Hello, I am in a hurry to generate a surface object with 2FJG complex to be exported in a STL format for 3D printing. This item will be presented for a local event organized by the Ligue contre le Cancer. I have download Chimera as absolute beginner and I am facing a need for splitting the (too big ?, multi-chain) complex. The function Action / Surface / show generates the splitting solution. Could you help me and guide me ? Thanks in advance Regards Olivier Sire -- *Olivier SIRE * / Professeur à l'Université de Bretagne-Sud / ------------------------------------------------------------------------ Laboratoire d'Ingénierie des Matériaux de Bretagne Campus de Tohannic BP575 56017 VANNES cedex Tél. 02 97 01 71 48 Fax. 02 97 01 70 70 Mob. 06 89 48 25 24 olivier.sire@univ-ubs.fr UNIVERSITÉ DE BRETAGNE-SUD http://www-limatb.univ-ubs.fr/ <http://www.univ-ubs.fr/>
Hello Olivier, I'm not sure exactly what you mean. Here are some guesses. (1) If you mean the structure is too big and you are interested in only part of it, you could delete the other part. I see from the information at the RCSB PDB including the cited paper <http://www.rcsb.org/pdb/explore/explore.do?structureId=2fjg> ...that this is two Fabs bound to the VEGF dimer. There are 6 chains: chains A,B are one Fab, chains H,L are another Fab, chains V,W are VEGF. If you only wanted one Fab, you could, for example delete chains H,L,V,W. If you wanted one Fab plus VEGF dimer, you could, for example, delete chains H,L (example command: delete :.H:.L ) <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#deletion> (2) If you wanted a surface of the whole structure in that PDB file, but you mean that the surface has too many triangles… i. you could decrease the vertex density of the molecular surface, for example command: setattr s density 0.5 <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html> - or - ii. instead of molecular surface, you could calculate a low-res density map and use an isosurface of that density map, for example command: molmap protein 8 (where the 8 is an adjustable parameter) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html> You mentioned splitting. However, that will not make a surface with fewer triangles, it will make MORE triangles because it will enclose each chain separately instead of trying to enclose all of the chains together. It might also make a 3D model that falls apart because each chain is enclosed separately. So I suspect that isn't what you really wanted. However, to split you could just use command: split <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/split.html> Splittting a surface calculation is mainly for when the overall (un-split) surface calculation fails and you need surface displays for purposes other than 3D models (interactive use of Chimera, or images and movies), or even if the overall calculation works but you want to show interface surfaces. Discussion about surface failures and workarounds here, including more about the "split" and "molmap" commands: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jun 26, 2014, at 7:39 AM, Olivier Sire <olivier.sire@univ-ubs.fr> wrote:
Hello, I am in a hurry to generate a surface object with 2FJG complex to be exported in a STL format for 3D printing. This item will be presented for a local event organized by the Ligue contre le Cancer. I have download Chimera as absolute beginner and I am facing a need for splitting the (too big ?, multi-chain) complex. The function Action / Surface / show generates the splitting solution. Could you help me and guide me ? Thanks in advance Regards Olivier Sire
Hello Olivier, I'm not sure exactly what you mean. Here are some guesses. (1) If you mean the structure is too big and you are interested in only part of it, you could delete the other part. I see from the information at the RCSB PDB including the cited paper <http://www.rcsb.org/pdb/explore/explore.do?structureId=2fjg> ...that this is two Fabs bound to the VEGF dimer. There are 6 chains: chains A,B are one Fab, chains H,L are another Fab, chains V,W are VEGF. If you only wanted one Fab, you could, for example delete chains H,L,V,W. If you wanted one Fab plus VEGF dimer, you could, for example, delete chains H,L (example command: delete :.H:.L ) <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#deletion> (2) If you wanted a surface of the whole structure in that PDB file, but you mean that the surface has too many triangles… i. you could decrease the vertex density of the molecular surface, for example command: setattr s density 0.5 <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html> - or - ii. instead of molecular surface, you could calculate a low-res density map and use an isosurface of that density map, for example command: molmap protein 8 (where the 8 is an adjustable parameter) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html> You mentioned splitting. However, that will not make a surface with fewer triangles, it will make MORE triangles because it will enclose each chain separately instead of trying to enclose all of the chains together. It might also make a 3D model that falls apart because each chain is enclosed separately. So I suspect that isn't what you really wanted. However, to split you could just use command: split <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/split.html> Splittting a surface calculation is mainly for when the overall (un-split) surface calculation fails and you need surface displays for purposes other than 3D models (interactive use of Chimera, or images and movies), or even if the overall calculation works but you want to show interface surfaces. Discussion about surface failures and workarounds here, including more about the "split" and "molmap" commands: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jun 26, 2014, at 7:39 AM, Olivier Sire <olivier.sire@univ-ubs.fr> wrote:
Hello, I am in a hurry to generate a surface object with 2FJG complex to be exported in a STL format for 3D printing. This item will be presented for a local event organized by the Ligue contre le Cancer. I have download Chimera as absolute beginner and I am facing a need for splitting the (too big ?, multi-chain) complex. The function Action / Surface / show generates the splitting solution. Could you help me and guide me ? Thanks in advance Regards Olivier Sire
Hi Olivier, If you are getting the surface calculation error and your goal is STL for a 3D model, use the "molmap" command mentioned in (2)ii of the previous reply. Show the Command Line by choosing it from the Favorites menu. man page for molmap command
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html>
another molmap example is #3 in this page
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html>
Best, Elaine On Jun 26, 2014, at 1:37 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hello Olivier, I'm not sure exactly what you mean. Here are some guesses.
(1) If you mean the structure is too big and you are interested in only part of it, you could delete the other part. I see from the information at the RCSB PDB including the cited paper <http://www.rcsb.org/pdb/explore/explore.do?structureId=2fjg> ...that this is two Fabs bound to the VEGF dimer. There are 6 chains: chains A,B are one Fab, chains H,L are another Fab, chains V,W are VEGF. If you only wanted one Fab, you could, for example delete chains H,L,V,W. If you wanted one Fab plus VEGF dimer, you could, for example, delete chains H,L (example command: delete :.H:.L ) <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#deletion>
(2) If you wanted a surface of the whole structure in that PDB file, but you mean that the surface has too many triangles…
i. you could decrease the vertex density of the molecular surface, for example command: setattr s density 0.5 <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html> - or - ii. instead of molecular surface, you could calculate a low-res density map and use an isosurface of that density map, for example command: molmap protein 8 (where the 8 is an adjustable parameter) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html>
You mentioned splitting. However, that will not make a surface with fewer triangles, it will make MORE triangles because it will enclose each chain separately instead of trying to enclose all of the chains together. It might also make a 3D model that falls apart because each chain is enclosed separately. So I suspect that isn't what you really wanted. However, to split you could just use command: split <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/split.html>
Splittting a surface calculation is mainly for when the overall (un-split) surface calculation fails and you need surface displays for purposes other than 3D models (interactive use of Chimera, or images and movies), or even if the overall calculation works but you want to show interface surfaces. Discussion about surface failures and workarounds here, including more about the "split" and "molmap" commands: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html>
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 26, 2014, at 7:39 AM, Olivier Sire <olivier.sire@univ-ubs.fr> wrote:
Hello, I am in a hurry to generate a surface object with 2FJG complex to be exported in a STL format for 3D printing. This item will be presented for a local event organized by the Ligue contre le Cancer. I have download Chimera as absolute beginner and I am facing a need for splitting the (too big ?, multi-chain) complex. The function Action / Surface / show generates the splitting solution. Could you help me and guide me ? Thanks in advance Regards Olivier Sire
Hi Olivier, If you are getting the surface calculation error and your goal is STL for a 3D model, use the "molmap" command mentioned in (2)ii of the previous reply. Show the Command Line by choosing it from the Favorites menu. man page for molmap command
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html>
another molmap example is #3 in this page
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html>
Best, Elaine On Jun 26, 2014, at 1:37 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hello Olivier, I'm not sure exactly what you mean. Here are some guesses.
(1) If you mean the structure is too big and you are interested in only part of it, you could delete the other part. I see from the information at the RCSB PDB including the cited paper <http://www.rcsb.org/pdb/explore/explore.do?structureId=2fjg> ...that this is two Fabs bound to the VEGF dimer. There are 6 chains: chains A,B are one Fab, chains H,L are another Fab, chains V,W are VEGF. If you only wanted one Fab, you could, for example delete chains H,L,V,W. If you wanted one Fab plus VEGF dimer, you could, for example, delete chains H,L (example command: delete :.H:.L ) <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#deletion>
(2) If you wanted a surface of the whole structure in that PDB file, but you mean that the surface has too many triangles…
i. you could decrease the vertex density of the molecular surface, for example command: setattr s density 0.5 <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html> - or - ii. instead of molecular surface, you could calculate a low-res density map and use an isosurface of that density map, for example command: molmap protein 8 (where the 8 is an adjustable parameter) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html>
You mentioned splitting. However, that will not make a surface with fewer triangles, it will make MORE triangles because it will enclose each chain separately instead of trying to enclose all of the chains together. It might also make a 3D model that falls apart because each chain is enclosed separately. So I suspect that isn't what you really wanted. However, to split you could just use command: split <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/split.html>
Splittting a surface calculation is mainly for when the overall (un-split) surface calculation fails and you need surface displays for purposes other than 3D models (interactive use of Chimera, or images and movies), or even if the overall calculation works but you want to show interface surfaces. Discussion about surface failures and workarounds here, including more about the "split" and "molmap" commands: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html>
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 26, 2014, at 7:39 AM, Olivier Sire <olivier.sire@univ-ubs.fr> wrote:
Hello, I am in a hurry to generate a surface object with 2FJG complex to be exported in a STL format for 3D printing. This item will be presented for a local event organized by the Ligue contre le Cancer. I have download Chimera as absolute beginner and I am facing a need for splitting the (too big ?, multi-chain) complex. The function Action / Surface / show generates the splitting solution. Could you help me and guide me ? Thanks in advance Regards Olivier Sire
Hello Elaine, I am amazed by the rapidity and precision you adressed my needs. Reducing the mesh for triangulation did not succeed (always the same fail). On opposite I got what I need with the molmap protein 5 command. I send you a picture of it. If you are interested, I shall send you also in a few days a photograph of the 3D printed protein which will be used for public sensibilisation to cancer in our city. Kind Regards Olivier Sire Le 26/06/2014 22:37, Elaine Meng a écrit :
Hello Olivier, I'm not sure exactly what you mean. Here are some guesses.
(1) If you mean the structure is too big and you are interested in only part of it, you could delete the other part. I see from the information at the RCSB PDB including the cited paper <http://www.rcsb.org/pdb/explore/explore.do?structureId=2fjg> ...that this is two Fabs bound to the VEGF dimer. There are 6 chains: chains A,B are one Fab, chains H,L are another Fab, chains V,W are VEGF. If you only wanted one Fab, you could, for example delete chains H,L,V,W. If you wanted one Fab plus VEGF dimer, you could, for example, delete chains H,L (example command: delete :.H:.L ) <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#deletion>
(2) If you wanted a surface of the whole structure in that PDB file, but you mean that the surface has too many triangles…
i. you could decrease the vertex density of the molecular surface, for example command: setattr s density 0.5 <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html> - or - ii. instead of molecular surface, you could calculate a low-res density map and use an isosurface of that density map, for example command: molmap protein 8 (where the 8 is an adjustable parameter) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html>
You mentioned splitting. However, that will not make a surface with fewer triangles, it will make MORE triangles because it will enclose each chain separately instead of trying to enclose all of the chains together. It might also make a 3D model that falls apart because each chain is enclosed separately. So I suspect that isn't what you really wanted. However, to split you could just use command: split <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/split.html>
Splittting a surface calculation is mainly for when the overall (un-split) surface calculation fails and you need surface displays for purposes other than 3D models (interactive use of Chimera, or images and movies), or even if the overall calculation works but you want to show interface surfaces. Discussion about surface failures and workarounds here, including more about the "split" and "molmap" commands: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html>
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 26, 2014, at 7:39 AM, Olivier Sire <olivier.sire@univ-ubs.fr> wrote:
Hello, I am in a hurry to generate a surface object with 2FJG complex to be exported in a STL format for 3D printing. This item will be presented for a local event organized by the Ligue contre le Cancer. I have download Chimera as absolute beginner and I am facing a need for splitting the (too big ?, multi-chain) complex. The function Action / Surface / show generates the splitting solution. Could you help me and guide me ? Thanks in advance Regards Olivier Sire
-- *Olivier SIRE * / Professeur à l'Université de Bretagne-Sud / ------------------------------------------------------------------------ Laboratoire d'Ingénierie des Matériaux de Bretagne Campus de Tohannic BP575 56017 VANNES cedex Tél. 02 97 01 71 48 Fax. 02 97 01 70 70 Mob. 06 89 48 25 24 olivier.sire@univ-ubs.fr UNIVERSITÉ DE BRETAGNE-SUD http://www-limatb.univ-ubs.fr/ <http://www.univ-ubs.fr/>
Hello Olivier, Great, I'm glad you were able to get a result quickly! If it's easy, you could certainly send a picture of the printed model, either to the list or just to me (if the latter, I'll share it with my coworkers). Best regards, Elaine On Jun 26, 2014, at 11:19 PM, Olivier Sire wrote:
Hello Elaine, I am amazed by the rapidity and precision you adressed my needs. Reducing the mesh for triangulation did not succeed (always the same fail). On opposite I got what I need with the molmap protein 5 command. I send you a picture of it. If you are interested, I shall send you also in a few days a photograph of the 3D printed protein which will be used for public sensibilisation to cancer in our city. Kind Regards
Olivier Sire
participants (2)
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Elaine Meng -
Olivier Sire