From: Alexander R. <ale...@we...> - 2012-10-14 17:02:02
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Hi, I'd like to do some work on Jmol's cartoon style. Attached is an images showing cross-sections of various cartoon style. We have (1) and now also (2), with cartoonFancy. For the java-version there is also (3), but not when exported to WebGL as for JSmol. I think having (3) as a mesh-based version that works for WebGL is good performance wise, which can be seen in e.g. GLmol thin ribbons. (4) and (5) provide greater variety, artistically and for finding the most clear depiction. I would start with the mesh version of (3). What do you think, any suggestions? Best Alexander |
From: Rolf H. <rh...@fl...> - 2012-10-15 10:13:32
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On 10/14/2012 07:01 PM, Alexander Rose wrote: > Hi, > > I'd like to do some work on Jmol's cartoon style. Attached is an images showing > cross-sections of various cartoon style. We have (1) and now also (2), with > cartoonFancy. For the java-version there is also (3), but not when exported to > WebGL as for JSmol. I think having (3) as a mesh-based version that works for > WebGL is good performance wise, which can be seen in e.g. GLmol thin ribbons. > (4) and (5) provide greater variety, artistically and for finding the most clear > depiction. > > I would start with the mesh version of (3). What do you think, any suggestions? > Aren't 4 and 5 already there? 4: 'rockets' 5: 'cartoon' with 'set ribbonborder on' Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rh...@fl... Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 296, Amtsgericht Jena Tax Number: 162/141/08228 |
From: Alexander R. <ale...@we...> - 2012-10-15 13:25:19
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Hi Rolf, Am 15.10.2012 um 12:13 schrieb Rolf Huehne: > On 10/14/2012 07:01 PM, Alexander Rose wrote: >> Hi, >> >> I'd like to do some work on Jmol's cartoon style. Attached is an images showing >> cross-sections of various cartoon style. We have (1) and now also (2), with >> cartoonFancy. For the java-version there is also (3), but not when exported to >> WebGL as for JSmol. I think having (3) as a mesh-based version that works for >> WebGL is good performance wise, which can be seen in e.g. GLmol thin ribbons. >> (4) and (5) provide greater variety, artistically and for finding the most clear >> depiction. >> >> I would start with the mesh version of (3). What do you think, any suggestions? >> > Aren't 4 and 5 already there? > 4: 'rockets' > 5: 'cartoon' with 'set ribbonborder on' Yes and no. 'rockets' gives something like (4) for the beta-sheets but that does not take the C-alpha trace into account as the rectangular box is, well, straight. I mean something like (1), i.e. 'cartoon; hermiteLevel=1;', but without the half-barrels/rounded corners. 'cartoon' with 'set ribbonborder on' works not for hermiteLevel != 0 and also not for exports (e.g. WebGL) Alex |
From: Alexander R. <ale...@we...> - 2012-10-15 15:49:57
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Hi, Here are some more explanations and thoughts regarding cartoons. If there are no objections, I would now start with (3) and send a patch, hoping to get some of Bob's attention so he has a look at it. Although I know he is currently working on an infinitely more exciting projects. [g3d] is Jmols own software based renderer (i.e. no accelerated by a graphics card). It contains specialized methods to draw e.g. balls (atoms) or cylinders (bonds) that are one of the reasons that make it so fast despite the lack of graphics card acceleration. [mesh] here it describes the representation of 3d objects by lots of adjacent triangles in 3d space that can be rendered more or less as is by any 3d program/library. (1) [g3d] N/A [mesh] cartoon; set hermiteLevel 3; (2) [g3d] N/A NEW [mesh] cartoon; set hermiteLevel 3; set cartoonFancy; (3) [g3d] cartoon; TODO [mesh] cartoon; set hermiteLevel 3; set cartoonThin true; (3b) [g3d] cartoon; set ribbonBorder true; TODO [mesh] cartoon; set hermiteLevel 3; set cartoonThin true; set ribbonBorder true; (4) [g3d] N/A (there is some hidden source code, but it does not produce ok-looking results) TODO [mesh] cartoon; set hermiteLevel 3; set cartoonThick true; (5) [g3d] N/A TODO [mesh] cartoon; set hermiteLevel 3; set cartoonThick true; set ribbonBorder true; As for the set ribbonBorder true; option it would be nice to switch it of for sheets: set ribbonBorder [true, "helix", "sheet"]. Another thing (also previously implemented in various other programs) is two sided coloring of the cartoons, especially helices. Alex Am 14.10.2012 um 19:01 schrieb Alexander Rose: > Hi, > > I'd like to do some work on Jmol's cartoon style. Attached is an images showing cross-sections of various cartoon style. We have (1) and now also (2), with cartoonFancy. For the java-version there is also (3), but not when exported to WebGL as for JSmol. I think having (3) as a mesh-based version that works for WebGL is good performance wise, which can be seen in e.g. GLmol thin ribbons. (4) and (5) provide greater variety, artistically and for finding the most clear depiction. > > I would start with the mesh version of (3). What do you think, any suggestions? > > > Best > Alexander > > > > <cartoon_cross_sections.png> > ------------------------------------------------------------------------------ > Don't let slow site performance ruin your business. Deploy New Relic APM > Deploy New Relic app performance management and know exactly > what is happening inside your Ruby, Python, PHP, Java, and .NET app > Try New Relic at no cost today and get our sweet Data Nerd shirt too! > http://p.sf.net/sfu/newrelic-dev2dev_______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers |