How to visualize a pdb-like file

horacio at NOSPAMum.es horacio at NOSPAMum.es
Thu Nov 13 03:55:50 EST 2003


Thnaks.

It is good, but my problem is how to specify the different radius for every
bead.


"D.K." <no.email at thanks.to.spam.net> escribió en el mensaje
news:bouk1j$arl$1 at news.doit.wisc.edu...
> 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:
>
> http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html
>
> 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
> 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





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