Hello,
One can use PARST to check the geometry of the molecules.
The idea is to compare geometries with a standard molecule.
-Divya
On 3/11/11, gauri misra <[log in to unmask]> wrote:
> Hi,
> Swiss-pdb viewer works well for small peptides, you can check if it serves
> your objective too...
> Even WHAT IF provides clues to bond angles, bond length and torsion angles.
>
> Gauri
>
> On Thu, Mar 10, 2011 at 3:56 PM, Robert Immormino
> <[log in to unmask]>wrote:
>
>> Hi Halliang,
>> If the ligands are in the pdb het dictionary I think MolProbity will
>> look at bonds and angles...maybe even dihedrals.
>> Cheers,
>> -bob
>>
>> On Thu, Mar 10, 2011 at 12:23 PM, Hailiang Zhang <[log in to unmask]> wrote:
>> > Hi there,
>> >
>> > I want to found some bad geometry for my ligand (sugar rings). The
>> > procheck .out file seems only shows the bad bond length or angles for
>> > protein. Is there any way we can get these information for sugar rings?
>> >
>> > Thanks in advance!
>> >
>> > Hailiang
>> >
>>
>
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