Re: [ccp4bb] i2run crank2 problem
Dear Stuart,
Thank you very much for your prompt and helpful response. I apologize for my
delayed reply. Your guidance offered a solid foundation, enabling me to
successfully implement the procedures you suggested. However, I've encountered
additional challenges that were not resolved. Specifically, I need to run the
process with the --noDb feature, which operates outside an existing project and
generates all output files in the current directory. This requirement continues
to pose a problem.
I am unsure of the correct way to specify the mtz file and sequence file.
Despite following the formats suggested in the
Documentation<https://ccp4i2.gitlab.io/rstdocs/i2run/i2run.html>, my attempts
have been unsuccessful, and I noticed there are no examples for Crank2 in this
documentation.
Nonetheless, I am grateful for your assistance.
Best regards,
Xin
From: CCP4 bulletin board on behalf of Stuart
McNicholas <19a0c5f649e5-dmarc-requ...@jiscmail.ac.uk>
Sent: 20 February 2024 23:01
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] i2run crank2 problem
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
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk<mailto:176a9d5ebad7-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<mailto:zx2...@connect.hku.hk>
mailto: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 coeficient
Re: [ccp4bb] i2run crank2 problem
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 <
176a9d5ebad7-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
> 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
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
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i2_run_crank.sh
Description: Bourne shell script
Re: [ccp4bb] i2run crank2 problem
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
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
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
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