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 <CCP4BB@JISCMAIL.AC.UK> on behalf of Stuart McNicholas <000019a0c5f649e5-dmarc-requ...@jiscmail.ac.uk> Sent: 20 February 2024 23:01 To: CCP4BB@JISCMAIL.AC.UK <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 <0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk<mailto: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<mailto:zx2...@connect.hku.hk> <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 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&A=1 ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
