Re: [PyMOL] Mutating an Ion in Pymol and Displaying van der waals Radii

[Buz B. <bu...@ma...>]

Thanks Warren!

That worked really well.

All the best,

--Buz


On Dec 18, 2008, at 10:08 PM, DeLano Scientific wrote:

> Buz,
>
> alter elem Na, elem='K'
>
> iterate elem K, print vdw
>
> show spheres, elem K
>
> alter elem K, vdw=1.4
>
> rebuild
>
> iterate elem K, print vdw
>
> color yellow, elem K
>
> Cheers,
> Warren
>
>
> --
> DeLano Scientific LLC
> Subscriber Support Services
> mailto:su...@de...
>
>
>
>> -----Original Message-----
>> From: Buz Barstow [mailto:bu...@ma...]
>> Sent: Thursday, December 18, 2008 2:30 PM
>> To: pym...@li...
>> Subject: [PyMOL] Mutating an Ion in Pymol and Displaying van
>> der waals Radii
>>
>> Dear All,
>>
>> I'd like to mutate an ion in pymol from a potassium to a
>> sodium. Is there an easy way to do this from the command line
>> without having to edit the pdb file of the structure?
>>
>> Also, when one displays an atom (for instance a K atom) using
>> the spheres representation, is the radius of the sphere equal
>> to the Pauling radius of the atom (under the assumption that
>> it is ionized)?
>> For K, it looks like it is.
>>
>> Thanks! and all the best,
>>
>> --Buz
>>
>>
>>
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