We are having trouble saving images to look a certain way. More specifically we are trying to make an image with the distance from a residue to a metal ion shown. The problem arises when we save the image the 'thickness' of the distance line doesn't change on the actual saved image. So no matter what the thickness is on chimera the image will always show the distance line as being less thick. Thanks Eric -- Merlin Eric Hobbs | Graduate Student, Biochemistry and Biophysics | Raushel Lab | Rm 2510 | Texas A&M University | College Station, TX 77842 | 979-845-9163 | eric0zero@tamu.edu
Hi Eric, When you save an image with supersampling, initially the image is drawn larger and then sampled down to the final requested size. The problem is that graphics drivers have an upper bound on linewidth that can be drawn, so the line can only be so fat in the initial image, and then when it is sampled down, it is thinner. The image dialog will report (near the bottom) the maximum attainable linewidth in the final image given the requested image dimensions and the supersampling level. Decreasing the supersampling level and/or image dimensions will increase the attainable line fatness. Generally supersampling is nice because it smooths edges (pixel stairsteps less visible), so I would first see if 2x2 supersampling ameliorates the problem before turning it off entirely. For further discussion/explanation, see this previous post: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-December/004642.html> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Aug 7, 2012, at 2:09 PM, Hobbs, Merlin Eric wrote:
We are having trouble saving images to look a certain way. More specifically we are trying to make an image with the distance from a residue to a metal ion shown. The problem arises when we save the image the 'thickness' of the distance line doesn't change on the actual saved image. So no matter what the thickness is on chimera the image will always show the distance line as being less thick. Thanks Eric
Also some older Chimera versions simply didn't fatten up the lines when using supersampling so they always came out too thin independent of the upper limit on line thickness Elaine mentions. So if you are running an older Chimera or a daily build of any vintage you might try the latest production release 1.6.2. Tom
Hi Eric, When you save an image with supersampling, initially the image is drawn larger and then sampled down to the final requested size. The problem is that graphics drivers have an upper bound on linewidth that can be drawn, so the line can only be so fat in the initial image, and then when it is sampled down, it is thinner. The image dialog will report (near the bottom) the maximum attainable linewidth in the final image given the requested image dimensions and the supersampling level.
Decreasing the supersampling level and/or image dimensions will increase the attainable line fatness. Generally supersampling is nice because it smooths edges (pixel stairsteps less visible), so I would first see if 2x2 supersampling ameliorates the problem before turning it off entirely.
For further discussion/explanation, see this previous post: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-December/004642.html>
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 7, 2012, at 2:09 PM, Hobbs, Merlin Eric wrote:
We are having trouble saving images to look a certain way. More specifically we are trying to make an image with the distance from a residue to a metal ion shown. The problem arises when we save the image the 'thickness' of the distance line doesn't change on the actual saved image. So no matter what the thickness is on chimera the image will always show the distance line as being less thick. Thanks Eric
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Hi Eric, One further idea is that you can use sticks instead of lines, although the sticks can't be dotted or dashed. Distance monitors, H-bonds, metal complexation lines etc. are all pseudobonds. One way to change a pseudobond into a stick is to Ctrl-click to select it, then use the Selection Inspector (open by clicking the green magnifying glass icon near bottom right of Chimera window) to change "bond style" from "wire" to "stick". You can make the stick thinner by reducing the "radius" in that same dialog. All this can also be done with the "setattr" command, as explained in a recent post: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-August/007843.html> Elaine On Aug 8, 2012, at 11:39 AM, Tom Goddard wrote:
Also some older Chimera versions simply didn't fatten up the lines when using supersampling so they always came out too thin independent of the upper limit on line thickness Elaine mentions. So if you are running an older Chimera or a daily build of any vintage you might try the latest production release 1.6.2.
Tom
Hi Eric, When you save an image with supersampling, initially the image is drawn larger and then sampled down to the final requested size. The problem is that graphics drivers have an upper bound on linewidth that can be drawn, so the line can only be so fat in the initial image, and then when it is sampled down, it is thinner. The image dialog will report (near the bottom) the maximum attainable linewidth in the final image given the requested image dimensions and the supersampling level.
Decreasing the supersampling level and/or image dimensions will increase the attainable line fatness. Generally supersampling is nice because it smooths edges (pixel stairsteps less visible), so I would first see if 2x2 supersampling ameliorates the problem before turning it off entirely.
For further discussion/explanation, see this previous post: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-December/004642.html>
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 7, 2012, at 2:09 PM, Hobbs, Merlin Eric wrote:
We are having trouble saving images to look a certain way. More specifically we are trying to make an image with the distance from a residue to a metal ion shown. The problem arises when we save the image the 'thickness' of the distance line doesn't change on the actual saved image. So no matter what the thickness is on chimera the image will always show the distance line as being less thick. Thanks Eric
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Le 08/08/12 22:59, Elaine Meng a écrit :
Hi Eric, One further idea is that you can use sticks instead of lines, although the sticks can't be dotted or dashed.
Hi Elaine, Maybe a silly question, but could they be converted to bild objects? If so, perhaps a short script could produce something like dashed sticks (which is something we usually want) Best regards, -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR7257) CNRS, Aix-Marseille Université Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 mailto:miguel.ortiz-lombardia@afmb.univ-mrs.fr http://w2.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia
Hi Miguel, Not silly at all... but you would have to figure out the coordinates for each "dash" (cylinder) or "dot" (sphere). Also, these objects are not editable once created, so there may need to be some iterations of deletion and re-creation to get the proper size and color. Bild format description: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html> Another alternative is to use the "shape" command to make cylinder- or sphere-shaped surfaces. These are not shape/size editable but the colors can be changed easily. For example, open 2mnr; focus ions; rep wire shape sphere color yellow radius .1 center 27,4.8,17.4 modelid 2 shape sphere color yellow radius .1 center 27.5,5.3,17.6 modelid 2 shape sphere color yellow radius .1 center 28,5.8,17.8 modelid 2 color hot pink #2 <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html> Thanks for the thought, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Aug 9, 2012, at 1:19 AM, Miguel Ortiz Lombardía wrote:
Le 08/08/12 22:59, Elaine Meng a écrit :
Hi Eric, One further idea is that you can use sticks instead of lines, although the sticks can't be dotted or dashed.
Hi Elaine, Maybe a silly question, but could they be converted to bild objects? If so, perhaps a short script could produce something like dashed sticks (which is something we usually want) Best regards, Miguel
El 09/08/12 18:47, Elaine Meng escribió:
Hi Miguel, Not silly at all... but you would have to figure out the coordinates for each "dash" (cylinder) or "dot" (sphere). Also, these objects are not editable once created, so there may need to be some iterations of deletion and re-creation to get the proper size and color. Bild format description: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html>
In fact, all one would need is the coordinates of the end positions (the atoms engaged in the H-bond), a script could determine by interpolation the position of the dashes/spheres. Once one finds a combination to her taste for the distance between the interpolated points the script could be reused with the end poistions as the only input. The same goes for the color of the dashes or spheres. Perhaps all this could be done within the Chimera code (to directly recover the end-positions)?
Another alternative is to use the "shape" command to make cylinder- or sphere-shaped surfaces. These are not shape/size editable but the colors can be changed easily. For example,
open 2mnr; focus ions; rep wire shape sphere color yellow radius .1 center 27,4.8,17.4 modelid 2 shape sphere color yellow radius .1 center 27.5,5.3,17.6 modelid 2 shape sphere color yellow radius .1 center 28,5.8,17.8 modelid 2 color hot pink #2
That's also a nice possibility. Just need time to explore them!!! Best regards, -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR7257) CNRS, Aix-Marseille Université Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 mailto:miguel.ortiz-lombardia@afmb.univ-mrs.fr http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia
participants (5)
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Elaine Meng -
Hobbs, Merlin Eric -
Miguel Ortiz Lombardia -
Miguel Ortiz Lombardía
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Tom Goddard