Re: [ccp4bb] xds undefined data_range error

[Kay Diederichs]

Hi Sangeetha,


3)  SPOT_RANGE=7  18
    SPOT_RANGE=20 20
should be valid.

5) no idea how to run XDS viewer on a Mac.

HTH,

Kay

Sangeetha Vedula schrieb:

1) when I open the XDS.INP that you posted with a text-mode program like vi , it looks very messy - like one long line, with ctrl-M control characters at the putative linebreaks. I just realize that Tim Grüne found that out in the same way! 2) Christopher Buhl's JOB= line does not have the first steps (XYCORR INIT COLSPOT IDXREF) that are required to be run before DEFPIX INTEGRATE CORRECT. That explains the !!! ERROR !!! CANNOT READ XPARM.XDS error message (XPARM.XDS is actually written by IDXREF). 4) XDS viewer does not let you see how the program is progressing. There is no online viewer available for XDS. Probably there will never be one, as this would e.g. not be compatible with multiple XDS jobs processing the data, and not even with multiple processors (in a multi-core machine). It is however possible to extract from an existing XDS_ASCII.HKL the information that lets adxv (starting with one of the latest beta versions) show you boxes around the reflections, so you can see which reflections XDS reduced, and where XDS calculated their position. If there is interest, I'll post the little helper program in the XDS wiki.

I am just now editing it again using nedit. I edited it before in textedit. That was probably my problem! And no, when I look at it using more, it is all messed up.

I edited Chris's file. New error.

 !!! ERROR !!! CANNOT READ XPARM.XDS









I did consider the editor problem but (idiot!) dismissed it.

So now, I followed Jurgen's advice of JOB=ALL and it is running. But will JOB = ALL try to make me strategize data collection after the fact? I am yet to figure out how to work XDS viewer to see how it is progressing. *Is it possible to see progress by looking at images in real time like for denzo and d*trek?* To Mark Brooks: SMV may not be required because it did say that XDS figures it out on its own. This may be entirely different issue or, I don't know (yet) what it is. Doesn't running xds generate these files for use in successive steps? On Thu, Jun 11, 2009 at 11:53 AM, Tim Gruene <t...@shelx.uni-ac.gwdg.de <mailto:t...@shelx.uni-ac.gwdg.de>> wrote:

    Dear Sangeetha,

    the attached screenshot is what the XDS.INP looks like when I open
    it with vi. Are you sure you did not edit it with e.g. a
    windows-editor, or maybe some other editor which might have caused
    this apperance?


    Tim


    --
    Tim Gruene
    Institut fuer anorganische Chemie
    Tammannstr. 4
    D-37077 Goettingen

    GPG Key ID = A46BEE1A


    On Thu, 11 Jun 2009, Sangeetha Vedula wrote:

        I checked:

        1. I did name it XDS.INP; no problem there.
        2. The path along with file name template is only about 30
        characters.
        3. No. of files = 156 (DATA_RANGE=1 156)
        4. Edited Nx, Ny, Qx, Qy (unless the image header is wrong,
        which could cause problems,
        but why does it have a problem with data range?).

        I am attaching the file, XDS.INP that I am using. Thank you so
        much in advance for taking
        the time.

        Regards,

        Sangeetha.

        On Thu, Jun 11, 2009 at 3:23 AM, Kay Diederichs
        <kay.diederi...@uni-konstanz.de
        <mailto:kay.diederi...@uni-konstanz.de>> wrote:
             Sangeetha Vedula schrieb:

             Hello all,

             Apologies for the non-CCP4 question.

             I am trying to process some data collected at X6A in March.
        I edited the
             XDS.inp file for ADSC detector. When I try to run xds,
        however, it gives
             an error immediately:

             !!! ERROR !!! UNDEFINED DATA_RANGE=

             I checked the data range and the image path and template I
        gave. Doesn't
             appear to be anything wrong. What could be causing the
        error, though?

             Thanks for any input and suggestions!

             Sangeetha.


        Hello Sangeetha,

        please post your XDS.INP for us to check.

        Kay
        --

Kay Diederichs http://strucbio.biologie.uni-konstanz.de

        email: kay.diederi...@uni-konstanz.de
        <mailto:kay.diederi...@uni-konstanz.de>     Tel +49 7531 88 4049
        Fax 3183
        Fachbereich Biologie, Universitaet Konstanz, Box M647, D-78457
        Konstanz

--
Kay Diederichs                 http://strucbio.biologie.uni-konstanz.de
email: kay.diederi...@uni-konstanz.de     Tel +49 7531 88 4049 Fax 3183
Fachbereich Biologie, Universitaet Konstanz, Box M647, D-78457 Konstanz

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