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Re: [PyMOL] Making transparent boxes with colored surfaces?
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From: Dean W. <wa...@ch...> - 2008-04-24 15:38:28
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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, > > Tsjerk > > On Thu, Apr 24, 2008 at 3:41 PM, Dean Waldow <wa...@ch...> > 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 >>> <wa...@ch...> 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 <wa...@ch...> >> 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 wa...@ch... >>>> >>>> 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 >>>> PyM...@li... >>>> 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 wa...@ch... >>>> >>>> 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 -- ------------------------------------------------------------------------ Dean Waldow, Professor (253) 535-7533 Department of Chemistry (253) 536-5055 (FAX) Pacific Lutheran University wa...@ch... Tacoma, WA 98447 USA http://www.chem.plu.edu/waldow/ ------------------------------------------------------------------------ ---> CIRRUS and the Chemistry homepage: <http://www.chem.plu.edu/> <---- ------------------------------------------------------------------------ |