Thanks Thomas
I've just one extra question about ligand sites.
As I've said previously I can obtain information about polar contacts
between ligand and its surrounding residues via Present- ligand sites.
On the next step I mask all other non relevant parts of the protein ( wich
are represented as the cartoon) by
hide cartoon
so as the consequence I have only ligand and its environment ( other
residues and some water)
How I could select all this visible (relevant) part and save it in the
separate pdb?
I've not found such simple selection by the visible part in the selection
algebra :(
James
2012/1/20 Thomas Holder <spel...@users.sourceforge.net>
> Hi James,
>
>
> 1- Some of my proteins consist of ligand wich include some of amino
>> acids from sequence of my protein ( e.g fluorophores in GFP). So I'd
>> like to assign some residue motif as the ligand group ( e.g Ser Tyr Gly
>> motif in GFP). How I could do it?
>>
>
> The preset selects hetatoms as ligands, so you could do:
>
> select motif, (pepseq SYG) and not (name C+N+O)
> alter motif, type="HETATM"
>
>
> 2- In some cases there are relatively long distances between polar
>> ligand groups and protein's polar residues where H-bond must be formed (
>> eg in some cases up to 3.5-3.7 A ). So the default a-> present->ligands
>> sites-> cartoon does not recognize that long H-bonds. How I could set
>> the H-bond cutoff distance in the above method?
>>
>
> there are several h_bond_* settings that control this. (I recommend
> http://pymolwiki.org/index.**php/Grepset<http://pymolwiki.org/index.php/Grepset>to
> find settings) For example:
>
> set h_bond_cutoff_center, 5.0
> set h_bond_cutoff_edge, 4.0
>
>
> Cheers,
> Thomas
>
> --
> Thomas Holder
> MPI for Developmental Biology
> Spemannstr. 35
> D-72076 Tübingen
>
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