I like Topdraw very much, have been using it since 2005. But as far as i understand it will not "make a topological
figure of my protein with a b-sheet and helix based on its crystal structure". It is a drawing tool to help you make
your own topology drawing. (I will be very happy to learn if I am wrong about that).
The correct answer from my point of view is Pro-Origami, which did not show up in the first page of hits. I had a chance
to play with it a little, and it does a very nice job of organizing beta sheets, for example with 1RIE. I would probably
take its output as a starting point for making my own diagram with topdraw. It is not so useful with helices - a
4-helix bundle which I would draw as parallel up and down cylinders was drawn in a straight line one after the other -
like chain C of 1ppj.
So there are at least 3 things people mean by a protein topology program- one that defines the secondary structure, like
espript, one that gives you drawing tools to make your own based on the output of those programs, like TopDraw, and one
with artificial intelligence that automates the whole thing like ProOrigami. I am aware that the pdbsum website has
nice topology drawings, didn't realize you could use it on your own undeposited structures.
eab
Anastassis Perrakis wrote:
My point was that the second hit in the google list, was the CCP4's own program
to make topology diagrams.
There was no issue of installing anything - it was an issue of looking if ccp4
has a program that makes
topology diagrams. If you don't like that program, you could ask "is there
another program other than ccp4's TopDraw
to make topological diagrams?". Asking the ccp4bb without looking at the ccp4
list of software
for what you are looking for, is - in my view - sloppy and shows lack of
effort. Possibly I am too demanding.
I should add, that if you type to google something like "topology diagram protein
structure" you get lots
of useful hits, including PDBSUM and Pro-Origami, in the first page.
I do not want to discourage people asking question in the bb, but at the same
time I think that
some problem solving hierarchy of the order 'google it' -> 'ask your lab-mates' ->
'ask your boss' ->
'mail 5,000 people' can save everybody lots of time, can help people to grow,
and might even make
the bb more fun.
My two cents - and sorry for the long and likely unnecessary and redundant
email.
A.
On Sat, Mar 9, 2013 at 1:02 PM, Edward A. Berry <ber...@upstate.edu
<mailto:ber...@upstate.edu>> wrote:
Still, I would second Lisa's question. Your google search gives a lot of
false hits, and one doesn't want to
download and install a dozen programs (with license forms to fill out in
some cases) to see which one works, when
Partha can tell us that Pro-origami will do it and provide a link to the
description. Seems to be just what I've
been looking for. Thanks, Partha!
Anastassis Perrakis wrote:
On 9 Mar 2013, at 12:11, Jon Agirre wrote:
Espript will do. http://espript.ibcp.fr <http://espript.ibcp.fr/>
Well, if you want a topology diagram, espipt will not do. Brilliant as
it may be, it will annotate the
topology linearly
on top of a set of aligned sequences (and more!).
As for a topology diagram, I could not resist pasting your question to
google - its a good thing to do before
pasting
the question
in your email client - it can give you a strange sense of satisfaction
and us (or at least me) less Saturday
morning fun.
http://lmgtfy.com/?q=%5Bccp4%__5D+how+to+make+protein+__topology+figure+based+on+its+__structure
<http://lmgtfy.com/?q=%5Bccp4%5D+how+to+make+protein+topology+figure+based+on+its+structure>
A.
Good luck,
Jon
On 9 Mar 2013 11:52, "LISA" <science...@gmail.com
<mailto:science...@gmail.com>
<mailto:science...@gmail.com <mailto:science...@gmail.com>>> wrote:
Hi all,
I want to make a topological figure of my protein with a b-sheet
and helix based on its crystal structure.
Please
recommend some online sever of software?
Thank you.
lisa
