Re: [Jmol-users] drums on jmol colors page
Phil wrote: > How about the colors used for water, as in WAT HOH and H2O PDB files generally do not have hydrogen atoms. Therefore WAT, HOH, and H2O groups generally contain only one atom ... the oxygen. So ... HOH usually shows up as red. > (seems to be blue in the Jmol default colors) I am puzzled as to why you think you have seen blue ... ? > and for OH (seems to render like H)? Q: I don't understand what you are asking here Miguel --- SF.Net email is Sponsored by the Better Software Conference & EXPO September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices Agile & Plan-Driven Development * Managing Projects & Teams * Testing & QA Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] drums on jmol colors page
> Very good start. I like the Periodic Table. > > Let me know if you need additional information. How about the colors used for water, as in WAT HOH and H2O (seems to be blue in the Jmol default colors), and for OH (seems to render like H)? I've been all over the constants file and can't pick it out. --Phil Barak --- SF.Net email is Sponsored by the Better Software Conference & EXPO September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices Agile & Plan-Driven Development * Managing Projects & Teams * Testing & QA Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] drums on jmol colors page
Thanks to my being an enthusiast of doing things in Javascript instead of repeating html, Rolf's suggestions have been too easy to implement :-o This starts to look real good! El 28 Jul 2005 a las 16:38, Rolf Huehne escribió: > I would suggest some additions: > > The color values should also be given in the form that is understood by > jmol (e.g. 255,17,125, maybe even in braces [255,17,125]) and not only > in hexadecimal form. > > In the periodic table it would be nice if the title of each cell would > be the color value. Then a popup would show the value if the mouse rests > over the cell. --- SF.Net email is Sponsored by the Better Software Conference & EXPO September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices Agile & Plan-Driven Development * Managing Projects & Teams * Testing & QA Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] drums on jmol colors page
> I have started to compile a page describing colors used by Jmol. > For now, it will be linked from the Wiki > http://wiki.jmol.org/JmolColors Very good start. I like the Periodic Table. Let me know if you need additional information. Miguel --- SF.Net email is Sponsored by the Better Software Conference & EXPO September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices Agile & Plan-Driven Development * Managing Projects & Teams * Testing & QA Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] drums on jmol colors page
Hi, De: "Angel Herraez" <[EMAIL PROTECTED]> > >I have started to compile a page describing colors used by Jmol. >For now, it will be linked from the Wiki >http://wiki.jmol.org/JmolColors Your draft is really nice :) The suggestion for a tooltip seems also good to me, or at least reorganizing the matrix to be less vertical (page has a lot of empty space on a big screen). If you're interested, you can modify the source pages of Jmol website to have something similar on the colors page. Otherwise, I will try to do it in August. Nicolas --- SF.Net email is Sponsored by the Better Software Conference & EXPO September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices Agile & Plan-Driven Development * Managing Projects & Teams * Testing & QA Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] drums on jmol colors page
Angel Herraez wrote: I have started to compile a page describing colors used by Jmol. For now, it will be linked from the Wiki http://wiki.jmol.org/JmolColors I looked at the draft version linked in the Wiki. It looks nice and really fills a gap in the jmol documentation. Especially the periodic table version shows nicely the reasoning behind the atom color scheme. I would suggest some additions: The color values should also be given in the form that is understood by jmol (e.g. 255,17,125, maybe even in braces [255,17,125]) and not only in hexadecimal form. In the periodic table it would be nice if the title of each cell would be the color value. Then a popup would show the value if the mouse rests over the cell. Regards, Rolf --- SF.Net email is Sponsored by the Better Software Conference & EXPO September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices Agile & Plan-Driven Development * Managing Projects & Teams * Testing & QA Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] drums on jmol colors page
I have started to compile a page describing colors used by Jmol. For now, it will be linked from the Wiki http://wiki.jmol.org/JmolColors El 29 May 2005 a las 12:41, Miguel escribió: > > This is why I proposed that it be linked to the jmol "Colors" page. > > Yes, we should do this. > > Per Nico's other email, we the Jmol colors page should also include the > default definitions of the Jmol element colors. --- SF.Net email is Sponsored by the Better Software Conference & EXPO September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices Agile & Plan-Driven Development * Managing Projects & Teams * Testing & QA Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] drums on jmol colors page
At 5/29/05, Miguel wrote: In addition, we should try to add support for DRuMS as a supported color scheme within Jmol in order to facilitate adoption of of a standard coloring scheme. Agreed! Eric Martz, Professor Emeritus, Dept Microbiology University of Massachusetts, Amherst MA US http://www.umass.edu/molvis/martz --- This SF.Net email is sponsored by Yahoo. Introducing Yahoo! Search Developer Network - Create apps using Yahoo! Search APIs Find out how you can build Yahoo! directly into your own Applications - visit http://developer.yahoo.net/?fr=offad-ysdn-ostg-q22005 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] drums on jmol colors page
> At 5/29/05, Nicolas Vervelle wrote: >>is the DRuMS color schemes widely used ? Eric wrote: > This is why I proposed that it be linked to the jmol "Colors" page. Yes, we should do this. Per Nico's other email, we the Jmol colors page should also include the default definitions of the Jmol element colors. > As time > permits, ideally the whole DRuMS site could be jmol-ized and added to > jmol.sourceforge.net. For now, I recommend a link to the existing site > http://www.umass.edu/molvis/drums/ . Agreed. In addition, we should try to add support for DRuMS as a supported color scheme within Jmol in order to facilitate adoption of of a standard coloring scheme. Miguel --- This SF.Net email is sponsored by Yahoo. Introducing Yahoo! Search Developer Network - Create apps using Yahoo! Search APIs Find out how you can build Yahoo! directly into your own Applications - visit http://developer.yahoo.net/?fr=offad-ysdn-ostg-q22005 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] drums on jmol colors page
At 5/29/05, Nicolas Vervelle wrote: is the DRuMS color schemes widely used ? Thanks for your reply, Nicolas. The name "DRuMS" (http://www.umass.edu/molvis/drums/) comes from Driscoll, Reichsman, Martz and Sayle. The core color schemes in DRuMS (elements, secondary structure) are those in RasMol (authored by Roger Sayle) and therefore also in Chime (because its rendering code is adapted from RasMol's public domain source). (See my recent revision of http://wiki.jmol.org/JmolScripting ) Driscoll (with Reichsman and Martz) extended these core schemes to be comprehensive, adding schemes for macromolecule type (protein vs. DNA vs. RNA vs. solvent vs. hetero), amino acid sidechain polarity/charge, purines, pyrimidines, DNA backbone, RNA backbone, and nucleotide bases. The schemes were carefully designed so that any combination of schemes can be used concurrently yet all colors are distinct. The DRuMS core schemes are built into RasMol and Chime. Full DRuMS is used by ProteinExplorer.Org (see the "Colored by DRuMS" button/link on its FrontDoor page), and in Chime-based tutorials for the popular Lehninger Principles of Biochemistry text, tutorials authored by Driscoll and Reichsman (http://www.worthpublishers.com/lehninger3d/index2.html). In my personal opinion, these tutorials (which I was not involved in authoring) set a high standard of scientific and pedagogic quality. The figures in each major biochemistry textbook (including Lehninger's) use different, and often internally inconsistent, color schemes. There is no agreed-upon standard for macromolecular colors, or for nucleotide base colors in sequences, and many different schemes are in wide use. DRuMS was proposed in 2000 partly because of the need for rational color schemes that could be used concurrently, and partly in response to this chaos in the field. The DRuMS color schemes, http://www.umass.edu/molvis/drums/ , are supported by downloadable Chime scripts, cascading style sheets for color-matched HTML, color charts with RGB codes, demonstration examples, and explicit rationales. To my knowledge, DRuMS is the only set of macromolecular color schemes with a website, or with this level of documentation and support. This is why I proposed that it be linked to the jmol "Colors" page. As time permits, ideally the whole DRuMS site could be jmol-ized and added to jmol.sourceforge.net. For now, I recommend a link to the existing site http://www.umass.edu/molvis/drums/ . -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis/martz Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop Biochem Structure Tutorials http://MolviZ.org World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List (molvis-list): http://bioinformatics.org/mailman/listinfo/molvis-list - - - - - - - - - - - - - - - - - - - - - - - - - - - */ --- This SF.Net email is sponsored by Yahoo. Introducing Yahoo! Search Developer Network - Create apps using Yahoo! Search APIs Find out how you can build Yahoo! directly into your own Applications - visit http://developer.yahoo.net/?fr=offad-ysdn-ostg-q22005 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] drums on jmol colors page
Hi, is the DRuMS color schemes widely used ? what do others think of adding this to the website ? I think that if we choose to add it, we should add the color schemes not only a link. IMHO, the colour page on the website should also be completed to add default colors used by Jmol. Nicolas Eric Martz wrote: To whom or where/how do I submit requests for changes to the jmol website at sourceforge.net? There's always the solution of using the tracker items on sourceforge.net. Just wait a little more to see if you have answers. BTW, the bugs tracker is more used than the RFE one. There is no contact info on the website that I can find. I received no response to this suggestion posted 5 days ago: On 5/23/05, Eric Martz wrote to jmol-users: I'd like to suggest that a new category be added to the "Colors" page at www.jmol.org, namely "Colors for Macromolecules". Under this heading I suggest a link to the DRuMS color schemes, http://www.umass.edu/molvis/drums From the main DRuMS page: "DRuMS is a set of seven standardized, intuitive color schemes applicable to macromolecular structures and designed for use on the Web. Color is an efficient and powerful method for conveying information about a macromolecule. Adopting a standard color scheme is important, to avoid confusion and present a clear message. DRuMS is freely available to all for use in noncommercial and commercial contexts. You are invited to use DRuMS in your own online resources." --- This SF.Net email is sponsored by Yahoo. Introducing Yahoo! Search Developer Network - Create apps using Yahoo! Search APIs Find out how you can build Yahoo! directly into your own Applications - visit http://developer.yahoo.net/?fr=offad-ysdn-ostg-q22005 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users --- This SF.Net email is sponsored by Yahoo. Introducing Yahoo! Search Developer Network - Create apps using Yahoo! Search APIs Find out how you can build Yahoo! directly into your own Applications - visit http://developer.yahoo.net/?fr=offad-ysdn-ostg-q22005 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] drums on jmol colors page
To whom or where/how do I submit requests for changes to the jmol website at sourceforge.net? There is no contact info on the website that I can find. I received no response to this suggestion posted 5 days ago: On 5/23/05, Eric Martz wrote to jmol-users: I'd like to suggest that a new category be added to the "Colors" page at www.jmol.org, namely "Colors for Macromolecules". Under this heading I suggest a link to the DRuMS color schemes, http://www.umass.edu/molvis/drums From the main DRuMS page: "DRuMS is a set of seven standardized, intuitive color schemes applicable to macromolecular structures and designed for use on the Web. Color is an efficient and powerful method for conveying information about a macromolecule. Adopting a standard color scheme is important, to avoid confusion and present a clear message. DRuMS is freely available to all for use in noncommercial and commercial contexts. You are invited to use DRuMS in your own online resources." --- This SF.Net email is sponsored by Yahoo. Introducing Yahoo! Search Developer Network - Create apps using Yahoo! Search APIs Find out how you can build Yahoo! directly into your own Applications - visit http://developer.yahoo.net/?fr=offad-ysdn-ostg-q22005 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] drums on jmol colors page
I'd like to suggest that a new category be added to the "Colors" page at www.jmol.org, namely "Colors for Macromolecules". Under this heading I suggest a link to the DRuMS color schemes, http://www.umass.edu/molvis/drums From the main DRuMS page: "DRuMS is a set of seven standardized, intuitive color schemes applicable to macromolecular structures and designed for use on the Web. Color is an efficient and powerful method for conveying information about a macromolecule. Adopting a standard color scheme is important, to avoid confusion and present a clear message. DRuMS is freely available to all for use in noncommercial and commercial contexts. You are invited to use DRuMS in your own online resources." __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis/martz Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop Biochem Structure Tutorials http://MolviZ.org World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List (molvis-list): http://bioinformatics.org/mailman/listinfo/molvis-list - - - - - - - - - - - - - - - - - - - - - - - - - - - */ --- This SF.Net email is sponsored by Oracle Space Sweepstakes Want to be the first software developer in space? Enter now for the Oracle Space Sweepstakes! http://ads.osdn.com/?ad_id=7412&alloc_id=16344&op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
