AMBER Archive (2008)

Subject: Re: AMBER: changing pdb structure

From: Taufik Al-Sarraj (taufik.alsarraj_at_utoronto.ca)
Date: Tue Oct 14 2008 - 15:26:33 CDT

Thank you to all those to replied. I am glad there were so many options
for me.

I have used Sirius before and mutating amino acids using the sequence
viewer is the most user friendly. mutating DNA was not available

I don't have Jmole or Chimera

Coot took a while to download (on Fedora) but i couldn't find the
function for mutating DNA or amino acids.

DeepView was easy to download on Windows. Mutating amino acids was
relatively easy but not as convenient as Sirius, DNA mutations should
work according to the software, but i was unable to get to work yet. I
will try to work through the tutorial because i like the way DeepView looks.

Many thanks again,
Taufik

Sally Pias wrote:
> Taufik,
>
> DeepView (Swiss PDB Viewer) can easily incorporate point mutations to
> standard amino acids.
>
> Sally
>
>
> On Thu, Oct 9, 2008 at 8:35 PM, <taufik.alsarraj_at_utoronto.ca> wrote:
>> Hello,
>> This is a general question.
>>
>> If i take a structure from the protein data bank, and the structure contains
>> a protein and a DNA, is there a a software or a relatively simple method for
>> modifying the protein sequence or the DNA sequence, e.g. changing an A to L
>> (Protein) or changing a T to A (DNA). Short of manual modification in xleap
>> or deleting the original DNA and creating a new one.
>>
>>
>> Best,
>> Taufik
>>
>>
>>
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