[buster-discuss] error running pipedream

[Wei-Chun Kao]

Dear Guenter,

I also tried to run pipedream with the same options Guenter had used, except -nofreeref  instead of -hklref, plus -remediate -sidechainrebuild and -runpepflip 

The run finished without any error messages. hydrogenate.log shows that the ccp4 program reduce was used.

By inspecting report.tsv, it seems that reduce is defined by BDG_TOOLS_MOLPOBITY_ROOT but the executable is from the ccp4 path?

Is it possible that one has also to setup molprobity (I did) in order to call reduce correctly?

My system is CentOS 7, CCP4 7.1.011, buster snapshot 20210224. molprobity was installed according to the method provided by the BUSTER installation guide.

Hope that helps,

Wei-Chun

—

Dr. rer. nat. Wei-Chun Kao
wei-chun.kao at biochemie.uni-freiburg.de
TEL: +49-761-203-5277 <tel:%2B49-761-203-5277>
orcid.org/0000-0001-8687-6334						

Institute for Biochemistry and Molecular Biology
AG Carola Hunte
Albert-Ludwigs-Universitaet Freiburg
Stefan-Meier-Str. 17
D-79104 Freiburg im Breisgau
Germany

> On 24. Feb 2021, at 21:10, Guenter Fritz <guenter.fritz.phenix.ccp4 at gmail.com> wrote:
> 
> Dear Buster developers,
> 
> I was trying to run pipedream, but get the notice that reduce is not in the path, although it is. 
> Below is my input and the output.  Any hintwhat I am doing wrong is welcome.
> System is Centos 8, CCP4 is 7.1, latest release of buster from today. 
> Many thanks and best regards,
> 
> Guenter
> [guenter at epikur pipedream_test]$ pipedream -hklin paefs_215.mtz -hklref paefs_215.mtz -xyzin paefs_215.pdb -rhofit grade-XXX.cif -nthreads 6 -d paefs_215_results 
> .......
> 
> Command run: pipedream  -hklin paefs_215.mtz -hklref paefs_215.mtz -xyzin paefs_215.pdb -rhofit grade-XXX.cif -nthreads 6 -d paefs_215_results
> For details see paefs_215_results/summary.out
> 
> ERROR: Unable to run hydrogenate - 'reduce' (in CCP4 distribution) not found on path!
> 
> [guenter at epikur pipedream_test]$ which reduce 
> /opt/software/CCP4/7.1/ccp4-7.1/bin/reduce
> 
> 
> _______________________________________________
> buster-discuss mailing list
> buster-discuss at globalphasing.com
> https://www.globalphasing.com/mailman/listinfo/buster-discuss

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.globalphasing.com/pipermail/buster-discuss/attachments/20210225/925fec09/attachment.html>