of coot and on the same machine. >> Hopefully this information will help in identifying the source of the >> problem. >> >> I have an mtz file containing dano and phwt columns (created by using cad >> to merge the phases from refmac with the original mtz file from truncate >> that contains dano). From coot, I open the mtz, select expert mode, select >> dano for the amplitudes and select fwt for the phases and then OK. Usually >> this will open up a perfectly good anomalous map with nice peaks on >> seleniums, etc. but now I have an empty map with no density - the contour >> level reads: nan3/A^3 ( nansigma). The terminal window looks like this: >> >> (filter-fileselection-filenames-state) >> (manage-column-selector /ccp4/dano-t.mtz) Making map from >> /1646b2/1646b2/DANO_1646b2inf and /1646b2/1646b2/PHWT >> making difference map from MTZ filename /ccp4/dano-t.mtz using >> /1646b2/1646b2/DANO_1646b2inf /1646b2/1646b2/PHWT >> CCP4MTZfile: Mtz column type mismatch: DANO_1646b2inf D-F >> Number of OBSERVED reflections: 46057 >> INFO:: finding ASU unique map points with sampling rate 2 >> INFO grid sampling...Nuvw = ( 324, 324, 324) >> INFO:: 0.6 seconds to read MTZ file >> INFO:: 0.009 seconds to initialize map >> INFO:: 1.474 seconds for FFT >> INFO:: 0.65 seconds for statistics >> Map mean: ........ nan >> Map sigma: ....... nan >> Map maximum: ..... -1e+10 >> Map minimum: ..... 1e+10 >> INFO:: 0.026 seconds for contour map >> INFO:: 2.759 seconds in total >> (make-and-draw-map-with-reso-with-refmac-params "/ccp4/dano-t.mtz" >> "/1646b2/1646b2/DANO_1646b2inf" "/1646b2/1646b2/PHWT" "" 0 1 0 >> "Fobs:None-specified" "SigF:None-specified" "RFree:None-specified" 0 1 0 >> -1.00 -1.00) >> >> >> several things about this strike me as a potential problem; 1) >> CCP4MTZfile: Mtz column type mismatch: DANO_1646b2inf D-F >> 2) Map mean: ........ nan >> Map sigma: ....... nan >> 3) " 0 1 0 "Fobs:None-specified" "SigF:None-specified" >> "RFree:None-specified" >> >> >> I try another mtz file created exactly the same way but with a different >> dataset to compare the terminal output with an mtz file that worked earlier >> for this same project and it looks like this: >> >> (filter-fileselection-filenames-state) >> (manage-column-selector /ccp4/job17-peak-dano.mtz) >> Making map from /1646b2/1646b2_2/DANO_1646b2pk and >> /1646b2renamed/1646b2/PHWT >> making difference map from MTZ filename /ccp4/job17-peak-dano.mtz using >> /1646b2/1646b2_2/DANO_1646b2pk /1646b2renamed/1646b2/PHWT >> CCP4MTZfile: Mtz column type mismatch: DANO_1646b2pk D-F >> Number of OBSERVED reflections: 41811 >> INFO:: finding ASU unique map points with sampling rate 2 >> INFO grid sampling...Nuvw = ( 324, 324, 324) >> INFO:: 0.445 seconds to read MTZ file >> INFO:: 0.009 seconds to initialize map >> INFO:: 0.451 seconds for FFT >> INFO:: 0.08 seconds for statistics >> Map mean: ........ -5.51326e-08 >> Map sigma: ....... 0.0100791 >> Map maximum: ..... 0.0944656 >> Map minimum: ..... -0.0629124 >> INFO:: 0.004 seconds for contour map >> INFO:: 0.989 seconds in total >> (make-and-draw-map-with-reso-with-refmac-params >> "/sgpp/data/process/Lmaj00847AAA/SeMet/1646b2/ccp4/job17-peak-dano.mtz" >> "/1646b2/1646b2_2/DANO_1646b2pk" "/1646b2renamed/1646b2/PHWT" "" 0 1 0 >> "Fobs:None-specified" "SigF:None-specified" "RFree:None-specified" 0 1 0 >> -1.00 -1.00) >> >> >> this time there are values for the map mean and sigma and I get a beautiful >> anomalous difference map. Again there are what I thought were signs of a >> problem (the column type mismatch and the None-specified column labels) in >> the terminal output so points 1 and 3 above are not the culprit. This >> suggests that there is a problem with the latest mtz file but it appears to >> be essentially the same as the earlier one that works so...??? >> Further confusing the matter, when I use fft in ccp4 to create an anomalous >> map using the "problematic" mtz file and the same DANO_1646b2inf and PHWT >> columns (which was the suggested "fix" to the problem last year!), it >> yields an anomalous map that opens up just fine in coot with the expected >> peaks on the seleniums suggesting that the "problematic" mtz file is fine - >> at least to ccp4 that is. >> >> The "work around" works fine but it is kind of annoying to have to do the >> extra fft step. Hopefully this information is useful. >> >> Please let me know if you need more information. >> >> Eric __________________________ >> Eric Larson, PhD >> Biomolecular Structure Center >> Department of Biochemistry >> Box 357742 >> University of Washington >> Seattle, WA 98195 > >
