Comments on: Publication quality pictures of biomolecules http://freelancingscience.com/2007/08/07/publication-quality-pictures-of-biomolecules/ protein science, open science and freelancing science Sat, 19 Jul 2008 18:40:34 +0000 http://wordpress.org/?v=MU By: A bad day in structure space « Suicyte Notes http://freelancingscience.com/2007/08/07/publication-quality-pictures-of-biomolecules/#comment-109 A bad day in structure space « Suicyte Notes Thu, 08 Nov 2007 12:36:40 +0000 http://freesci.wordpress.com/2007/08/07/publication-quality-pictures-of-biomolecules/#comment-109 [...] whereever you look. There are  free structure viewers (check the interesting posting on “Freelancing Science“), but if you read the fineprint, almost all viewers capable of producing publication-quality [...] [...] whereever you look. There are  free structure viewers (check the interesting posting on “Freelancing Science“), but if you read the fineprint, almost all viewers capable of producing publication-quality [...]

]]> By: Egon Willighagen http://freelancingscience.com/2007/08/07/publication-quality-pictures-of-biomolecules/#comment-81 Egon Willighagen Mon, 29 Oct 2007 20:18:00 +0000 http://freesci.wordpress.com/2007/08/07/publication-quality-pictures-of-biomolecules/#comment-81 Another name: Jmol.org does a pretty good PovRay export nowadays too. Another name: Jmol.org does a pretty good PovRay export nowadays too.

]]> By: baoilleach http://freelancingscience.com/2007/08/07/publication-quality-pictures-of-biomolecules/#comment-33 baoilleach Sun, 02 Sep 2007 11:34:05 +0000 http://freesci.wordpress.com/2007/08/07/publication-quality-pictures-of-biomolecules/#comment-33 iayork says: "I find PyMol’s attitude (” today’s PyMOL users can choose to either sponsor the project to enjoy incentives such as our precompiled executables, or they can choose to assume responsibility for obtaining their own FREE executables from the open-source code.“) off-putting. Of course, they can present their software any way they like, but the tone of aggrieved self-righteousness doesn’t make them look good, and it’s not like they have the only product around." Just to point out that PyMol is written by a single person, Warren DeLano, not a "they". Warren is trying to maintain a delicate balance between making it open source (for example, it's included in most major Linux distributions) and relying on it for income (you need to pay for Windows binaries, or figure out how to compile it yourself). Most of the other software discussed here (with the exception of Qutemol) is not even open source (which is why you can't port it, fix the bugs, or build on it), unlike PyMol. iayork says:
“I find PyMol’s attitude (” today’s PyMOL users can choose to either sponsor the project to enjoy incentives such as our precompiled executables, or they can choose to assume responsibility for obtaining their own FREE executables from the open-source code.“) off-putting. Of course, they can present their software any way they like, but the tone of aggrieved self-righteousness doesn’t make them look good, and it’s not like they have the only product around.”

Just to point out that PyMol is written by a single person, Warren DeLano, not a “they”. Warren is trying to maintain a delicate balance between making it open source (for example, it’s included in most major Linux distributions) and relying on it for income (you need to pay for Windows binaries, or figure out how to compile it yourself). Most of the other software discussed here (with the exception of Qutemol) is not even open source (which is why you can’t port it, fix the bugs, or build on it), unlike PyMol.

]]> By: My Biotech Life » Bio::Blogs #14 - The lightning edition http://freelancingscience.com/2007/08/07/publication-quality-pictures-of-biomolecules/#comment-32 My Biotech Life » Bio::Blogs #14 - The lightning edition Sat, 01 Sep 2007 19:36:38 +0000 http://freesci.wordpress.com/2007/08/07/publication-quality-pictures-of-biomolecules/#comment-32 [...] prediction tools, we have a great post by newcomer Paweł from Freelancing Science that discusses publication quality pictures of biomolecules and the tools used. Aside from this post, keep your eyes open for some great commenting going on [...] [...] prediction tools, we have a great post by newcomer Paweł from Freelancing Science that discusses publication quality pictures of biomolecules and the tools used. Aside from this post, keep your eyes open for some great commenting going on [...]

]]> By: Visualization software for molecular assemblies by Thomas Goddard and Thomas Ferrin « Freelancing science http://freelancingscience.com/2007/08/07/publication-quality-pictures-of-biomolecules/#comment-31 Visualization software for molecular assemblies by Thomas Goddard and Thomas Ferrin « Freelancing science Sat, 01 Sep 2007 11:02:24 +0000 http://freesci.wordpress.com/2007/08/07/publication-quality-pictures-of-biomolecules/#comment-31 [...] if the focus of this paper is not preparation of publication quality pictures, software cited there sounds familiar: Chimera, Pymol, VMD, Qutemol. The authors mention also VISION, which is a visual programming [...] [...] if the focus of this paper is not preparation of publication quality pictures, software cited there sounds familiar: Chimera, Pymol, VMD, Qutemol. The authors mention also VISION, which is a visual programming [...]

]]> By: naga http://freelancingscience.com/2007/08/07/publication-quality-pictures-of-biomolecules/#comment-26 naga Mon, 20 Aug 2007 13:06:45 +0000 http://freesci.wordpress.com/2007/08/07/publication-quality-pictures-of-biomolecules/#comment-26 hi all, pymol is good for visualization.. i liked it very much, becoz it provides the option to make molecular animation out of that..! its good wen i make presentation for my lab meets..! the ray fuction in the pymol provides a pretty good picture..! n sector (sgi) is also used to make pretty good pictures for publications..! naga hi all,

pymol is good for visualization.. i liked it very much, becoz it provides the option to make molecular animation out of that..! its good wen i make presentation for my lab meets..! the ray fuction in the pymol provides a pretty good picture..!

n sector (sgi) is also used to make pretty good pictures for publications..!

naga

]]> By: iayork http://freelancingscience.com/2007/08/07/publication-quality-pictures-of-biomolecules/#comment-25 iayork Sun, 19 Aug 2007 19:15:15 +0000 http://freesci.wordpress.com/2007/08/07/publication-quality-pictures-of-biomolecules/#comment-25 Pedro: <EM>I’ll put in another name, YASARA (www.yasara.org).</EM> Thanks for the pointer, Pedro. I had forgotten about YASARA since I moved to my Intel Macs. Now that I can run it, I'm impressed - pretty pictures and ease of use combined. Freesci: <EM>What kind of images you are trying to get?</EM> I'm usually after something like a PNG file (for slides or web viewing) and I'm usually trying to make pretty simple points. For example, I like to show my students MHC class I peptide complexes with the peptide's surface-exposed surfaces and anchor residues indicated. YASARA seems to make it quite easy to make those clear. Pedro: I’ll put in another name, YASARA (www.yasara.org).

Thanks for the pointer, Pedro. I had forgotten about YASARA since I moved to my Intel Macs. Now that I can run it, I’m impressed - pretty pictures and ease of use combined.

Freesci: What kind of images you are trying to get? I’m usually after something like a PNG file (for slides or web viewing) and I’m usually trying to make pretty simple points. For example, I like to show my students MHC class I peptide complexes with the peptide’s surface-exposed surfaces and anchor residues indicated. YASARA seems to make it quite easy to make those clear.

]]> By: freesci http://freelancingscience.com/2007/08/07/publication-quality-pictures-of-biomolecules/#comment-24 freesci Sun, 19 Aug 2007 17:57:53 +0000 http://freesci.wordpress.com/2007/08/07/publication-quality-pictures-of-biomolecules/#comment-24 Deepak, I'm sorry that publishing of your comment took so long - it was somehow identified by Akismet as spam :). Deepak, I’m sorry that publishing of your comment took so long - it was somehow identified by Akismet as spam :).

]]> By: freesci http://freelancingscience.com/2007/08/07/publication-quality-pictures-of-biomolecules/#comment-23 freesci Sun, 19 Aug 2007 17:50:38 +0000 http://freesci.wordpress.com/2007/08/07/publication-quality-pictures-of-biomolecules/#comment-23 Iayork, in my group Molscript, Pymol and VMD have been used for publications with at least acceptable results. Advanced features of Pymol/Chimera/VMD (several layers of the visualization, like transparent surfaces and such) look very well on the screen, but unfortunately often not on the paper. I really like the output of Molscript, but it takes hours to prepare a single figure (I've tested various interfaces to the Molscript, but at least on the linux, I haven't found anything that suited me). What kind of images you are trying to get? Pedro, thanks for pointing that. I've used Yasara for various things (the Dynamics package), but never thought to think about it in terms of producing images. I may want to try. :) Iayork, in my group Molscript, Pymol and VMD have been used for publications with at least acceptable results. Advanced features of Pymol/Chimera/VMD (several layers of the visualization, like transparent surfaces and such) look very well on the screen, but unfortunately often not on the paper. I really like the output of Molscript, but it takes hours to prepare a single figure (I’ve tested various interfaces to the Molscript, but at least on the linux, I haven’t found anything that suited me). What kind of images you are trying to get?

Pedro, thanks for pointing that. I’ve used Yasara for various things (the Dynamics package), but never thought to think about it in terms of producing images. I may want to try. :)

]]> By: Deepak http://freelancingscience.com/2007/08/07/publication-quality-pictures-of-biomolecules/#comment-22 Deepak Sun, 19 Aug 2007 17:41:07 +0000 http://freesci.wordpress.com/2007/08/07/publication-quality-pictures-of-biomolecules/#comment-22 YASARA looks good to. Never tried it but it was always intriguing as was <a href="http://www.ddl.unimi.it/vega/index3.htm" rel="nofollow">VEGA</a> which I last used about 7 years ago. Re DSViewer ... it got completely re-written a couple of years ago, so the performance should be better. It's essentially WLViewer resurrected. It does have more features than a lot of people need though, and is probably more useful if you are doing drug design. I have mixed feelings on PyMol. It's the best visualization software I've used, but I feel Warren has lost a lot of goodwill with the current approach, especially in the academic community. YASARA looks good to. Never tried it but it was always intriguing as was VEGA which I last used about 7 years ago.

Re DSViewer … it got completely re-written a couple of years ago, so the performance should be better. It’s essentially WLViewer resurrected. It does have more features than a lot of people need though, and is probably more useful if you are doing drug design.

I have mixed feelings on PyMol. It’s the best visualization software I’ve used, but I feel Warren has lost a lot of goodwill with the current approach, especially in the academic community.

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