I got i2run to work with this data by: * Importing the data with "Import merged" * Importing the 2 sequences one at a time with 2 import sequence jobs * Running a 'Define AU contents' job with both sequences added to the contents. * Creating a Crank2 job, then clicking the "Show i2 run command" to produce script. * I tweaked the i2run script to put double quotes around strings with brackets "()<>"
I have attached my script.
On Tue, 20 Feb 2024 at 12:05, Eleanor Dodson <
0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
> 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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>
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i2_run_crank.sh
Description: Bourne shell script
