Dear Hong,
As Eugene mentioned, you should be able to build the full virus assembly using
PISA.
Another option is to use the multiscale model menu of UCSF Chimera (default
setting is "Biological Assembly") to generate the complete virus assembly from
PDB BIOMT records.
If this is a new struct
Would PISA not do this? -- Eugene
On 25 Apr 2013, at 09:20, abhimanyu singh wrote:
Hi Hong,
In your PDB file if the BIOMT transformation matrix (under remark 350) is
provided, you can use this script to generate the biological assembly :
http://watcut.uwaterloo.ca/cgi-bin/makemultimer/
Greeti
ology
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 usin
Hi Hong,
In your PDB file if the BIOMT transformation matrix (under remark 350) is
provided, you can use this script to generate the biological assembly :
http://watcut.uwaterloo.ca/cgi-bin/makemultimer/
Greetings,
Abhi
On Thu, Apr 25, 2013 at 9:31 AM, sujata halder wrote:
> Hi,
>
> In continu
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 r
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
proc
Hi Hong,
you can usually download the 'biological assembly' from the PDBe, be
warned that for viruses this is rather large, cheers, Matt.
On 25/04/2013 08:19, Guan Hong Hsiang wrote:
Dear all:
I have one subunit PDB of one virus with a NCS record. Which
program should I use to gener
