tag:blogger.com,1999:blog-7844526396210378482.post6403710413909105298..comments2024-01-31T09:23:26.925+00:00Comments on Noel O'Blog: Using Jmol for Drug Design - Depict Ligand in Active SiteNoel O'Boylehttp://www.blogger.com/profile/03288289351940689018noreply@blogger.comBlogger9125tag:blogger.com,1999:blog-7844526396210378482.post-58924239053008332592007-12-13T16:16:00.000+00:002007-12-13T16:16:00.000+00:00I've done the ray trace, but the image above is mo...I've done the ray trace, but the image above is more informative (the lighting is too much in the ray trace; also a small bug with the text). The image is <A HREF="http://www.redbrick.dcu.ie/~noel/blog/jmol/1p62_pov.png" REL="nofollow">here</A>.Noel O'Boylehttps://www.blogger.com/profile/03288289351940689018noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-73236921801644606482007-12-13T16:12:00.000+00:002007-12-13T16:12:00.000+00:00Felix, please see:http://chem-bla-ics.blogspot.com...Felix, please see:<BR/><BR/>http://chem-bla-ics.blogspot.com/2007/10/bob-improved-pov-ray-export-of-jmol.htmlEgon Willighagenhttps://www.blogger.com/profile/07470952136305035540noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-64356354809959357232007-12-13T16:08:00.000+00:002007-12-13T16:08:00.000+00:00so how about ray-tracing in povray?or are you plan...so how about ray-tracing in povray?<BR/>or are you planning to do that anyway?Felixhttps://www.blogger.com/profile/05138335803929997277noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-76216421746138680692007-12-13T10:25:00.000+00:002007-12-13T10:25:00.000+00:00Brilliant! Very nice!Brilliant! Very nice!Egon Willighagenhttps://www.blogger.com/profile/07470952136305035540noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-16558530532837311802007-12-13T09:21:00.000+00:002007-12-13T09:21:00.000+00:00@Egon: I've updated the post with links to a low q...@Egon: I've updated the post with links to a low quality and high quality applet. But if I find out that you've just been spinning that molecule...:-)Noel O'Boylehttps://www.blogger.com/profile/03288289351940689018noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-53733396811680886552007-12-13T08:10:00.000+00:002007-12-13T08:10:00.000+00:00"One of the points of this series is to show that ..."One of the points of this series is to show that Jmol's functionality is not limited to spinning molecules around on a webpage. Hence, no applet."<BR/><BR/>Mmm... and you can't rotate or zoom in on an active site? That's what I am interested in. Hence, the applet. :)Egon Willighagenhttps://www.blogger.com/profile/07470952136305035540noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-21986037957455976102007-12-13T07:54:00.000+00:002007-12-13T07:54:00.000+00:00@karol: It can also do isosurfaces of Gaussian .cu...@karol: It can also do isosurfaces of Gaussian .cube files.<BR/><BR/>@egon:<BR/>1. Hydrogens removed for clarity<BR/>2. One of the points of this series is to show that Jmol's functionality is not limited to spinning molecules around on a webpage. Hence, no applet. Ok, maybe that's not a great excuse, but it took me a while just to get this blog post together...<BR/><BR/>Felix (and others?) have embedded Jmol in blogger.Noel O'Boylehttps://www.blogger.com/profile/03288289351940689018noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-91022539294003871782007-12-13T07:21:00.000+00:002007-12-13T07:21:00.000+00:00Very nice demo! Two comments:1. where are the liga...Very nice demo! Two comments:<BR/>1. where are the ligands hydrogens?<BR/>2. where is the Jmol applet??<BR/><BR/>I know Jmol can be embedded in Wordpress [1], but have to admit that I have not tried in blogger.com myself.<BR/><BR/>1.http://www.openscience.org/blog/?p=208Egon Willighagenhttps://www.blogger.com/profile/07470952136305035540noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-28465923879859589492007-12-12T21:43:00.000+00:002007-12-12T21:43:00.000+00:00That is pretty nifty... never used JMol much, mayb...That is pretty nifty... never used JMol much, maybe I should :)Karolhttps://www.blogger.com/profile/17032498937126368914noreply@blogger.com