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Re: [ccp4bb]: Error in running arp_warp.sh
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Huiying Li wrote:
>
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> *** CCP4 home page http://www.ccp4.ac.uk ***
>
> We tried to submit a run with "arp_warp.sh mode warpNtrace" for a
> small protein at 1.75A resolution using an MTZ file generated by
> SHARP/SOLOMON. Program crashed with the following
> message:
>
> Starting arp_warp in mode warpNtrace
>
> warp_free.brk from "files" directory will be used.
>
> Remove atoms if below 1.4 sigmas in 2mFoDFc map.
> Add atoms in density above 3.2 sigmas in mFoDFc map.
> 100 ARP refinent cycles will be run in total.
> Rebuilding of the model will happen every 20 cycles.
>
> Refmac_5.0.36: Too little time to do everything
>
> QUITING ... CHECK ERROR MESSAGE
>
> We couldn't find any other error messages from the log files output by
> ARP/wARP. Can someone tell us what the message means. The warp.par file is
> as follows:
>
> set datafile = merge.mtz
> set fp = FP
> set sigfp = SIGFP
> set protsize = 1632
> set wilsonb = 21
> set fbest = FPsha
> set phibest = PHIshasol
> set fom = FOMshasol
> set restrcyc = 100
> set restrref = 10
> set cgr = 2
> set wmat = 0.7
> set wgrad = 1.0
> set rc1 = 15
> set rc2 = 15
> set rc3 = 15
> set models = 1
> set procs = 1
> set machine1 = kirin
> set machine2 = DUMMY
> set machine3 = DUMMY
> set machine4 = DUMMY
> set machine5 = DUMMY
> set machine6 = DUMMY
> set sym = 20
> set cell = ' 49.9140 74.8770 107.8140 90.0000 90.0000 90.0000 '
> set xyzlim = ' 0 0.5 0 0.5 0 0.5 '
> set refmax = MLKF
> set refmeth = CDIR
> set freer = N
> set freerml = N
> set damp = ' 0.99 0.99 '
> set rrcyc = 1
> set bulkls = 'SBULk -0.75 BBULk 150'
> set bulkml = 'SBULk -0.25 BBULk 80'
> set fixbulk = '\#'
> set scale = BULK
> set scanis = Y
> set eresol =
> set phaseres = N
> set phasblur = 0.5
> set resol = ' 20 1.750 '
>
> Many thanks,
>
> Huiying Li
> --------------------------------------------------
> Huiying Li, Ph. D
> Department of Molecular Biology and Biochemistry
> University of California at Irvine
> Irvine, CA 92697, USA
> Tel: 949-824-4322(or -1797); Fax: 949-824-3280
> email: hli@bragg.bio.uci.edu
> --------------------------------------------------
I just happened to see the same error message earlier this week when I
tried to use CDIR in refmac5.1. When I changed to CGMAT everything was
OK. But you are using refmc 5.0.36, so I don't know.
Jinsong
--
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"The DAO is not a real DAO when it can be talked about."
---(DAO DE JING)
Jinsong Liu, Ph.D.
Tularik Inc. Phone: 650 825-7054
Two Corporate Drive Fax: 650 825-7320
South San Francisco, CA 94080, USA Email: jsliu@tularik.com
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