Hmm - I can't help with the scripting question, but it solved easily from
the I2 interface?
This is run on a Mac.
CRANK2 called SHELX - found SE with weak signal..
Some difference between hand
It traced ALA - R factor 41%
Then BUCCANEER or MODELFIR quickly built and sequenced the rest..
Eleanor
On Thu, 15 Feb 2024 at 09:07, zx2...@connect.hku.hk <zx2...@connect.hku.hk>
wrote:
> Dear Colleagues,
>
> I hope this message finds you well. I am reaching out to inquire if anyone
> has experience with *running Crank2 using the CCP4i2 i2run command*.
> Unfortunately, I've encountered some difficulties and would greatly
> appreciate any guidance or advice.
>
> For context, I've attached the script and files utilized in my attempts.
> Specifically, I'm interested in understanding how to address the errors
> I've encountered and would like to know the minimum input requirements for
> successfully running this script.
>
> Below are the errors I've received:
>
>
> Error in wrapper crank2 0.02: -ERROR- crank2:0 Error in wrapper crank2
> 0.02::
> *Anomalous scattering coeficients could not be determined. Please input
> them or the wavelength.*
>
> Traceback (most recent call last):
> File
> "/home/Xin/programs/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/pipelines/crank2/crank2/ccp4i2crank.py",
> line 41, in CallCrankFromCCP4i2
> raise
> RuntimeError: No active exception to reraise
>
> During handling of the above exception, another exception occurred:
>
> Traceback (most recent call last):
> File
> "/home/Xin/programs/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/pipelines/crank2/script/crank2_script.py",
> line 466, in process
> crank2 = ccp4i2crank.CallCrankFromCCP4i2(self, inpfile=inpfile,
> defaults=defaults, rvapi_style=rvapi_style)
> File
> "/home/Xin/programs/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/pipelines/crank2/crank2/ccp4i2crank.py",
> line 43, in CallCrankFromCCP4i2
> raise error
> File
> "/home/Xin/programs/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/pipelines/crank2/crank2/ccp4i2crank.py",
> line 29, in CallCrankFromCCP4i2
> crank =
> parser.ParseAndRun(ccp4i2crank,defaults,rvapi_style=rvapi_style)
> File
> "/home/Xin/programs/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/pipelines/crank2/crank2/parse.py",
> line 58, in ParseAndRun
> crank_prep.Run()
> File
> "/home/Xin/programs/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/pipelines/crank2/crank2/process.py",
> line 1017, in Run
>
> self.RunPreprocess(rundir=rundir,clear_out=clearout,save=restore,*args,**kwargs)
> File
> "/home/Xin/programs/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/pipelines/crank2/crank2/manager.py",
> line 107, in RunPreprocess
> self.GetAnomScatCoefs()
> File
> "/home/Xin/programs/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/pipelines/crank2/crank2/manager.py",
> line 327, in GetAnomScatCoefs
> common.Error('Anomalous scattering coeficients could not be
> determined. Please input them or the wavelength.')
> File
> "/home/Xin/programs/ccp4-8.0/lib/python3.7/site-packages/ccp4i2/pipelines/crank2/crank2/common.py",
> line 34, in Error
> raise CrankError(message)
> common.CrankError: Anomalous scattering coeficients could not be
> determined. Please input them or the wavelength.
>
> I would be grateful for any insights or suggestions you might have
> regarding this issue. Thank you very much for your time and assistance.
>
> Best regards,
> Xin
>
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