Woops, sorry. See, that's why it's so much better to put things on the user list :)
Tsjerk On Thu, Apr 24, 2008 at 6:23 PM, DeLano Scientific <del...@delsci.info> wrote: > > Pymol (at least up to 0.99rc6) has a problem with multiple > > transparencies in ray-tracing. > > That's news to me. Combination of multiple transparent surfaces is indeed > broken in the OpenGL viewer up into 1.x. However, the ray tracer has been > able to do this almost since the beginning. > > The thing is, with PyMOL, you get to choose whether or not you see multiple > transparent layers. Given the geometric intricacy of molecular surfaces, it > is often preferable to only see the front-most transparent surface, so that > is the default behavior: > > set transparency_mode, 2 > > If, instead, you want to render all transparent layers: > > set transparency_mode, 1 > > If you want increased contrast when rendering: > > set ray_transparency_contrast, 1.5 > > If you want to factor in surface normals: > > set ray_transparency_oblique, 1.1 > > If you don't want transparent surfaces casting a shadow: > > set ray_transparency_shadow, 0 > > If you don't want any shadows at all: > > set ray_shadow, 0 > > Cheers, > Warren > > > > > If you really need it, you can > > export the scene to povray, which will allow you to build > > complex scenes with multiple transparent objects. This may be > > the same issue as losing the shaded face between two boxes. > > There it may help to define each plane uniquely, rather than > > placing two boxes with the faces coinciding. Or you can try > > to add a little bit of space between the boxes. But I should > > add that I haven't tried these things yet. > > > > By the way, I also bounce this mail the pymol user list, so > > that others may add their comments and/or can learn from it. > > > > Best, > > > > Tsjerk > > > > On Thu, Apr 24, 2008 at 3:41 PM, Dean Waldow > > <wal...@chem.plu.edu> wrote: > > > Tsjerk, > > > > > > Thanks, perhaps that might related to other things I have > > noticed.... > > > > > > I have noticed some oddities (which I think I can work > > around) when I > > > place multiple boxes next to each other and then do a ray. Have you > > > seen anything like these and not that I expect you to have the > > > answers... :) I thought I would mention them in case you > > have seen them. I'm using .99r6 I think. > > > > > > 1) Looking through one of the middle boxes molecules in > > there get a 'snow' > > > look if the color settings are 1 but when I most the color > > settings a > > > little lower than 1 that seems to got away. > > > 2) One other obj (spheroid) which I had set at transparent > > disappears > > > when viewed through a transparent box after issuing the ray command. > > > 3) Also when I issue the ray command, I can't see the shadowed > > > boundary between boxes like I can before before the ray command. > > > > > > Thanks again. I really appreciate the tips! > > > > > > Dean > > > > > > > > > > > > On Apr 24, 2008, at 2:21 AM, Tsjerk Wassenaar wrote: > > > > > > > > > > Hi Dean, > > > > > > > > Good that it works. I suspect the only real difference is > > the use of > > > > ALPHA, which sets the transparency. Do mind the position of the > > > > ALPHA keyword and it's value, as these are important. > > > > > > > > Best, > > > > > > > > Tsjerk > > > > > > > > On Wed, Apr 23, 2008 at 8:08 PM, Dean Waldow > > <wal...@chem.plu.edu> wrote: > > > > > > > > > Hi Tsjerk, > > > > > > > > > > It works Great! Thanks so much. I'll have to study > > your code to > > > > > see > > > where I > > > > > was going wrong. > > > > > > > > > > Dean > > > > > > > > > > > > > > > On Apr 23, 2008, at 10:39 AM, Tsjerk Wassenaar wrote: > > > > > > > > > > > > > > > Hi Dean, > > > > > > > > > > Funny, really. Last week I was just playing around a bit with > > > > > creating boxes in pymol, e.g. to create a bounding box, and I > > > > > wanted to have it transparent. So here's a script, giving you a > > > > > function 'rect', which takes two tuples, specifying the > > far edges of the box: > > > > > > > > > > rect( [x0,y0,z0], [x1,y1,z1],name="box",rgbt=[1,1,0,0.5]) > > > > > > > > > > The rgbt argument specifies the color and transparency. > > Feel free > > > > > to go through the code to see how things are done (although you > > > > > won't hear me say it's perfect). In case you have any > > suggestions, > > > > > also feel free to contact me, either on or off list. > > > > > > > > > > I hope it helps. Cheers, > > > > > > > > > > Tsjerk > > > > > > > > > > On Wed, Apr 23, 2008 at 5:22 PM, Dean Waldow > > <wal...@chem.plu.edu> > > > wrote: > > > > > Hi Folks, > > > > > > > > > > I am very new to pymol and have been learning a lot about using > > > (mac)pymol. > > > > > However, I seem to be unable to make a box which is transparent > > > > > and has color. I have been able to make a box with the > > *.py script > > > > > below but > > > when I > > > > > do the ray tracing to get a nice image the box turns to grey / > > > > > black. I > > > have > > > > > also been able to to make prolate and oblate spheriods > > using ideas > > > > > from > > > the > > > > > pymol wiki. > > > > > > > > > > My eventual goal is to have about three slabs or boxes with > > > > > spheroids at > > > the > > > > > interface of these slabs and my pdb results from a monte carlo > > > simulation > > > > > where the spheriods highlight the changes in shape of my > > > > > copolymers at > > > the > > > > > interface. > > > > > > > > > > Has anyone succeeded in making colored transparent > > boxes? Or might > > > > > there > > > be > > > > > another strategy? > > > > > > > > > > Thanks, > > > > > > > > > > Dean Waldow > > > > > > > > > > Here is the script (modified from one that makes a > > bounding box I > > > believe) > > > > > that makes my current solid box which turns grey with I > > issue the > > > > > ray > > > > > command: > > > > > > > > > > > > > > > from pymol.cgo import * > > > > > from pymol import cmd > > > > > # > > > > > # SEGMENT 1 > > > > > box = [ > > > > > LINEWIDTH, 1.0, > > > > > BEGIN, VERTEX, > > > > > COLOR, 0.0, 0.0, 0.0, > > > > > > > > > > # Face 1 > > > > > VERTEX, 55.000, 55.000, 55.000, > > > > > VERTEX, 55.000, 5.000, 55.000, > > > > > VERTEX, 55.000, 5.000, 5.000, > > > > > > > > > > VERTEX, 55.000, 5.000, 5.000, > > > > > VERTEX, 55.000, 55.000, 5.000, > > > > > VERTEX, 55.000, 55.000, 55.000, > > > > > > > > > > # Face 2 > > > > > VERTEX, 5.000, 55.000, 55.000, > > > > > VERTEX, 5.000, 5.000, 55.000, > > > > > VERTEX, 5.000, 5.000, 5.000, > > > > > > > > > > VERTEX, 5.000, 5.000, 5.000, > > > > > VERTEX, 5.000, 55.000, 5.000, > > > > > VERTEX, 5.000, 55.000, 55.000, > > > > > > > > > > # Face 3 > > > > > VERTEX, 55.000, 55.000, 55.000, > > > > > VERTEX, 5.000, 55.000, 55.000, > > > > > VERTEX, 5.000, 55.000, 5.000, > > > > > > > > > > VERTEX, 5.000, 55.000, 5.000, > > > > > VERTEX, 55.000, 55.000, 5.000, > > > > > VERTEX, 55.000, 55.000, 55.000, > > > > > > > > > > # Face 4 > > > > > VERTEX, 55.000, 5.000, 55.000, > > > > > VERTEX, 5.000, 5.000, 55.000, > > > > > VERTEX, 5.000, 5.000, 5.000, > > > > > > > > > > VERTEX, 5.000, 5.000, 5.000, > > > > > VERTEX, 55.000, 5.000, 5.000, > > > > > VERTEX, 55.000, 5.000, 55.000, > > > > > > > > > > # Face 5 > > > > > VERTEX, 55.000, 55.000, 55.000, > > > > > VERTEX, 5.000, 55.000, 55.000, > > > > > VERTEX, 5.000, 5.000, 55.000, > > > > > > > > > > VERTEX, 5.000, 5.000, 55.000, > > > > > VERTEX, 55.000, 5.000, 55.000, > > > > > VERTEX, 55.000, 55.000, 55.000, > > > > > > > > > > # Face 6 > > > > > VERTEX, 55.000, 55.000, 5.000, > > > > > VERTEX, 5.000, 55.000, 5.000, > > > > > VERTEX, 5.000, 5.000, 5.000, > > > > > > > > > > VERTEX, 5.000, 5.000, 5.000, > > > > > VERTEX, 55.000, 5.000, 5.000, > > > > > VERTEX, 55.000, 55.000, 5.000, > > > > > > > > > > END > > > > > ] > > > > > > > > > > obj = box > > > > > > > > > > cmd.load_cgo(obj,'segment', 1) > > > > > > > > > > > > > > > > > > > > -- > > > > > > > > > > > > ------------------------------------------------------------------ > > > > > ------ > > > > > > > > > > Dean Waldow, Professor (253) 535-7533 > > > > > > > > > > Department of Chemistry (253) 536-5055 (FAX) > > > > > > > > > > Pacific Lutheran University wal...@chem.plu.edu > > > > > > > > > > Tacoma, WA 98447 USA > > http://www.chem.plu.edu/waldow/ > > > > > > > > > > > > ------------------------------------------------------------------ > > > > > ------ > > > > > > > > > > ---> CIRRUS and the Chemistry homepage: > > <http://www.chem.plu.edu/> > > > > > ---> <---- > > > > > > > > > > > > ------------------------------------------------------------------ > > > > > ------ > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > ---------------------------------------------------------------------- > > > --- > > > > > This SF.net email is sponsored by the 2008 JavaOne(SM) > > Conference > > > > > Don't miss this year's exciting event. There's still > > time to save $100. > > > > > Use priority code J8TL2D2. > > > > > > > > > > > > > > > http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com > > > /javaone > > > > > _______________________________________________ > > > > > PyMOL-users mailing list > > > > > PyMOL-users@lists.sourceforge.net > > > > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > Tsjerk A. Wassenaar, Ph.D. > > > > > Junior UD (post-doc) > > > > > Biomolecular NMR, Bijvoet Center > > > > > Utrecht University > > > > > Padualaan 8 > > > > > 3584 CH Utrecht > > > > > The Netherlands > > > > > P: +31-30-2539931 > > > > > F: +31-30-2537623<rect.py> > > > > > > > > > > -- > > > > > > > > > > > > > > > > > ------------------------------------------------------------------ > > > > > ------ > > > > > > > > > > Dean Waldow, Professor (253) 535-7533 > > > > > > > > > > Department of Chemistry (253) 536-5055 (FAX) > > > > > > > > > > Pacific Lutheran University wal...@chem.plu.edu > > > > > > > > > > Tacoma, WA 98447 USA > > http://www.chem.plu.edu/waldow/ > > > > > > > > > > > > ------------------------------------------------------------------ > > > > > ------ > > > > > > > > > > ---> CIRRUS and the Chemistry homepage: > > <http://www.chem.plu.edu/> > > > > > ---> <---- > > > > > > > > > > > > ------------------------------------------------------------------ > > > > > ------ > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > Tsjerk A. Wassenaar, Ph.D. > > > > Junior UD (post-doc) > > > > Biomolecular NMR, Bijvoet Center > > > > Utrecht University > > > > Padualaan 8 > > > > 3584 CH Utrecht > > > > The Netherlands > > > > P: +31-30-2539931 > > > > F: +31-30-2537623 > > > > > > > > > > > > > > > > > > -- > > Tsjerk A. Wassenaar, Ph.D. > > Junior UD (post-doc) > > Biomolecular NMR, Bijvoet Center > > Utrecht University > > Padualaan 8 > > 3584 CH Utrecht > > The Netherlands > > P: +31-30-2539931 > > F: +31-30-2537623 > > > > -------------------------------------------------------------- > > > > ----------- > > This SF.net email is sponsored by the 2008 JavaOne(SM) > > Conference Don't miss this year's exciting event. There's > > still time to save $100. > > Use priority code J8TL2D2. > > http://ad.doubleclick.net/clk;198757673;13503038;p?http://java > .sun.com/javaone > > _______________________________________________ > > PyMOL-users mailing list > > PyMOL-users@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623
