Hi Tsjerk,
The first issue I haven't encountered yet. I can't really say where that's coming from. As for the second issue, that is a known glitch. Pymol (at least up to 0.99rc6) has a problem with multiple transparencies in ray-tracing. 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.
I should get the current open source code and compile it (which I think it possible or purchase a compiled version - I have to look into these things) to see if any of these issues go away. I'll have to learn about povray to try that suggestion. I have tried putting spaces between the 'slabs' so to speak and there was no difference. I even put a very thin slab of a nearly opaque layer at the interface with the same result. As you suggest, I suspect it may be related to the one partially transparent object disappearing when viewed through the partially transparent slab or box.
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.
Sure... sorry I didn't notice. Thanks again, Dean
Best, TsjerkOn 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 littlelower than 1 that seems to got away.2) One other obj (spheroid) which I had set at transparent disappears whenviewed through a transparent box after issuing the ray command.3) Also when I issue the ray command, I can't see the shadowed boundarybetween 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 ofALPHA, which sets the transparency. Do mind the position of the ALPHAkeyword and it's value, as these are important. Best, TsjerkOn 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 seewhere Iwas 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', whichtakes 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 togo through the code to see how things are done (although you won'thear me say it's perfect). In case you have any suggestions, also feelfree 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 butwhen Ido the ray tracing to get a nice image the box turns to grey / black. Ihavealso been able to to make prolate and oblate spheriods using ideas fromthepymol wiki.My eventual goal is to have about three slabs or boxes with spheroids attheinterface of these slabs and my pdb results from a monte carlosimulationwhere the spheriods highlight the changes in shape of my copolymers attheinterface.Has anyone succeeded in making colored transparent boxes? Or might therebeanother strategy? Thanks, Dean Waldow Here is the script (modified from one that makes a bounding box Ibelieve)--------------------------------------------------------------------- ----that makes my current solid box which turns grey with I issue the raycommand: 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.eduTacoma, WA 98447 USA http://www.chem.plu.edu/ waldow/------------------------------------------------------------------- --------> CIRRUS and the Chemistry homepage: <http://www.chem.plu.edu/ > <----------------------------------------------------------------------- -----http://ad.doubleclick.net/clk;198757673;13503038;p?http:// java.sun.com/javaoneThis SF.net email is sponsored by the 2008 JavaOne(SM) ConferenceDon't miss this year's exciting event. There's still time to save $100.Use priority code J8TL2D2._______________________________________________ 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.eduTacoma, 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
-- ------------------------------------------------------------------------ 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/> <---- ------------------------------------------------------------------------
