[sharp-discuss] various Sharp problems

[Clemens Vonrhein]

Hi Jan,

On Thu, Feb 23, 2006 at 03:35:58PM -0800, Jan Abendroth wrote:
> a) Installation on a single user machine:
> - downloaded all the files in fresh directory
> - added new .licence file in this directory
> - added $BDG_home in .bashrc, sourced .bashrc

I recommend adding

  [ -f /where/ever/sharp/setup.sh ] && \
    . /where/ever/sharp/setup.sh

into your ~/.bashrc. You only ever need BDG_home set if 

 - you want to run things from the command line
 - you want to use the autoSHARP CCP4i interface
 - you want to do some administrative tasks

> - installSHARP -F in $BDG_home
> - .. useSHARP ...

Was already done during the 'installSHARP -F' step: but running it
again doesn't hurt anyway.

> - the examples stop w/ the following error message:
> ***SHARP-ERR-0002: Unknown return status = 6 ***

You are probably running on a machine for which no valid licence key
is found in $BDG_home/.licence. Are you sure you did request a licence
key for that particular machine? You can always try:

  % cd /where/ever/sharp
  % . ./setup.sh
  % bin/linux_exe/sharp -l       # assuming it is Linux

to see if your $BDG_home/.licence file contains a valid licence
key. If not: just request an additional key at

  http://www.globalphasing.com/sharp/restricted/request.html

> Problems b) and c) occur on our main server on which Sharp itself seems 
> to run nicely:
> 
> b) density modification including partial model:
> - after initial dm run fft quits with the following error message:
> 
> Permutation of axes: (program=input)  x= X,  y= Y,  z= Z
> 
> >>>>>>CCP4 library signal library_file:Cannot open file (Error)
> 	 raised in ccp4_file_open2 <<<<<<
> >>>>>>CCP4 library signal mtz:Cannot open file (Error)
> 	 raised in MtzOpenForWrite <<<<<<
> 
> $TEXT:Warning: $$ comment $$ 
> WARNING: LWOPEN_NOEXIT: failed to open output file FFTHKLSCR
> $$
> FFT:  LWOPEN: failed to open output file
> FFT:  LWOPEN: failed to open output file

During installation, the SHARP/autoSHARP-internal CCP4 configuration
uses various values of your current environment: and it seems that you
had $CCP4_SCR set to a non-existent directory. This can easily happen,
since the default CCP4-way is to have /tmp/$USER (which I don't like,
since your operating system might delete directories in /tmp on a
regular basis. The idea I guess is to have something user-unique, so
that scratch files written by one user don't interfere with scratch
files from another user ... I prefer programming applications to
actually produce unique scratch files ... anyway).

Anyway, have a look at $BDG_home/machines/*/ccp4.setup for the values
of CCP4_SCR (and maybe BINSORT_SCR as well) and make sure these
directories will always exist.

Problem c) is most likely based on the same problem.

Hope that helps ....

Cheers

Clemens


> c) extracting phases from model:
> 
> 
>      1. Generating structure factors from model model_26oLEGO.pdb
> 
>     (details) 
> <http://kudu.bmsc.washington.edu:8080/users/jan/logfiles/periL-DAD-4Se-inv-HR.1/mkabcd_sfall.log>
> 
>    scale and overall B-factor:  
>    R-factor: 
> 
> 
>      2. Scaling of generated structure factors
> 
>     (details) 
> <http://kudu.bmsc.washington.edu:8080/users/jan/logfiles/periL-DAD-4Se-inv-HR.1/mkabcd_rstats.log>
> 
>    R-factor: 
> 
> ------------------------------------------------------------------------
> 
> *ERROR in /usr/local/sharp/sushi/cgi-bin/mkabcd.cgi*
> 
>    The following return values are set:
> 
>    * Child error = 256
>    * OS error = No such file or directory
>    * Eval error = 0
> 
> *Error message  :  * File "mkabcd.mtz1" not found or not readable
> 
> Any ideas?
> Thanks a lot
> Jan
> 
> -- 
> Jan Abendroth
> Howard Hughes Medical Institute and
> University of Washington
> 1959 NE Pacific Street, K-426
> Box 357742
> Seattle, WA-98195
> phone: +1-206-616-4510
> fax:   +1-206-685-7002
> 
> 

> _______________________________________________
> sharp-discuss mailing list
> sharp-discuss at globalphasing.com
> http://www.globalphasing.com/mailman/listinfo/sharp-discuss


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