Nico wrote: > I see that you have worked on the povray output. Thanks for working on this!
> I made myself some modifications to Jmol code to work on the povray output > > The modifications I have made : > > Concerning the output of only the visible items, you can now choose to > output only the currently displayed model (rendered as 1 frame) or all the > models (rendered as n frames, n being the number of models) I had some troubles with this on Linux. It hangs when I try to generate all the frames. povray 3.6 seems to hang after the first frame povray 3.5 seems to hang after the second frame > Concerning the output of bonds : > - output of hydrogen bonds is added I was unable to see this. I loaded samples/pdb/1CRN.pdb and said 'hbonds on' I think I know what the problem is ... there is more than one type of HBOND. So the bond-mask needs to check for a whole set of hbonds (by doing some binary masking), not just == > - output of aromatic bonds is added but the position of the full cylinder > and the dashed cylinder are not always the same when seen in Jmol. I don't > know if it is a problem Very nice! Yes, I see that the dotted lines are not inside the ring. We should fix this. > - output of s-bonds is not added because I didn't find a sample with one > of them to look at how it was displayed s-bonds are displayed as normal bonds. There is nothing special about them. The fact that they receive 'special treatment' is an historical artifact. > - in the SticksRenderer, I saw that there was also a case for > BOND_STEREO_FAR and BOND_STEREO_NEAR (rendered as triangle ?), but I > didn't find a sample to to look at them. We should not put any energy into this. Jmol's support for 2d is weak/poor/incorrect/wrong. > Concerning the output of secondary structure, I am not familiar with how > data is organized in Jmol so I had problems to find what was the data to > output. I made a test with 'polymer' : it seems that I get the points used > to draw the 'trace'. I will try to help you with this ... but I will be quite busy for the next week or two. > I couldn't find a simple way to render correctly the trace in povray. I > tried the sphere_sweep object but it is limited to the following splines : > - linear_spline : draws straight lines between each point We will start by doing 'backbone' as a linear spline. load samples/pdb/1CRN.pdb backbone .5 color backbone structure > - b_spline or cubic_splice : draw curves but the curves do not pass any > more through the points This could be a problem. I chose to use hermite curves in Jmol because the curve will pass through the control points that you specify. load samples/pdb/1CRN.pdb; trace .5; color trace amino; spacefill off; wireframe; select alpha; spacefill 25%; color atoms lime The trace passes through the mid-points between the alpha carbon atoms We should post messages to some mailing lists ... perhaps the povray list ... and ask how to make a b_spline or cubic_spline pass through a particular point. Miguel ------------------------------------------------------- The SF.Net email is sponsored by: Beat the post-holiday blues Get a FREE limited edition SourceForge.net t-shirt from ThinkGeek. It's fun and FREE -- well, almost....http://www.thinkgeek.com/sfshirt _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
