silentfrompdbs new errors

[brystingjosephine]

Hello All, hoping you can help me out withe following errors:

$ /silent_tools
$ ./silentfrompdbs /ldlr_outputs *.pdb > my_designs.silent

ERRORS:

./silentfrompdbs: line 51: pyjd2: command not found
./silentfrompdbs: line 53: silentls: command not found
./silentfrompdbs: line 53: silentrename: command not found
rm: cannot remove 'tmp_Dz3m8aHKsdUUN.silent': No such file or directory
rm: cannot remove 'tmp_Dz3m8aHKsdUUN.silent.idx': No such file or directory

My silent_tools directory looks like this (also contains pyjd2 so I do not understand why it is not found?):

brians_score_jd2 silentfrompdbs_test
extract_pdbs silentgreppdbinfolabels
extra_residues.list silentinjectscores
_helpers silentls
in.silent silentmodelcount
ldlr_ppi_designs.silent silentoopsdropcorruptmodels
pycache silentoopsdropcorruptmodelsrename
pyextract_pdbs silentoopsscoreslice
pyjd2 silentorigls
README.md silentrandomslice
silentappendwaters silentremovewatersequence
silentassertuniquetags silentrename
silentclearscores silentscorefile
silentdd silentsequence
silentdropcorruptmodels silentsketchextractca
silentdropduplicatesequences silentsketchextractcaprotein
silentdropduplicatesequencesch1 silentsketchextractch1
silentextract silentslice
silentextractlig silentsliceinverse
silentextractparallel silentsplit
silentextractparalleloverdrive silentsplitbylength
silentextractRM_waters silentsplitdd
silentextractspecific silentsplitnoshuf
silentfasterslice silentsplitshuf
silentfastslice silenttaginverse
silentfrompdbs silent_tools.py
silentfrompdbsparallel silent_tools.pyc
silentfrompdbsRM_waters tmp_u4ldTjx13dE0l.list

[sophievincoff]

I encountered the same error! I was able to fix it by going into the silentfrompdbs file and making the following changes:

inserted a new line 9: cwd=$(pwd)
changed line 44 (used to be 43 before this insertion^) to: jd2_program=$cwd/pyjd2
changed line 54 (used to be 53 before the insertion^^) by adding $cwd/ before silentls and silentrename