[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
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
Re: [ccp4bb] making a paper model
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
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