Hi all,
There's also a tool available for converting PDB files into the viper format available at http://viperdb.scripps.edu/pdbToViper.php Brad --- Bradley Kearney, Research Associate The Scripps Research Institute Department of Integrative Structural and Computational Biology Jack Johnson Laboratory From: sujata halder [mailto:halder.suj...@gmail.com] Sent: Thursday, April 25, 2013 12:32 AM To: Bradley Kearney Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] How to generate a complete viirus PDB Hi, In continuation to the previous suggestion about using the 'Oligomer Generator' in viperdb. To use viperdb, your pdb needs to be in the viper format. So download any pdb (example this one :http://viperdb.scripps.edu/cgi-bin/viper_coord.cgi?VDB=1z14) and then superpose your monomer onto this reference viper format pdb....and then upload your 'moved' pdb into the Oligomer generator 'browse' option. Then select the T number and the option for 60mer, 30mer etc. If this is an already published pdb then just input the id in the homepage and then the next page will have options for you to download a whole capsid or half capsid. -Tina On Thu, Apr 25, 2013 at 2:48 AM, Bradley Kearney <bmkea...@ncsu.edu> wrote: Hi Hong, I would recommend that you check out the services at the VIPERdb website http://viperdb.scripps.edu. It looks like the oligomer tool (http://viperdb.scripps.edu/oligomer_multi.php) might be useful for what you want to do. They have many of the virus structures from the PDB already processed for you, or you could upload your own PDB coordinate file. Brad --- Bradley Kearney, Research Associate The Scripps Research Institute Department of Integrative Structural and Computational Biology Jack Johnson Laboratory From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Guan Hong Hsiang Sent: Wednesday, April 24, 2013 11:19 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] How to generate a complete viirus PDB Dear all: I have one subunit PDB of one virus with a NCS record. Which program should I use to generate a complete virus PDB using the NCS? Thank you Hong Hsiang
