How to visualize a pdb-like file

D.K. no.email at thanks.to.spam.net
Wed Nov 12 19:43:11 EST 2003

In article <6e6c00d7.0311110221.606cc1ee at posting.google.com>, 
horacio at um.es (Horacio  horacio at um.es) wrote:
>Hi everybody.
>I have a pdb-like file which represents the model of a molecule.
>The exact format is the following:
>x1, y1, z1, r1
>xn, yn, zn, rn
>where each line corresponds to each bead of the model and it describes the
>Cartesian coordinates of the bead and its radius.
>My questions are:
>Does anybody know how to visualize this file in a similar way that in rasmol
>you can visualize a pdb structure ?

Why not make a real PDB file out of it? Here is the format: 


For example:

ATOM      7  CG2 THR A  15      20.613  65.449  44.328  1.00 55.84

In your case you can all atoms UNK (it is "CG2" above), number 
atoms sequentially ("7"), give them all any 3 letter residue name 
("THR"), use any chain ID and number ("A" and "15"), keep occupancy 
as 1.00 and set temperature factors ("55.84") as anything (20.00 is 
common for no real value). "20.613  65.449  44.328" are cartesian 

Rasmol will be happy, as will be 90% of all other programs. All in 
all, it's a copy and paste job that can be done in Word using 
vertical copy selection. 


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