-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Li,
you find a list of programs with a short description at http://www.ccp4.ac.uk/dist/html/INDEX.html 1. areaimol: Analyse solvent accessible areas I am not sure you can reliably derive (partial) side chain charges from a (X-ray) crystal structure, especially when hydrogen positions are only calculated, although this may depend on the level of accuracy you seek. You could use pdb2pqr, which is not part of ccp4i, to write (tabulated) partial charge into the B-factor column of the pdb-file. 2. I don't know. 3. refmac5 can do this. Best, Tim On 03/04/2015 11:20 AM, Li Xue wrote: > Hi, > > I am new to ccp4. I am writing to check the possibility to use ccp4 > as a platform to develop my software. > > I was wondering whether I could get the following information from > ccp4 after I input a pdb file: > > 1. chemico-physical properties of each residue, such as > hydrophobicity, side chain charge, relative solvent accessibility > and so on. 2. the nearest 5 neighbor residues of each residue in > the pdb file > > 3. add hydrogen to the pdb file > > Although I can calculate the above information myself without using > ccp4, it would be great thatccp4 has already all the packages that > I need. I'd appreciate it very much if someone could point out > where I should start with. > > Thanks. > > Li > > - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iD8DBQFU9vI1UxlJ7aRr7hoRAq46AJ9YiMtWvzmg+5PyXPvs/+F9J+Ys5ACg/sv/ UYaslb+qXKvZflX7QMh0hT0= =a0c6 -----END PGP SIGNATURE-----
