Re: [ccp4bb] Parameters for phenix.refine in phenix 1.21
Dear Dennis,
As Elke wrote, some parameters were changed... I'm not sure but I think
that now definitions are even more sensitive to be specified
hierarchically. I would try to this:
phenix.refine model.pdb data.mtz params.def
where params.def are:
data_manager {
fmodel {
xray_data {
r_free_flags.generate=
force_anomalous_flag_to_be_equal_to=
}
}
miller_array {
file=data.mtz
labels.name=
}
}
output.prefix=
output.serial=
output.serial_format=
Best wishes,
Martin
On 12/04/2024 16:25, Elke De Zitter wrote:
Hi,
If you indeed run phenix.refine --show-defaults=3 you will see that
many parameter names have been changed as compared to 1.20,
e.g. refinement.input.xray_data.r_free_flags.generate has been
replaced by data_manager.fmodel.xray_data.r_free_flags.generate
I haven't checked all of your parameters, but I think you will be able
to find the corresponding new names in a similar way.
I went over the unrecognized parameters for my scripts, adapted them
accordingly and it worked.
All the best,
Elke
*From: *"Dennis Brookner"
*To: *"CCP4BB"
*Sent: *Friday, April 12, 2024 4:49:39 PM
*Subject: *[ccp4bb] Parameters for phenix.refine in phenix 1.21
Hey all,
I’m wondering if anyone has an example .eff script that works with
phenix.refine 1.21. My software package writes a parameters.eff file
to be run through phenix.refine, and it works fine with phenix 1.20,
but throws the error seen below with phenix 1.21 due to missing
parameters.
Based on the information here:
https://phenix-online.org/documentation/reference/refinement.html#list-of-all-available-keywords I
have gathered that the parameters listed below are in fact not
recognized by phenix 1.21’s phenix.refine. However, I’m unable to
locate the new versions of these parameters! Does anyone know what is
going on here?
Best,
Dennis
Here’s the error message thrown by phenix.refine:
Unrecognized PHIL parameters:
-
refinement.input.pdb.file_name (file "params.eff", line 9)
refinement.input.xray_data.file_name (file "params.eff", line 12)
refinement.input.xray_data.labels (file "params.eff", line 13)
refinement.input.xray_data.r_free_flags.generate (file "params.eff",
line 15)
refinement.input.xray_data.force_anomalous_flag_to_be_equal_to (file
"params.eff", line 17)
refinement.output.prefix (file "params.eff", line 24)
refinement.output.serial (file "params.eff", line 25)
refinement.output.serial_format (file "params.eff", line 26)
Sorry: Some PHIL parameters are not recognized by phenix.refine.
Please run this program with the --show-defaults option to see what
parameters
are available.
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Re: [ccp4bb] Parameters for phenix.refine in phenix 1.21
Hi, If you indeed run phenix.refine --show-defaults=3 you will see that many parameter names have been changed as compared to 1.20, e.g. refinement.input.xray_data.r_free_flags.generate has been replaced by data_manager.fmodel.xray_data.r_free_flags.generate I haven't checked all of your parameters, but I think you will be able to find the corresponding new names in a similar way. I went over the unrecognized parameters for my scripts, adapted them accordingly and it worked. All the best, Elke From: "Dennis Brookner" To: "CCP4BB" Sent: Friday, April 12, 2024 4:49:39 PM Subject: [ccp4bb] Parameters for phenix.refine in phenix 1.21 Hey all, I’m wondering if anyone has an example .eff script that works with phenix.refine 1.21. My software package writes a parameters.eff file to be run through phenix.refine, and it works fine with phenix 1.20, but throws the error seen below with phenix 1.21 due to missing parameters. Based on the information here: [ https://phenix-online.org/documentation/reference/refinement.html#list-of-all-available-keywords | https://phenix-online.org/documentation/reference/refinement.html#list-of-all-available-keywords ] I have gathered that the parameters listed below are in fact not recognized by phenix 1.21’s phenix.refine. However, I’m unable to locate the new versions of these parameters! Does anyone know what is going on here? Best, Dennis Here’s the error message thrown by phenix.refine: Unrecognized PHIL parameters: - refinement.input.pdb.file_name (file "params.eff", line 9) refinement.input.xray_data.file_name (file "params.eff", line 12) refinement.input.xray_data.labels (file "params.eff", line 13) refinement.input.xray_data.r_free_flags.generate (file "params.eff", line 15) refinement.input.xray_data.force_anomalous_flag_to_be_equal_to (file "params.eff", line 17) refinement.output.prefix (file "params.eff", line 24) refinement.output.serial (file "params.eff", line 25) refinement.output.serial_format (file "params.eff", line 26) Sorry: Some PHIL parameters are not recognized by phenix.refine. Please run this program with the --show-defaults option to see what parameters are available. To unsubscribe from the CCP4BB list, click the following link: [ https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 | 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 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/
[ccp4bb] Parameters for phenix.refine in phenix 1.21
Hey all, I’m wondering if anyone has an example .eff script that works with phenix.refine 1.21. My software package writes a parameters.eff file to be run through phenix.refine, and it works fine with phenix 1.20, but throws the error seen below with phenix 1.21 due to missing parameters. Based on the information here: https://phenix-online.org/documentation/reference/refinement.html#list-of-all-available-keywords I have gathered that the parameters listed below are in fact not recognized by phenix 1.21’s phenix.refine. However, I’m unable to locate the new versions of these parameters! Does anyone know what is going on here? Best, Dennis Here’s the error message thrown by phenix.refine: Unrecognized PHIL parameters: - refinement.input.pdb.file_name (file "params.eff", line 9) refinement.input.xray_data.file_name (file "params.eff", line 12) refinement.input.xray_data.labels (file "params.eff", line 13) refinement.input.xray_data.r_free_flags.generate (file "params.eff", line 15) refinement.input.xray_data.force_anomalous_flag_to_be_equal_to (file "params.eff", line 17) refinement.output.prefix (file "params.eff", line 24) refinement.output.serial (file "params.eff", line 25) refinement.output.serial_format (file "params.eff", line 26) Sorry: Some PHIL parameters are not recognized by phenix.refine. Please run this program with the --show-defaults option to see what parameters are available. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
Re: [ccp4bb] "pandda.analyse ground_state_datasets=" fails with "Error: No shell partitions generated"
Hi Filippo, try reducing the number of min_build_datasets: pandda.analyse min_build_datasets=20 ... The default value is 30 (you can see this by running pandda.analyse --show-defaults). HTH, Christian Am 12.04.24 um 10:00 schrieb Filippo Vascon: Hi, I am experiencing the same issue running pandda with 30 ground-state datasets and 26 datasets obtained in the presence of different ligands. As already reported by Christian, the pandda run exits with "No shell partitions generated" error. Does anybody know how to overcome this problem? Thank you and best regards. Filippo Vascon To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
Re: [ccp4bb] Request for assistance with structure solution
Good morning Adewumi Adeyeye, I'll look at the problem but I need the raw data. Please upload the *.h5 files from this crystal to some cloud service, and send me the link. Best wishes, Kay Am 12.04.24 um 10:40 schrieb Adewumi Adeyeye: Good day, I am writing to seek your help with resolving the problems I have been having solving the structure of my protein. I collected my data on the Beamline I04 of the Diamond Light Source. There were at least 4 different types of crystals in the collection. Unfortunately, I couldn't get a solution. However, with the assistance of yourself and other experts, we identified that my best data belong to a contaminant protein. Afterwards, I decided to inspect all the other dataset. I noticed there is a dataset which reported 85% completeness. Upon analysis with Xtriage it suggested indexing at a lower space group. I suspect this dataset might belong to my protein of interest. The images show that it is my crystal of interest that was loaded giving this dataset. I would really love to explore this. I have downloaded the dataset and tried using XDS to index but my results have been inconsistent. Initially, the process was smooth all the way through and yielded hkl file. Subsequent attempt failed to even proceed beyond IDXREF. I don't know what I am doing wrong. Any help would be so much appreciated Thank you. Inline image Inline image Kind Regards, Adewumi Adeyeye, (PhD Candidate) Department of Biochemistry, Genetics, and Microbiology Structural Biology Group, Room 3-7, Agricultural Sciences Building, University of Pretoria c/o University & Lynnwood Roads Hatfield Pretoria 0083 Cell: +27638643131 South Africa -- Kay Diederichshttp://strucbio.biologie.uni-konstanz.de email: kay.diederi...@uni-konstanz.de Tel +49 7531 88 4049 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz This e-mail is digitally signed. If your e-mail client does not have the necessary capabilities, just ignore the attached signature "smime.p7s". To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/ smime.p7s Description: Kryptografische S/MIME-Signatur
Re: [ccp4bb] "pandda.analyse ground_state_datasets=" fails with "Error: No shell partitions generated"
Hi, I am experiencing the same issue running pandda with 30 ground-state datasets and 26 datasets obtained in the presence of different ligands. As already reported by Christian, the pandda run exits with "No shell partitions generated" error. Does anybody know how to overcome this problem? Thank you and best regards. Filippo Vascon To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
