Design

Hi there,

I have a pdb file from CHARMM format. When I use

fixbb.default.linuxgccrelease -in:file:s step1_pdbreader.pdb -in:file:fullatom -resfile resfile_2 -ex1 -ex2 -extrachi_cutoff 1 -nstruct 50 >out

I got this:

core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] skipping pdb residue b/c it's missing too many mainchain atoms:    1 A TRP TRP:NtermProteinFull:triazolamerC
core.io.pose_from_sfr.PoseFromSFRBuilder: missing:  CT1

and it skipped the first residue TRP.

Hello!

While doing protein minimization, I found that the terminal amino acids of gap (let say 80 and 110) have incomplete valency e.g. -C(O) and -NH instead of -C(O)O-/H and NH2/H+ as rosetta consider them very neighbours during renumbering step. 

I tried modifying both residues (let say 80 and 110) in different protein visualization plateforma and fed to Rosetta, but it modifies them to -C(O) and -NH. 

Could you suggest how to deal with it?

Dear all,

I have recently upgraded to the newest PyRosetta version (156) because my machine was upgraded to Unbuntu Artful, that uses Python 3.6 (and 144 was compiled for 3.5).

My packing script worked fine in the previous PyRosetta version I used (144) but now fails on rosetta.core.pack.pack_rotamers_setup with the following message.

I am trying to replicate the work of the paper: http://www.nature.com/nature/journal/vaop/ncurrent/full/nature23912.html?foxtrotcallback=true

It seems the Rosetta Script in the supplimentary meterials is old because when I try to use it I get a lot of typo errors, anyway I changed it but I could not find a way to fix this error: