Hi Ethan, Thanks for the information. My guess is that in MTZ only F-float is expected, because it is the only 32bit form? Zhijie
> On Nov 13, 2018, at 3:44 PM, Ethan A Merritt <[email protected]> wrote: > >> On Tuesday, November 13, 2018 11:51:55 AM PST Zhijie Li wrote: >> If somebody is going to send these files by email, please send one to me >> too. Thanks in advance. I actually prefer to get a MTZ file because the >> miller indices would serve as good clues for understanding the encodings. >> Even the first 1024 bytes of an MTZ would do (data array starts at byte 80 >> in MTZ). >> >> In my life I had only seen ieee754. According to what I can find, VAX has >> an exponent bias of 128 (ieee754 uses 127). Then it seems to me that when >> converting from vax to ieee a division of 2 is involved. > > It's more complicated than that. VAXen supported multiple floating point > formats, > F-floating G-floating and H-floating. > They had differed by how many bits were used for the exponent, and hence how > many bits were left for the mantissa. > I can pull out the architecture manuals if necessary. > > ah, nostalgia > > Ethan > > >> However all procedures I have seen use a division of 4, which is quite >> puzzling to me. A real data file containing meaningful numbers (eg., HKL >> indices) would be very helpful. Thanks in advance. >> >> Zhijie >> >>> On Nov 13, 2018, at 2:21 PM, Johan Hattne <[email protected]> wrote: >>> >>> Related by not exactly on topic: would anybody on the list be able to share >>> old map files (not MTZ:s) with Convex, Cray, Fujitsu, or VAX reals/strings? >>> I’d be interested to see what those files actually look(ed) like. >>> >>> // Best wishes; Johan >>> >>>> On Nov 9, 2018, at 18:38, Zhijie Li <[email protected]> wrote: >>>> >>>> Hi all, >>>> >>>> On linux there are a few good GUI HEX editors. Here I’d like to recommend >>>> BLESS, which conveniently displays all possible numerical interpretations >>>> of the four bytes under cursor. It also allows the user to switch between >>>> big endian or little endian through a checkbox. Unfortunately all floats >>>> are assumed to be IEEE754, therefore VAX floats won’t be interpreted >>>> correctly. ( The simplest way to convert vax to ieee float would be to >>>> write a little program to do some bit operations. I’d be happy to take >>>> that as my weekend project) >>>> >>>> >>>> BTW, along the line of space efficiency, I can’t help noticing that the >>>> miller indices are saved as float32 in mtz, as all other numbers in mtz. >>>> This certainly have made mtz format a beautiful homogeneous data format >>>> ;). In this particular case, if we have doubts about the reliability of >>>> the machine stamp, trying to restore the miller indices would be a good >>>> way to test hypotheses. >>>> >>>> Zhijie >>>> >>>>> On Nov 9, 2018, at 9:04 PM, James Holton >>>>> <[email protected]> wrote: >>>>> >>>>> As a beamline scientist I must say I am glad that diffraction image data >>>>> is not usually stored as ASCII text. In fact, I am slowly warming to the >>>>> idea of storing it as not just binary, but compressed formats. Problem, >>>>> I'm sure will be that it won't be long before we forget how to >>>>> decompress them, as most of the algorithms we are using aren't all that >>>>> widespread. Probably around the same time future generations will curse >>>>> us for using ASCII instead of unicode, which is a 16-bit standard. I'm >>>>> sure we will be reviled for limiting ourselves so, just to save a factor >>>>> of two in disk space. >>>>> In situations like this I always use the unix "od" command. It makes >>>>> everything "human readable" by converting the bytes into strings you can >>>>> read. Then it is just a matter of figuring out what the bytes are. >>>>> Unfortunately, "od" only decodes floats on the native platform, so if the >>>>> mtz is from another platform (Windows vs Linux, for example), then you >>>>> might need to do some swapping. Thus far, I have encountered files that >>>>> require one of a few swapping strategies in order to make them work: >>>>> >>>>> 1 2 3 4 - no swapping >>>>> >>>>> 4 3 2 1 - reverse all bytes >>>>> >>>>> 3 4 1 2 - swap words and swap bytes within the words >>>>> 2 1 4 3 - reverse of previous >>>>> >>>>> 2-1 1 4 3 - same as last, but if not all zero, decrement byte #2 before >>>>> swapping >>>>> 3 4 1 2+1 - same as 3412, but if not all zero increment byte #2 before >>>>> swapping >>>>> I'm sure there are other combinations, but the oldest MTZ I have is only >>>>> from 1996. >>>>> >>>>> -James Holton >>>>> MAD Scientist >>>>> >>>>> >>>>>> On 11/9/2018 4:47 AM, Eleanor Dodson wrote: >>>>>> Anyone any idea what to do about this?? Created in 1992!! >>>>>> Seems unreadable.. >>>>>> >>>>>> No CTYP lines input for file: 1 >>>>>> Indices output even if all data items flagged "missing" >>>>>> Warning, NOT all LABOUT data lines given >>>>>> Warning: Machine stamp corrupted? Assuming native format. >>>>>>>>>>>> CCP4 library signal library_file:End of File (Error) >>>>>> >>>>>> >>>>>> To unsubscribe from the CCP4BB list, click the following link: >>>>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 >>>>>> >>>>> >>>>> >>>>> To unsubscribe from the CCP4BB list, click the following link: >>>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 >>>>> >>>> >>>> To unsubscribe from the CCP4BB list, click the following link: >>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 >>>> >>> >>> Research Specialist @ Gonen Lab >>> ____________________________________________________ >>> UCLA * 615 Charles E. Young Drive South >>> BSRB #347 * Los Angeles, CA 90095 >>> >>> ######################################################################## >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 >> >> ######################################################################## >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 >> > > > -- > Ethan A Merritt > Biomolecular Structure Center, K-428 Health Sciences Bldg > MS 357742, University of Washington, Seattle 98195-7742 > > > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
