Re: [ccp4bb] making a paper model

[Clement Angkawidjaja]

Dear Alice,

Instead of printing on paper, why not 3D-print it?

Cheers,
Clement

-Original Message- 
From: Alice Clark

Sent: Friday, March 10, 2017 1:18 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] making a paper model

Dear All,
How can I get a 2D net diagram from a 3D PDB structure, to make a paper 
model?


What I want to do is: take a 3D structure (GFP for Eg, PDB:4xow) make
a 2D image, print it on paper, roll it up to give the 3D structure of
the beta barrel - made of paper.

I have tried conventional topology programs but they "straighten" the
strands, so when you roll it up, the strands do not curve round the
barrel as they should. I can force this manually (cut and paste etc) -
but was hoping someone knows a way of doing it, in one step, within a
program. Perhaps using a 2D net image generator or similar?

All the best,
Alice 

Re: [ccp4bb] making a paper model

[Edward A. Berry]

On 03/09/2017 11:45 AM, Alice Dawson (Staff) wrote:

you can find a paper model of GFP at the RCSB PDB
https://cdn.rcsb.org/pdb101/learn/resources/gfp-model.pdf



Hmm- that seems to involve quite a bit of cut-and-pasting too - or rather 
cut-and taping!

2D topology diagrams are really schematics, to show the connections of the
secondary structure elements, the arrangement of strands within sheets,
and perhaps of helices within a helix bundle.
For a more complex protein than GFP, putting these secondary structure
assemblies together in a way that somehow reflects their position in the
3D structure is a very objective process, not readily amenable to
computational automation without a lot of artificial intelligence.



On 09/03/2017, 16:18, "CCP4 bulletin board on behalf of Alice Clark"
 wrote:


Dear All,
How can I get a 2D net diagram from a 3D PDB structure, to make a paper
model?

What I want to do is: take a 3D structure (GFP for Eg, PDB:4xow) make
a 2D image, print it on paper, roll it up to give the 3D structure of
the beta barrel - made of paper.

I have tried conventional topology programs but they "straighten" the
strands, so when you roll it up, the strands do not curve round the
barrel as they should. I can force this manually (cut and paste etc) -
but was hoping someone knows a way of doing it, in one step, within a
program. Perhaps using a 2D net image generator or similar?

All the best,
Alice



The University of Dundee is a registered Scottish Charity, No: SC015096

Re: [ccp4bb] making a paper model

[Alice Dawson (Staff)]

you can find a paper model of GFP at the RCSB PDB
https://cdn.rcsb.org/pdb101/learn/resources/gfp-model.pdf


--
Alice Dawson

WNH Lab
Division of Biological Chemistry and Drug Discovery
School of Life Sciences
University of Dundee
01382 385744





On 09/03/2017, 16:18, "CCP4 bulletin board on behalf of Alice Clark"
 wrote:

>Dear All,
>How can I get a 2D net diagram from a 3D PDB structure, to make a paper
>model?
>
>What I want to do is: take a 3D structure (GFP for Eg, PDB:4xow) make
>a 2D image, print it on paper, roll it up to give the 3D structure of
>the beta barrel - made of paper.
>
>I have tried conventional topology programs but they "straighten" the
>strands, so when you roll it up, the strands do not curve round the
>barrel as they should. I can force this manually (cut and paste etc) -
>but was hoping someone knows a way of doing it, in one step, within a
>program. Perhaps using a 2D net image generator or similar?
>
>All the best,
>Alice


The University of Dundee is a registered Scottish Charity, No: SC015096

[ccp4bb] making a paper model

[Alice Clark]

Dear All,
How can I get a 2D net diagram from a 3D PDB structure, to make a paper model?

What I want to do is: take a 3D structure (GFP for Eg, PDB:4xow) make  
a 2D image, print it on paper, roll it up to give the 3D structure of  
the beta barrel - made of paper.


I have tried conventional topology programs but they "straighten" the  
strands, so when you roll it up, the strands do not curve round the  
barrel as they should. I can force this manually (cut and paste etc) -  
but was hoping someone knows a way of doing it, in one step, within a  
program. Perhaps using a 2D net image generator or similar?


All the best,
Alice