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Hello Thao-- > I tested run the file "protG_mkpsf.inp" to create the extended > structure of a protein; the output file is "template_protG.pdb." When > I display the extended structure in Rasmol or in Pymol I got the amino > acid sequence with the correct amino acids, but there are not peptide > bonds. The peptide bonds are not formed. I used the default file > "protG_mkpsf.inp" without any modifications. What statement should I > change or what is wrong with this file "protG_mkpsf.inp"? I used > "XPLOR-NIH 2.19 version", run in MAC OS. > That script also writes out a psf file, and this file actually contains bonding information (the pdb contains only coordinates). Rasmol and Pymol have to guess at bonding if given only a pdb, and probably get confused by the strange configuration of the extended strand. I suspect that nothing is wrong with protG_mkpsf.inp, but the python psf generation scripts (mostly in eginput/PSF_generation) are more featureful. best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.9 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iD8DBQFIsEkOPK2zrJwS/lYRAuqHAJ4w/yb8KhRaMNajcLxSqkYPmcap1wCeLKGg 2PajcSOYVeF1wH4ffWfkBBM= =R1Gx -----END PGP SIGNATURE-----
