Dear Li Xue, The questions you are asking are more the domain of protein structure bioinformatics than X-ray crystallography. The CCP4 has a series of these programs available, but their collection is limited. May I suggest that you also look at http://swift.cmbi.ru.nl/gv/facilities/. There you can find pointers to a series of web servers that do things like you ask with PDB files as input. Most of the web servers are also available as a web service that you can call directly from your software. Further, several of the calculations you ask for we routinely perform once per week on all new PDB files and store the results in easy-to-parse files, one per PDB file.
Greetings Gert 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 -- Xue, Li Bijvoet Center for Biomolecular Research Utrecht University Email: [email protected]<mailto:[email protected]> Web site: http://www.cs.iastate.edu/~lixue/<http://www.cs.iastate.edu/%7Elixue/> Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.
