Re: [Jmol-users] filter only certain HETATM

[Rolf H. <rh...@fl...>]

On 06/11/2012 03:40 PM, Daniel Carbajo wrote:
> Any idea anyone?
>
> 2012/6/11 Daniel Carbajo<dan...@gm...>
>
>> Hello everyone,
>> I am wondering whether I could filter filter HETATMS so I get only those
>> which are peptide-linking and not others, like waters, etc. surrounding or
>> interacting the protein (I only want those part of the protein). I want
>> those embedded in the normal ATOM records, and not after the TER line in
>> the PDB file.
>> For example http://www.rcsb.org/pdb/files/3NUR.pdb Here I want the MSE to
>> appear, but not the CA and HOH; as I load many structures I never know
>> which are the ones I need to filter.
>> Is there a general way I can say "filter only those HETATMS after the TER
>> line in the PDB file"? Or should I provide a list of non-peptide linking
>> HETATMS that should be filtered? I already have my own list (associative
>> array in php) of peptide linking HETATMS in the PDB... how could I say
>> "filter all those HETATMS except the ones on such list"?
>> Thanks a lot!
>> Daniel
>>
With these atom expressions you should be able to discriminate them in 
Jmol (tested for 3NUR):

"hetero and protein"
"hetero and not protein"

Example command:
   hide hetero and not protein

Regards,
Rolf