In the Prime Comparative Modeling workflow, Edit Alignment stage, the secondary structure prediction fails. What should I do?
First, check that you have the third-party software and databases properly installed — see the the Installation Guide for more information. • Check that the special Schrödinger and Prime environment variables are set with the commands: env | grep SCHRODINGER env | grep PSP Compare the results with the environment variables listed in the Installation Guide. • Check that PsiPred is properly installed. The following command should list the files in the installation. If the directory is missing, or there are no files in these directories, or if some files are missing, you will need to reinstall PsiPred. ls -l $SCHRODINGER/thirdparty/bin/platform/psipred/bin ls -l $SCHRODINGER/thirdparty/bin/platform/psipred/data Next, check whether you are running out of memory during the secondary structure prediction: these calculations can be memory-intensive. Perform the prediction again, and run the command top. Watch the output from top for a while to see if memory limitation is a problem. Finally, r
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