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Hello Jeff Ellena <jfe at virginia.edu> wrote: > Hi, > > > I used eginput/prot_prot/mkpfs_both.inp to make a two segment psf file > (with xplornih2.19). My pdb file formats are not compatible with > xplornih so I have used eginput/PSF_generation/addAtoms.py to obtain > pdb files that are compatible with xplornih. The psf file I obtained > from mkpfs_both.inp has HIS HD1 atoms. I input a pdb file for one of > the segments used to make the psf file into addAtoms.py and the output > pdb file has no HIS HD1 atoms even though the input pdb file had HIS > HD1 atoms. What do I need to do to obtain a pdb file that contains HIS > HD1 and is compatible with xplornih or a psf file that has no HIS HD1? > so keep the HIS HD1, in addAtoms.py add the following: deprotonateHIS=False to the argument list of seqToPSF. best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.9 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iD8DBQFItdk0PK2zrJwS/lYRAsasAJ45fcruYGRthEitYQfbPiAjDkc+WgCeNTsG 8i1wKpGk7Gt8vBBEGNZpODU= =QRJe -----END PGP SIGNATURE-----
