How to visualize a pdb-like file

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3 total messages Started by Horacio horacio Tue, 11 Nov 2003 14:43

#77

Author: Horacio horacio
Date: Tue, 11 Nov 2003 14:43

25 lines
1790 bytes

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 !

Re: How to visualize a pdb-like file

#78

Author: horacio
Date: Thu, 13 Nov 2003 08:55

52 lines
2872 bytes

Thnaks.

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


"D.K." <no.email@thanks.to.spam.net> escribi� en el mensaje
news:bouk1j$arl$1@news.doit.wisc.edu...
> In article <6e6c00d7.0311110221.606cc1ee@posting.google.com>,
> horacio@um.es (Horacio  horacio@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

Re: How to visualize a pdb-like file

#76

Author: George Elkins
Date: Wed, 21 Jan 2004 00:45

37 lines
2607 bytes

"D.K." <no.email@thanks.to.spam.net> wrote in message
news:bouk1j$arl$1@news.doit.wisc.edu...
> In article <6e6c00d7.0311110221.606cc1ee@posting.google.com>,
> horacio@um.es (Horacio  horacio@um.es) wrote:
> >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
>
> 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

And you can write a Perl script in 10 minutes which will automate this
conversion.

George Elkins

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