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From: Dean W. <wa...@ch...> - 2008-04-23 15:23:34
|
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/> <----
------------------------------------------------------------------------
|
|
From: Tsjerk W. <ts...@gm...> - 2008-04-23 17:39:23
Attachments:
rect.py
|
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 |
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From: Dean W. <wa...@ch...> - 2008-04-23 18:11:05
|
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/> <---- ------------------------------------------------------------------------ |
|
From: Tsjerk W. <ts...@gm...> - 2008-04-24 13:56:32
|
Hi Dean, 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. 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 <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 |
|
From: DeLano S. <de...@de...> - 2008-04-24 16:23:54
|
> 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 > <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 > > -------------------------------------------------------------- > ----------- > 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 |
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From: Tsjerk W. <ts...@gm...> - 2008-04-24 17:15:46
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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 <de...@de...> 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 > > <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 > > > > -------------------------------------------------------------- > > > > ----------- > > 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 |
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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/> <---- ------------------------------------------------------------------------ |
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