Thanks for your prompt answer,
numbers resets in every chain - and there is a lot of nucleobases in the
beginning (A,C,U,G) and MG at the end and these atoms mess up the residues
number additionally !
can I remove them via pymol ? Thank you
<http://en.wikipedia.org/wiki/Nucleobase>
On Sat, Dec 13, 2014 at 5:45 PM, Andreas Warnecke <
4ndreas.warne...@gmail.com> wrote:
>
> Hi,
>
> There is a script available on the pymol wiki called "zero_residues". This
> will allow you to easily renumber any AA sequence.
> As far as other heteroatoms are concerned you could consider removing them
> (remove hetatm), or extract them into a second object.
> Another alternative is to simply adjust the coloring command according to
> the pdb.
>
> Hope that helps,
>
> Andreas
> On Dec 13, 2014 4:41 PM, "Alireza Kashani" <alireza.kashanip...@gmail.com>
> wrote:
>
>> Dear All,
>>
>> I would like to colour different regions of a protein in different
>> colour; say region one, amino acid number 1 to 100 and region two amino
>> acid 101 to 150; However, when I look into a pdb file using pymol; by
>> displaying the residuals, I see the residue number 1, does not correspond
>> to the first amino acid; I assume, because of other atoms (metals, ions and
>> etc).
>>
>> I was wondering if I should filter the pdb file, beforehand to be free
>> from these metals, or is there any command that I can put them away and
>> make a selection based on set of amino acids ?
>>
>> I appreciate your help,
>>
>>
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