On Thu, 13 Nov 2003 09:55:50 +0100, <horacio at NOSPAMum.es> wrote:
>Thnaks.
>>It is good, but my problem is how to specify the different radius for every
>bead.
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
>> 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
>
