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 ?
or
Does anybody know how to convert this file to a pdb (or pdb-like) format ?
Thanks !
Why not make a real PDB file out of it? Here is the format:
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 coordinates.
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.
DK
Thnaks.
It is good, but my problem is how to specify the different radius for every bead.
"D.K." escribió en el mensaje news:bouk1j$arl$ snipped-for-privacy@news.doit.wisc.edu...
Call different bead different atom names. Rasmol is aware of VDV radii of many atoms and will assigns them automatically. In other, more powerful software, like Pymol, you could directly specify radius for each given atom type.
DK
And you can write a Perl script in 10 minutes which will automate this conversion.
George Elkins
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