Dear community,
Thanks for your helpful answers.
@Xavier: Obviously, I knew TopDraw, but as mentioned by Andy “TOPDRAW doesn't
interpret a pdb file, it just allows you to draw your own topology diagram.”
And I wanted it to be as simple as possible for my biochemist colleague with no
access
Dear Lionel,
If you want a programme that takes a PDB file and automatically generates a
topology diagram, then Pro-origami may be the software you need
(https://sites.google.com/site/alexdstivala/home/pro-origami) - it generates
prettier diagrams than PDBsum, and the diagrams are output as .sv
Dear Lionel,
I would say it depends what do you intend to use the topology diagram for?
I personally like Overprot (https://overprot.ncbr.muni.cz/) as you can
also see topological diagram for the CATH protein family.
Kind regards,
Deborah
On 30/05/2024 16:32, Lionel wrote:
Dear community,
From: CCP4 bulletin board on behalf of Xavier
Brazzolotto
Sent: 30 May 2024 16:39
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Topology diagram
External Sender: Use caution.
My Google search led directly to
<https://www.ccp4.ac.uk/html/topdraw.html>
TOPDRAW (CCP4: Supported
My Google search led directly to
https://www.ccp4.ac.uk/html/topdraw.html
HTH
> Le 30 mai 2024 à 17:32, Lionel a écrit :
>
> Dear community,
>
> A biochemist asks me if I knew a webserver/tool to draw topology diagram of
> protein from a deposited pdb or part of it, ideally allowing edition
Dear community,
A biochemist asks me if I knew a webserver/tool to draw topology diagram of
protein from a deposited pdb or part of it, ideally allowing edition (label,
colour, etc...).
For a better understanding, the topology diagram’s representation is as the
picture attached, which I belie
. Juni 2008 17:07
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] topology diagram
Hi all,
wondering if anyone knows of a user friendly and esy to use
program for generating topology diagrams for proteins. Any help would be
very useful to me.
thanks,
Neeraj
--
Neeraj Kapoor
TPCB Graduate Fellow
Hi Neeraj,
CCP4 has a program which allows one to draw topology diagram manually...it's
easy to learn and use.
http://stein.bioch.dundee.ac.uk/~charlie/software/topdraw/
There is another program called "TOPS" (website is currently under
maintenance) which generates topology diagram according to y
Hi all,
wondering if anyone knows of a user friendly and esy to use
program for generating topology diagrams for proteins. Any help would be
very useful to me.
thanks,
Neeraj
--
Neeraj Kapoor
TPCB Graduate Fellow
Sakmar Lab/ Molecular Biology & Biochemistry
The Rockefeller University
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