Thanks Thomas!
I've already tried use this command.
I want just ask about Hbond representation between 2 selected regions.
E.g I want to represent Hbonds beetween 2 helices
Firstly I've added donor Hydrogens
H_add donors
and than
distance 3sn6 and resi 197-220, 3sn6 and resi 275-298, cutoff=4, mode=2
where first selection is the 1st helix and second selection is another
helix of my protein.
I've noticed that in some cases there are errors in the h-bond network. How
I could fix it ?
James
2012/1/24 Thomas Holder <spel...@users.sourceforge.net>
> Hi James,
>
> use the distance command:
> http://pymolwiki.org/index.**php/Distance<http://pymolwiki.org/index.php/Distance>
>
> For the potential h-bonds, use it with mode=2.
>
> Cheers,
> Thomas
>
>
> On 01/24/2012 05:15 PM, James Starlight wrote:
>
>> Dear PyMol Users!
>>
>> In the PyMol Wizard I've found very userful option called distance
>> measurements beyween selected atoms.
>>
>> I wounder to know how I could realize such operation via PyMol console
>> in the simplest manner.
>>
>> My current task consist of making different point mutations and
>> subsiquent quick measurement of the new distance between new mutated
>> residue and some other native residue.
>>
>> In addition I'd like to measure potential H-bond distance between above
>> residues (polar contacts between electronegative groups) as well as
>> tight packing forces ( distance between non-polar residues).
>>
>> Is there any simplest method for that purpose ?
>>
>> Thanks,
>>
>> James
>>
>
> --
> Thomas Holder
> MPI for Developmental Biology
> Spemannstr. 35
> D-72076 Tübingen
>
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