Re: [Jmol-developers] cartoons in povray

[Nicolas V. <nve...@cl...>]

From: "Miguel" <mi...@jm...>
> > 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