From: "Miguel" <[EMAIL PROTECTED]> > > 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.
I tested it with only one sample (35 frames) under XP with povray 3.6.1 It worked for me > > 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' What I did with hbonds is similar to regular bonds : they are not sent to povray when they are displayed as wireframe. It may be the problem, could you try giving a radius to the hbonds ? > 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 == It may also be a problem, but I don't know which values could be considered as hbonds. > > - 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 > > Yes, I see that the dotted lines are not inside the ring. We should fix this. Yes, we should find a better way to put the dotted lines in the correct position. But the problem lies also on the Jmol side when things get more complicated. For example, see samples/hin/dan002.hin. > > - 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. Ok > > - 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. Ok > > 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. Ok, no problem, I think I will also be busy > > - 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. A few years ago I found a way to render a bspline that goes through defined points. I remember I was computing n + 2 control points so that the spline goes through the n points. The result was nice. Have to search in my archives to see if I can find this work. Nicolas ------------------------------------------------------- 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
