Re: [chimerax-users] [Chimera-users] Autodock Vina plugin
Hi, I've been trying out ChimeraX v. 1.3 vs. Chimera v. 1.15 on the same computer and notice that the publication presets for Chimera (Preset publication 1) look to my eye far superior to the preset publication setting for ChimeraX. This is really noticeable when comparing side by side at 400% enlargement. The attached tif file was created from powerpoint at 300 dpi comparing the same set of pdbs superimposed using Matchmaker from similar vantage points (but colored differently) and saved as tiff files or copied using screenshots. To my eye, the screenshot of the Chimera image is better than the ChimeraX tiff and the Chimera tiff is the best of all. The alpha helices in ChimeraX look washed out and the shading is less defined. Is there any way to get comparable images to the Chimera preset publication 1 in ChimeraX? Also, although these images are from the same pdb sources, it seems that the backbone ribbon is much more jagged in ChimeraX. Is there more smoothing in the algorithm for Chimera? Not that it matters that much, but I'd just like to know. Thanks, Ralph Loring Associate Professor of Pharmacology Department of Pharmaceutical Sciences 166 TF Northeastern University 360 Huntington Avenue Boston, MA 02115 USA 617-373-3216 office 617-373-8886 fax r.loring@northeastern.edu
On Wed, Jan 5, 2022 at 12:13 PM Elaine Meng via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
You can remove hydrogens from the protein part only using Chimera (or ChimeraX) command:
delete H & protein
That would not include the water, however. You could also do this to remove water hydrogens:
delete H & solvent
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 5, 2022, at 12:50 AM, Enrico Martinez via Chimera-users <
chimera-users@cgl.ucsf.edu> wrote:
[...] one question: how I could remove only protein's Hydrogen atoms using Chimera's command line (keeping them on the ligand)???
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
Hi Ralph, It looks like the difference between the pub presets of Chimera and ChimeraX is all in the silhouette edges (black outlines), and that what you want is for them to be thicker and drawn in more places. These are the silhouette linewidth and depthJump parameters, which can be controlled in the ChimeraX "graphics silhouettes" command: https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#silhouettes
E.g. to make them fatter in ChimeraX
graphics silhouettes width 3
....and drawn in more places
graphics silhouettes depthJump 0.01
As I understand it, the reason the preset can't make these exactly 1-to-1 between the two programs in all situations is that it depends on the graphics windowsize, the size of the image that you save, and depth (Z-range) of the data that is shown, since depth jump is a fraction of that rather than a specific distance. So if you had a smaller protein it would be better about drawing the silhouettes around individual parts of the ribbon.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 5, 2022, at 9:56 AM, Ralph Loring rhloring@gmail.com wrote:
Hi, I've been trying out ChimeraX v. 1.3 vs. Chimera v. 1.15 on the same computer and notice that the publication presets for Chimera (Preset publication 1) look to my eye far superior to the preset publication setting for ChimeraX. This is really noticeable when comparing side by side at 400% enlargement. The attached tif file was created from powerpoint at 300 dpi comparing the same set of pdbs superimposed using Matchmaker from similar vantage points (but colored differently) and saved as tiff files or copied using screenshots. To my eye, the screenshot of the Chimera image is better than the ChimeraX tiff and the Chimera tiff is the best of all. The alpha helices in ChimeraX look washed out and the shading is less defined. Is there any way to get comparable images to the Chimera preset publication 1 in ChimeraX? Also, although these images are from the same pdb sources, it seems that the backbone ribbon is much more jagged in ChimeraX. Is there more smoothing in the algorithm for Chimera? Not that it matters that much, but I'd just like to know. Thanks, Ralph Loring Associate Professor of Pharmacology Department of Pharmaceutical Sciences 166 TF Northeastern University 360 Huntington Avenue Boston, MA 02115 USA 617-373-3216 office 617-373-8886 fax r.loring@northeastern.edu
I should also mention that if you have a favorite set of parameters that gives you consistently good results, instead of having to repeatedly type those same commands, you could make them into your own custom preset.
For example, you could put a series of commands in a plain-text ".cxc" file, e.g.
preset pub graphics silhouettes width 3 graphics silhouettes depthJump 0.01
... and then in the Preferences, category: Startup, tell ChimeraX where to find this file. If you named it mypub.cxc then it would put an entry in the menu: Presets... Custom... Mypub
Explanation of custom presets: https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 5, 2022, at 10:17 AM, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Ralph, It looks like the difference between the pub presets of Chimera and ChimeraX is all in the silhouette edges (black outlines), and that what you want is for them to be thicker and drawn in more places. These are the silhouette linewidth and depthJump parameters, which can be controlled in the ChimeraX "graphics silhouettes" command: https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#silhouettes
E.g. to make them fatter in ChimeraX
graphics silhouettes width 3
....and drawn in more places
graphics silhouettes depthJump 0.01
As I understand it, the reason the preset can't make these exactly 1-to-1 between the two programs in all situations is that it depends on the graphics windowsize, the size of the image that you save, and depth (Z-range) of the data that is shown, since depth jump is a fraction of that rather than a specific distance. So if you had a smaller protein it would be better about drawing the silhouettes around individual parts of the ribbon.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 5, 2022, at 9:56 AM, Ralph Loring rhloring@gmail.com wrote:
Hi, I've been trying out ChimeraX v. 1.3 vs. Chimera v. 1.15 on the same computer and notice that the publication presets for Chimera (Preset publication 1) look to my eye far superior to the preset publication setting for ChimeraX. This is really noticeable when comparing side by side at 400% enlargement. The attached tif file was created from powerpoint at 300 dpi comparing the same set of pdbs superimposed using Matchmaker from similar vantage points (but colored differently) and saved as tiff files or copied using screenshots. To my eye, the screenshot of the Chimera image is better than the ChimeraX tiff and the Chimera tiff is the best of all. The alpha helices in ChimeraX look washed out and the shading is less defined. Is there any way to get comparable images to the Chimera preset publication 1 in ChimeraX? Also, although these images are from the same pdb sources, it seems that the backbone ribbon is much more jagged in ChimeraX. Is there more smoothing in the algorithm for Chimera? Not that it matters that much, but I'd just like to know. Thanks, Ralph Loring Associate Professor of Pharmacology Department of Pharmaceutical Sciences 166 TF Northeastern University 360 Huntington Avenue Boston, MA 02115 USA 617-373-3216 office 617-373-8886 fax r.loring@northeastern.edu
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Ralph,
It looks like the Chimera 'publication 1' preset turns off depth cueing, while the ChimeraX 'publication' preset does not change depth cueing (it looks like it's turned on in these images). Depth cueing could be contributing to the washed-out look of features that are farther from the screen. You can turn it off in ChimeraX with
lighting depthCue false
It might also have something to do with lighting intensity. I'm not sure how Chimera and ChimeraX differ in that regard.
The Chimera models also look more reflective. You can try running
material shiny
to see if that looks better.
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/lighting.html
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/material.html
Best,
Tony ________________________________ From: ChimeraX-users chimerax-users-bounces@cgl.ucsf.edu on behalf of Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu Sent: Wednesday, January 5, 2022 1:17 PM To: Ralph Loring rhloring@gmail.com Cc: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu; chimera-users@cgl.ucsf.edu List chimera-users@cgl.ucsf.edu Subject: [chimerax-users] pub preset: Chimera vs. ChimeraX silhouettes
[EXTERNAL SENDER - PROCEED CAUTIOUSLY]
Hi Ralph, It looks like the difference between the pub presets of Chimera and ChimeraX is all in the silhouette edges (black outlines), and that what you want is for them to be thicker and drawn in more places. These are the silhouette linewidth and depthJump parameters, which can be controlled in the ChimeraX "graphics silhouettes" command: https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#silhouettes
E.g. to make them fatter in ChimeraX
graphics silhouettes width 3
....and drawn in more places
graphics silhouettes depthJump 0.01
As I understand it, the reason the preset can't make these exactly 1-to-1 between the two programs in all situations is that it depends on the graphics windowsize, the size of the image that you save, and depth (Z-range) of the data that is shown, since depth jump is a fraction of that rather than a specific distance. So if you had a smaller protein it would be better about drawing the silhouettes around individual parts of the ribbon.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 5, 2022, at 9:56 AM, Ralph Loring rhloring@gmail.com wrote:
Hi, I've been trying out ChimeraX v. 1.3 vs. Chimera v. 1.15 on the same computer and notice that the publication presets for Chimera (Preset publication 1) look to my eye far superior to the preset publication setting for ChimeraX. This is really noticeable when comparing side by side at 400% enlargement. The attached tif file was created from powerpoint at 300 dpi comparing the same set of pdbs superimposed using Matchmaker from similar vantage points (but colored differently) and saved as tiff files or copied using screenshots. To my eye, the screenshot of the Chimera image is better than the ChimeraX tiff and the Chimera tiff is the best of all. The alpha helices in ChimeraX look washed out and the shading is less defined. Is there any way to get comparable images to the Chimera preset publication 1 in ChimeraX? Also, although these images are from the same pdb sources, it seems that the backbone ribbon is much more jagged in ChimeraX. Is there more smoothing in the algorithm for Chimera? Not that it matters that much, but I'd just like to know. Thanks, Ralph Loring Associate Professor of Pharmacology Department of Pharmaceutical Sciences 166 TF Northeastern University 360 Huntington Avenue Boston, MA 02115 USA 617-373-3216 office 617-373-8886 fax r.loring@northeastern.edu
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Tony and Elaine, These are very helpful suggestions and with some fiddling, I was able to get comparable results between ChimeraX and Chimera publication preset 1. However, it seems that ChimeraX is more sensitive to image size and so more fiddling may be required depending on the size of the image. These are the settings I ended up with (but others may like different looks):
graphics silhouettes width 2
graphics silhouettes depthJump 0.007
lighting depthCue false The default setting for material seemed fine. I'll try to set this up as a custom preset as you indicated. Thanks! Ralph
On Wed, Jan 5, 2022 at 1:43 PM Anthony James Schaefer tony.schaefer@uga.edu wrote:
Ralph,
It looks like the Chimera 'publication 1' preset turns off depth cueing, while the ChimeraX 'publication' preset does not change depth cueing (it looks like it's turned on in these images). Depth cueing could be contributing to the washed-out look of features that are farther from the screen. You can turn it off in ChimeraX with
lighting depthCue false
It might also have something to do with lighting intensity. I'm not sure how Chimera and ChimeraX differ in that regard.
The Chimera models also look more reflective. You can try running
material shiny
to see if that looks better.
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/lighting.html
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/material.html
Best,
Tony
*From:* ChimeraX-users chimerax-users-bounces@cgl.ucsf.edu on behalf of Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu *Sent:* Wednesday, January 5, 2022 1:17 PM *To:* Ralph Loring rhloring@gmail.com *Cc:* chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu; chimera-users@cgl.ucsf.edu List chimera-users@cgl.ucsf.edu *Subject:* [chimerax-users] pub preset: Chimera vs. ChimeraX silhouettes
[EXTERNAL SENDER - PROCEED CAUTIOUSLY]
Hi Ralph, It looks like the difference between the pub presets of Chimera and ChimeraX is all in the silhouette edges (black outlines), and that what you want is for them to be thicker and drawn in more places. These are the silhouette linewidth and depthJump parameters, which can be controlled in the ChimeraX "graphics silhouettes" command: < https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#silhouettes
E.g. to make them fatter in ChimeraX
graphics silhouettes width 3
....and drawn in more places
graphics silhouettes depthJump 0.01
As I understand it, the reason the preset can't make these exactly 1-to-1 between the two programs in all situations is that it depends on the graphics windowsize, the size of the image that you save, and depth (Z-range) of the data that is shown, since depth jump is a fraction of that rather than a specific distance. So if you had a smaller protein it would be better about drawing the silhouettes around individual parts of the ribbon.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 5, 2022, at 9:56 AM, Ralph Loring rhloring@gmail.com wrote:
Hi, I've been trying out ChimeraX v. 1.3 vs. Chimera v. 1.15 on the same
computer and notice that the publication presets for Chimera (Preset publication 1) look to my eye far superior to the preset publication setting for ChimeraX. This is really noticeable when comparing side by side at 400% enlargement. The attached tif file was created from powerpoint at 300 dpi comparing the same set of pdbs superimposed using Matchmaker from similar vantage points (but colored differently) and saved as tiff files or copied using screenshots. To my eye, the screenshot of the Chimera image is better than the ChimeraX tiff and the Chimera tiff is the best of all. The alpha helices in ChimeraX look washed out and the shading is less defined. Is there any way to get comparable images to the Chimera preset publication 1 in ChimeraX?
Also, although these images are from the same pdb sources, it seems that
the backbone ribbon is much more jagged in ChimeraX. Is there more smoothing in the algorithm for Chimera? Not that it matters that much, but I'd just like to know.
Thanks, Ralph Loring Associate Professor of Pharmacology Department of Pharmaceutical Sciences 166 TF Northeastern University 360 Huntington Avenue Boston, MA 02115 USA 617-373-3216 office 617-373-8886 fax r.loring@northeastern.edu
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
After some internal discussion, we've split the publication preset into two in order to cover more use cases:
publication 1 (silhouettes) publication 2 (depth-cued)
A shortcut you may not know about is that you can refer to a preset by any unique text in its name, so both "preset 1" and "preset sil" would run the first preset. These presets will be in tomorrow's daily build. They don't adjust silhouette (or depth-cue) parameters, just whether they are off or on.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jan 5, 2022, at 12:02 PM, Ralph Loring via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Tony and Elaine, These are very helpful suggestions and with some fiddling, I was able to get comparable results between ChimeraX and Chimera publication preset 1. However, it seems that ChimeraX is more sensitive to image size and so more fiddling may be required depending on the size of the image. These are the settings I ended up with (but others may like different looks): graphics silhouettes width 2
graphics silhouettes depthJump 0.007
lighting depthCue false
The default setting for material seemed fine. I'll try to set this up as a custom preset as you indicated. Thanks! Ralph
On Wed, Jan 5, 2022 at 1:43 PM Anthony James Schaefer <tony.schaefer@uga.edu mailto:tony.schaefer@uga.edu> wrote: Ralph,
It looks like the Chimera 'publication 1' preset turns off depth cueing, while the ChimeraX 'publication' preset does not change depth cueing (it looks like it's turned on in these images). Depth cueing could be contributing to the washed-out look of features that are farther from the screen. You can turn it off in ChimeraX with
lighting depthCue false
It might also have something to do with lighting intensity. I'm not sure how Chimera and ChimeraX differ in that regard.
The Chimera models also look more reflective. You can try running
material shiny
to see if that looks better.
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/lighting.html https://www.cgl.ucsf.edu/chimerax/docs/user/commands/lighting.html
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/material.html https://www.cgl.ucsf.edu/chimerax/docs/user/commands/material.html
Best,
Tony From: ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu mailto:chimerax-users-bounces@cgl.ucsf.edu> on behalf of Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> Sent: Wednesday, January 5, 2022 1:17 PM To: Ralph Loring <rhloring@gmail.com mailto:rhloring@gmail.com> Cc: chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu>; chimera-users@cgl.ucsf.edu mailto:chimera-users@cgl.ucsf.edu List <chimera-users@cgl.ucsf.edu mailto:chimera-users@cgl.ucsf.edu> Subject: [chimerax-users] pub preset: Chimera vs. ChimeraX silhouettes
[EXTERNAL SENDER - PROCEED CAUTIOUSLY]
Hi Ralph, It looks like the difference between the pub presets of Chimera and ChimeraX is all in the silhouette edges (black outlines), and that what you want is for them to be thicker and drawn in more places. These are the silhouette linewidth and depthJump parameters, which can be controlled in the ChimeraX "graphics silhouettes" command: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#silhouettes https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#silhouettes>
E.g. to make them fatter in ChimeraX
graphics silhouettes width 3
....and drawn in more places
graphics silhouettes depthJump 0.01
As I understand it, the reason the preset can't make these exactly 1-to-1 between the two programs in all situations is that it depends on the graphics windowsize, the size of the image that you save, and depth (Z-range) of the data that is shown, since depth jump is a fraction of that rather than a specific distance. So if you had a smaller protein it would be better about drawing the silhouettes around individual parts of the ribbon.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 5, 2022, at 9:56 AM, Ralph Loring <rhloring@gmail.com mailto:rhloring@gmail.com> wrote:
Hi, I've been trying out ChimeraX v. 1.3 vs. Chimera v. 1.15 on the same computer and notice that the publication presets for Chimera (Preset publication 1) look to my eye far superior to the preset publication setting for ChimeraX. This is really noticeable when comparing side by side at 400% enlargement. The attached tif file was created from powerpoint at 300 dpi comparing the same set of pdbs superimposed using Matchmaker from similar vantage points (but colored differently) and saved as tiff files or copied using screenshots. To my eye, the screenshot of the Chimera image is better than the ChimeraX tiff and the Chimera tiff is the best of all. The alpha helices in ChimeraX look washed out and the shading is less defined. Is there any way to get comparable images to the Chimera preset publication 1 in ChimeraX? Also, although these images are from the same pdb sources, it seems that the backbone ribbon is much more jagged in ChimeraX. Is there more smoothing in the algorithm for Chimera? Not that it matters that much, but I'd just like to know. Thanks, Ralph Loring Associate Professor of Pharmacology Department of Pharmaceutical Sciences 166 TF Northeastern University 360 Huntington Avenue Boston, MA 02115 USA 617-373-3216 office 617-373-8886 fax r.loring@northeastern.edu mailto:r.loring@northeastern.edu
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Awesome, thanks!
On Wed, Jan 5, 2022 at 6:52 PM Eric Pettersen pett@cgl.ucsf.edu wrote:
After some internal discussion, we've split the publication preset into two in order to cover more use cases:
publication 1 (silhouettes) publication 2 (depth-cued)
A shortcut you may not know about is that you can refer to a preset by any unique text in its name, so both "preset 1" and "preset sil" would run the first preset. These presets will be in tomorrow's daily build. They don't adjust silhouette (or depth-cue) parameters, just whether they are off or on.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jan 5, 2022, at 12:02 PM, Ralph Loring via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi Tony and Elaine, These are very helpful suggestions and with some fiddling, I was able to get comparable results between ChimeraX and Chimera publication preset 1. However, it seems that ChimeraX is more sensitive to image size and so more fiddling may be required depending on the size of the image. These are the settings I ended up with (but others may like different looks):
graphics silhouettes width 2
graphics silhouettes depthJump 0.007
lighting depthCue false The default setting for material seemed fine. I'll try to set this up as a custom preset as you indicated. Thanks! Ralph
On Wed, Jan 5, 2022 at 1:43 PM Anthony James Schaefer < tony.schaefer@uga.edu> wrote:
Ralph,
It looks like the Chimera 'publication 1' preset turns off depth cueing, while the ChimeraX 'publication' preset does not change depth cueing (it looks like it's turned on in these images). Depth cueing could be contributing to the washed-out look of features that are farther from the screen. You can turn it off in ChimeraX with
lighting depthCue false
It might also have something to do with lighting intensity. I'm not sure how Chimera and ChimeraX differ in that regard.
The Chimera models also look more reflective. You can try running
material shiny
to see if that looks better.
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/lighting.html
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/material.html
Best,
Tony
*From:* ChimeraX-users chimerax-users-bounces@cgl.ucsf.edu on behalf of Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu *Sent:* Wednesday, January 5, 2022 1:17 PM *To:* Ralph Loring rhloring@gmail.com *Cc:* chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu; chimera-users@cgl.ucsf.edu List chimera-users@cgl.ucsf.edu *Subject:* [chimerax-users] pub preset: Chimera vs. ChimeraX silhouettes
[EXTERNAL SENDER - PROCEED CAUTIOUSLY]
Hi Ralph, It looks like the difference between the pub presets of Chimera and ChimeraX is all in the silhouette edges (black outlines), and that what you want is for them to be thicker and drawn in more places. These are the silhouette linewidth and depthJump parameters, which can be controlled in the ChimeraX "graphics silhouettes" command: < https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#silhouettes
E.g. to make them fatter in ChimeraX
graphics silhouettes width 3
....and drawn in more places
graphics silhouettes depthJump 0.01
As I understand it, the reason the preset can't make these exactly 1-to-1 between the two programs in all situations is that it depends on the graphics windowsize, the size of the image that you save, and depth (Z-range) of the data that is shown, since depth jump is a fraction of that rather than a specific distance. So if you had a smaller protein it would be better about drawing the silhouettes around individual parts of the ribbon.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 5, 2022, at 9:56 AM, Ralph Loring rhloring@gmail.com wrote:
Hi, I've been trying out ChimeraX v. 1.3 vs. Chimera v. 1.15 on the same
computer and notice that the publication presets for Chimera (Preset publication 1) look to my eye far superior to the preset publication setting for ChimeraX. This is really noticeable when comparing side by side at 400% enlargement. The attached tif file was created from powerpoint at 300 dpi comparing the same set of pdbs superimposed using Matchmaker from similar vantage points (but colored differently) and saved as tiff files or copied using screenshots. To my eye, the screenshot of the Chimera image is better than the ChimeraX tiff and the Chimera tiff is the best of all. The alpha helices in ChimeraX look washed out and the shading is less defined. Is there any way to get comparable images to the Chimera preset publication 1 in ChimeraX?
Also, although these images are from the same pdb sources, it seems
that the backbone ribbon is much more jagged in ChimeraX. Is there more smoothing in the algorithm for Chimera? Not that it matters that much, but I'd just like to know.
Thanks, Ralph Loring Associate Professor of Pharmacology Department of Pharmaceutical Sciences 166 TF Northeastern University 360 Huntington Avenue Boston, MA 02115 USA 617-373-3216 office 617-373-8886 fax r.loring@northeastern.edu
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi, I'm updating protein problems for the upcoming semester and translating the instructions from Chimera to ChimeraX. I can't find the Ramachandran plot in ChimeraX. Is there an add-in that I'm missing? I don't see it mentioned in the guide and can't find it in the help section. If it's not there, is there a reason it was dropped? The students find it instructive. Thanks, Ralph
Ralph H. Loring Associate Professor of Pharmacology Department of Pharmaceutical Sciences 166 TF Northeastern University 360 Huntington Avenue Boston, MA 02115 USA 617-373-3216 office 617-373-8886 fax r.loring@northeastern.edu
On Wed, Jan 5, 2022 at 12:56 PM Ralph Loring rhloring@gmail.com wrote:
Hi, I've been trying out ChimeraX v. 1.3 vs. Chimera v. 1.15 on the same computer and notice that the publication presets for Chimera (Preset publication 1) look to my eye far superior to the preset publication setting for ChimeraX. This is really noticeable when comparing side by side at 400% enlargement. The attached tif file was created from powerpoint at 300 dpi comparing the same set of pdbs superimposed using Matchmaker from similar vantage points (but colored differently) and saved as tiff files or copied using screenshots. To my eye, the screenshot of the Chimera image is better than the ChimeraX tiff and the Chimera tiff is the best of all. The alpha helices in ChimeraX look washed out and the shading is less defined. Is there any way to get comparable images to the Chimera preset publication 1 in ChimeraX? Also, although these images are from the same pdb sources, it seems that the backbone ribbon is much more jagged in ChimeraX. Is there more smoothing in the algorithm for Chimera? Not that it matters that much, but I'd just like to know. Thanks, Ralph Loring Associate Professor of Pharmacology Department of Pharmaceutical Sciences 166 TF Northeastern University 360 Huntington Avenue Boston, MA 02115 USA 617-373-3216 office 617-373-8886 fax r.loring@northeastern.edu
On Wed, Jan 5, 2022 at 12:13 PM Elaine Meng via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
You can remove hydrogens from the protein part only using Chimera (or ChimeraX) command:
delete H & protein
That would not include the water, however. You could also do this to remove water hydrogens:
delete H & solvent
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 5, 2022, at 12:50 AM, Enrico Martinez via Chimera-users <
chimera-users@cgl.ucsf.edu> wrote:
[...] one question: how I could remove only protein's Hydrogen atoms using Chimera's command line (keeping them on the ligand)???
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
Hi Ralph, A missing tool (something in Chimera but not ChimeraX) should not be interpreted as intentionally chosen to be dropped... instead we may not have had time yet to add it. It's certainly fine to ask on this mailing list, and good for us to hear which features users are most eager to have in ChimeraX.
Since ChimeraX is built using entirely different frameworks than Chimera, tools need to be reimplemented mostly from scratch rather than simply copied and slotted in. We have somewhat limited manpower. Consider that Chimera tools were added over 15-20 years!
As for Ramachandran maps specifically, there may be something like that in the ISOLDE plugin. ISOLDE is generally for rather advanced users building atomic structures into cryoEM density, but I can investigate whether it could simply be used to show a Ramachandran map for protein structures and how difficult that might be for somebody at the student level.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 12, 2022, at 5:41 AM, Ralph Loring rhloring@gmail.com wrote:
Hi, I'm updating protein problems for the upcoming semester and translating the instructions from Chimera to ChimeraX. I can't find the Ramachandran plot in ChimeraX. Is there an add-in that I'm missing? I don't see it mentioned in the guide and can't find it in the help section. If it's not there, is there a reason it was dropped? The students find it instructive. Thanks, Ralph
Ralph H. Loring Associate Professor of Pharmacology Department of Pharmaceutical Sciences 166 TF Northeastern University 360 Huntington Avenue Boston, MA 02115 USA 617-373-3216 office 617-373-8886 fax r.loring@northeastern.edu
Hi all,
Yep - ISOLDE certainly does have a Ramachandran plot (a rather pretty one, I like to think!). See https://isolde.cimr.cam.ac.uk/static/isolde/doc/tools/gui/validate.html#the-....
Best regards, Tristan ________________________________ From: ChimeraX-users chimerax-users-bounces@cgl.ucsf.edu on behalf of Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu Sent: 12 January 2022 16:50 To: Ralph Loring rhloring@gmail.com Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu; chimera-users@cgl.ucsf.edu List chimera-users@cgl.ucsf.edu Subject: [chimerax-users] Ramachandran Map in ChimeraX?
Hi Ralph, A missing tool (something in Chimera but not ChimeraX) should not be interpreted as intentionally chosen to be dropped... instead we may not have had time yet to add it. It's certainly fine to ask on this mailing list, and good for us to hear which features users are most eager to have in ChimeraX.
Since ChimeraX is built using entirely different frameworks than Chimera, tools need to be reimplemented mostly from scratch rather than simply copied and slotted in. We have somewhat limited manpower. Consider that Chimera tools were added over 15-20 years!
As for Ramachandran maps specifically, there may be something like that in the ISOLDE plugin. ISOLDE is generally for rather advanced users building atomic structures into cryoEM density, but I can investigate whether it could simply be used to show a Ramachandran map for protein structures and how difficult that might be for somebody at the student level.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 12, 2022, at 5:41 AM, Ralph Loring rhloring@gmail.com wrote:
Hi, I'm updating protein problems for the upcoming semester and translating the instructions from Chimera to ChimeraX. I can't find the Ramachandran plot in ChimeraX. Is there an add-in that I'm missing? I don't see it mentioned in the guide and can't find it in the help section. If it's not there, is there a reason it was dropped? The students find it instructive. Thanks, Ralph
Ralph H. Loring Associate Professor of Pharmacology Department of Pharmaceutical Sciences 166 TF Northeastern University 360 Huntington Avenue Boston, MA 02115 USA 617-373-3216 office 617-373-8886 fax r.loring@northeastern.edu
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Thanks Tristan! Unfortunately, the students tell me that the 1 GB size of ChimeraX is about what their laptops can handle, so I'm reluctant to require them to install another program to do a small part of a larger exercise. Hopefully ChimeraX will have a Ramachandran plot at some point in the future, but I'll have other things for the students to do this year. Ralph
On Wed, Jan 12, 2022 at 11:55 AM Tristan Croll tic20@cam.ac.uk wrote:
Hi all,
Yep - ISOLDE certainly does have a Ramachandran plot (a rather pretty one, I like to think!). See https://isolde.cimr.cam.ac.uk/static/isolde/doc/tools/gui/validate.html#the-... .
Best regards, Tristan
*From:* ChimeraX-users chimerax-users-bounces@cgl.ucsf.edu on behalf of Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu *Sent:* 12 January 2022 16:50 *To:* Ralph Loring rhloring@gmail.com *Cc:* ChimeraX Users Help chimerax-users@cgl.ucsf.edu; chimera-users@cgl.ucsf.edu List chimera-users@cgl.ucsf.edu *Subject:* [chimerax-users] Ramachandran Map in ChimeraX?
Hi Ralph, A missing tool (something in Chimera but not ChimeraX) should not be interpreted as intentionally chosen to be dropped... instead we may not have had time yet to add it. It's certainly fine to ask on this mailing list, and good for us to hear which features users are most eager to have in ChimeraX.
Since ChimeraX is built using entirely different frameworks than Chimera, tools need to be reimplemented mostly from scratch rather than simply copied and slotted in. We have somewhat limited manpower. Consider that Chimera tools were added over 15-20 years!
As for Ramachandran maps specifically, there may be something like that in the ISOLDE plugin. ISOLDE is generally for rather advanced users building atomic structures into cryoEM density, but I can investigate whether it could simply be used to show a Ramachandran map for protein structures and how difficult that might be for somebody at the student level.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 12, 2022, at 5:41 AM, Ralph Loring rhloring@gmail.com wrote:
Hi, I'm updating protein problems for the upcoming semester and
translating the instructions from Chimera to ChimeraX. I can't find the Ramachandran plot in ChimeraX. Is there an add-in that I'm missing? I don't see it mentioned in the guide and can't find it in the help section. If it's not there, is there a reason it was dropped? The students find it instructive.
Thanks, Ralph
Ralph H. Loring Associate Professor of Pharmacology Department of Pharmaceutical Sciences 166 TF Northeastern University 360 Huntington Avenue Boston, MA 02115 USA 617-373-3216 office 617-373-8886 fax r.loring@northeastern.edu
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
No problem! For the record, ISOLDE adds another ~200 MB - but the installation is fairly trivial via the ChimeraX ToolShed (Tools/More Tools in the menu).
-- Tristan ________________________________ From: Ralph Loring rhloring@gmail.com Sent: 12 January 2022 17:17 To: Tristan Croll tic20@cam.ac.uk Cc: Tom Goddard via ChimeraX-users chimerax-users@cgl.ucsf.edu; Elaine Meng meng@cgl.ucsf.edu; chimera-users@cgl.ucsf.edu List chimera-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Ramachandran Map in ChimeraX?
Thanks Tristan! Unfortunately, the students tell me that the 1 GB size of ChimeraX is about what their laptops can handle, so I'm reluctant to require them to install another program to do a small part of a larger exercise. Hopefully ChimeraX will have a Ramachandran plot at some point in the future, but I'll have other things for the students to do this year. Ralph
On Wed, Jan 12, 2022 at 11:55 AM Tristan Croll <tic20@cam.ac.ukmailto:tic20@cam.ac.uk> wrote: Hi all,
Yep - ISOLDE certainly does have a Ramachandran plot (a rather pretty one, I like to think!). See https://isolde.cimr.cam.ac.uk/static/isolde/doc/tools/gui/validate.html#the-....
Best regards, Tristan ________________________________ From: ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edumailto:chimerax-users-bounces@cgl.ucsf.edu> on behalf of Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> Sent: 12 January 2022 16:50 To: Ralph Loring <rhloring@gmail.commailto:rhloring@gmail.com> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu>; chimera-users@cgl.ucsf.edumailto:chimera-users@cgl.ucsf.edu List <chimera-users@cgl.ucsf.edumailto:chimera-users@cgl.ucsf.edu> Subject: [chimerax-users] Ramachandran Map in ChimeraX?
Hi Ralph, A missing tool (something in Chimera but not ChimeraX) should not be interpreted as intentionally chosen to be dropped... instead we may not have had time yet to add it. It's certainly fine to ask on this mailing list, and good for us to hear which features users are most eager to have in ChimeraX.
Since ChimeraX is built using entirely different frameworks than Chimera, tools need to be reimplemented mostly from scratch rather than simply copied and slotted in. We have somewhat limited manpower. Consider that Chimera tools were added over 15-20 years!
As for Ramachandran maps specifically, there may be something like that in the ISOLDE plugin. ISOLDE is generally for rather advanced users building atomic structures into cryoEM density, but I can investigate whether it could simply be used to show a Ramachandran map for protein structures and how difficult that might be for somebody at the student level.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 12, 2022, at 5:41 AM, Ralph Loring <rhloring@gmail.commailto:rhloring@gmail.com> wrote:
Hi, I'm updating protein problems for the upcoming semester and translating the instructions from Chimera to ChimeraX. I can't find the Ramachandran plot in ChimeraX. Is there an add-in that I'm missing? I don't see it mentioned in the guide and can't find it in the help section. If it's not there, is there a reason it was dropped? The students find it instructive. Thanks, Ralph
Ralph H. Loring Associate Professor of Pharmacology Department of Pharmaceutical Sciences 166 TF Northeastern University 360 Huntington Avenue Boston, MA 02115 USA 617-373-3216 office 617-373-8886 fax r.loring@northeastern.edumailto:r.loring@northeastern.edu
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edumailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (5)
-
Anthony James Schaefer -
Elaine Meng -
Eric Pettersen -
Ralph Loring -
Tristan Croll