![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
#2978 closed defect (fixed)
Side view affects image saving
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | Greg Couch | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Windows-10-10.0.18362 ChimeraX Version: 0.93 (2020-03-19) Description I was using ChimeraX 0.92 for making figures in my lab PC without issues (specs below). I now have to work from home and use my lab PC remotely. I noticed that suddenly, when I control the ChimeraX session remotely, the images rendered with the same command are lower quality than normal (I'm attaching a comparison). I thought that it might be a connection problem, so I downloaded the last ChimeraX version in this laptop. For two days it worked normally (meaning that the images were saved at expected quality after opening ChimeraX session saved in the other PC). Suddenly today, the same problem started to happen in my laptop. After playing around, I noticed that the problem occurs when I open the Side View panel, change the view, and then save. If I instead modify the view, save the session, close the program, open the session and save directly (without opening the side view panel) the quality is normal. So: open session --> change view with side view --> save = image quality low; change view with side view --> save session --> close session --> open session --> save = image quality normal. This is the command I'm using: save C:\Users\Lucas\Desktop\sideview.png transparentBackground true supersample 3 The behaviour on my lab PC is not affected by this (it doesn't matter what I do, it is saving them at lower quality). I hope my description is legible. Thanks a lot in advance for your help. Log: UCSF ChimeraX version: 0.93 (2020-03-19) © 2016-2020 Regents of the University of California. All rights reserved. > open > C:\Users\Lucas\Desktop\ChimeraX_sessions\rheb_cartoon_activesite_zoom.cxs > format session Log from Thu Mar 26 11:07:41 2020UCSF ChimeraX version: 0.93 (2020-03-19) © 2016-2020 Regents of the University of California. All rights reserved. > open > C:\Users\Lucas\Desktop\ChimeraX_sessions\rheb_cartoon_activesite_zoom.cxs > format session Log from Thu Mar 26 10:48:08 2020UCSF ChimeraX version: 0.93 (2020-03-19) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open C:\Users\Lucas\Desktop\activesite_pras_s6k.cxs opened ChimeraX session > select #2 2154 atoms, 2175 bonds, 1 model selected > transparency #2/A,B 70 cartoons > select clear > save C:\Users\Lucas\Desktop\activesite_pras_rapa.png transparentBackground > true supersample 3 > transparency #2/A,B 50 cartoons > save C:\Users\Lucas\Desktop\activesite_pras_rapa.png transparentBackground > true supersample 3 > open C:/Users/Lucas/Desktop/ChimeraX_sessions/rheb_cartoon.cxs opened ChimeraX session > hide #!5 models > show #!5 models > select #1/B:3000 43 atoms, 45 bonds, 1 model selected > show sel atoms > hide sel atoms > select #1/A:3000 43 atoms, 45 bonds, 1 model selected > show sel atoms Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color sel byhetero > select clear > select #5/A:3000 43 atoms, 45 bonds, 1 model selected > show sel atoms > select clear > hide #!5 models > show #!5 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > mmaker #1/A:933-1260 to #5/A:933-1260 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 6bcu.cif, chain A (#5) with 6bcx.cif, chain A (#1), sequence alignment score = 1464.8 RMSD between 289 pruned atom pairs is 0.409 angstroms; (across all 290 pairs: 0.437) > toolshed show "Side View" > select #5/A:3000 43 atoms, 45 bonds, 1 model selected > color sel byhetero > select clear > hide #!1 models > select #5/A:2343,2357 26 atoms, 24 bonds, 1 model selected > select #5/A:2343,2357,2338,2340 56 atoms, 53 bonds, 1 model selected > show sel atoms > style sel stick Changed 56 atom styles > color sel byhetero > select #1/A:2343,2357,2338,2340 56 atoms, 53 bonds, 1 model selected > color sel byhetero > select #1/A:3001 1 atom, 1 model selected > show sel atoms > style sel sphere Changed 1 atom style > select #5/A:3001 1 atom, 1 model selected > show sel atoms > style sel stick Changed 1 atom style > style sel sphere Changed 1 atom style > color sel green > select clear > show #!1 models > hide #!5 models > select #1/A:2343,2357,2338,2340 56 atoms, 53 bonds, 1 model selected > show sel atoms > style sel stick Changed 56 atom styles > color sel byhetero > select #1/A:3001@MG 1 atom, 1 model selected > select up 35079 atoms, 35421 bonds, 1 model selected > select clear > select #1/A:3001@MG 1 atom, 1 model selected > color sel green > select clear > show #!5 models > hide #!5 models > show #!5 models > hide #!1 models > show #!1 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > mmaker #1/A:933-1260 to #5/A:933-1260 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 6bcu.cif, chain A (#5) with 6bcx.cif, chain A (#1), sequence alignment score = 1464.8 RMSD between 289 pruned atom pairs is 0.409 angstroms; (across all 290 pairs: 0.437) > save session > C:/Users/Lucas/Desktop/ChimeraX_sessions/rheb_cartoon_activesite.cxs > mmaker #1/A:2002-2549 to #5/A:2002-2549 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 6bcu.cif, chain A (#5) with 6bcx.cif, chain A (#1), sequence alignment score = 2543.8 RMSD between 441 pruned atom pairs is 1.060 angstroms; (across all 493 pairs: 1.282) > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > select #1/A:2187 22 atoms, 21 bonds, 1 model selected > show sel atoms > style sel stick Changed 22 atom styles > select #5/A:2187 22 atoms, 21 bonds, 1 model selected > show sel atoms > style sel stick Changed 22 atom styles > hide sel atoms > select #1/A:2187 22 atoms, 21 bonds, 1 model selected > hide sel atoms > select clear > mmaker #1/A:933-1260 to #5/A:933-1260 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 6bcu.cif, chain A (#5) with 6bcx.cif, chain A (#1), sequence alignment score = 1464.8 RMSD between 289 pruned atom pairs is 0.409 angstroms; (across all 290 pairs: 0.437) > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!1 models > show #!1 models > transparency #1 50 cartoons > transparency #1 50 atoms > select clear > select clear > save C:\Users\Lucas\Desktop\activesite_rheb.png transparentBackground true > supersample 3 > hide #!1 models > transparency #5 0 cartoons > show #!1 models > hide #!1 models > show #!1 models > save C:\Users\Lucas\Desktop\activesite_rheb.png transparentBackground true > supersample 3 > save session > C:/Users/Lucas/Desktop/ChimeraX_sessions/rheb_cartoon_activesite_zoom.cxs opened ChimeraX session > save C:\Users\Lucas\Desktop\activesite_rheb.png transparentBackground true > supersample 3 > toolshed show "Side View" > save C:\Users\Lucas\Desktop\activesite_rheb_test.png transparentBackground > true supersample 3 > save session > C:/Users/Lucas/Desktop/ChimeraX_sessions/rheb_cartoon_activesite_zoom.cxs opened ChimeraX session > save C:\Users\Lucas\Desktop\nosideview.png transparentBackground true > supersample 3 > hide #!1 models > save C:\Users\Lucas\Desktop\nosideview.png transparentBackground true > supersample 3 > toolshed show "Side View" > save C:\Users\Lucas\Desktop\sideview.png transparentBackground true > supersample 3 OpenGL version: 3.3.0 NVIDIA 388.73 OpenGL renderer: GeForce MX150/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: ASUSTeK COMPUTER INC. Model: UX430UNR OS: Microsoft Windows 10 Home Single Language (Build 18362) Memory: 8,443,699,200 MaxProcessMemory: 137,438,953,344 CPU: 8 Intel(R) Core(TM) i7-8550U CPU @ 1.80GHz" File attachment: example_ChimeraX.png
Attachments (1)
Change History (5)
by , 6 years ago
| Attachment: | example_ChimeraX.png added |
|---|
comment:1 by , 6 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Input/Output |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Side view affects image saving |
Reported by Lucas Tafur
comment:2 by , 6 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Fixed.
Your poor quality image was at half resolution, ie half the number of pixels in width and height when side view shown. A month or two ago I made ChimeraX image save on high DPI displays save an image with width and height in pixels matching the high DPI display resolution. Before that the saved image used half the display resolution (because Qt uses logical pixels that are twice as big on such high DPI displays). But side view was setting the opengl context framebuffer width and height using half resolution when it rendered. I fixed that code so it uses the full resolution.
On your lab Windows PC does it have a high DPI display? If not then the saved image width/height in pixels will be about half what you get on your Mac which has a high DPI retina display. But you can simply specify the image size in pixels when you save the image to get higher quality, "save myimage.png width 1500".
If you open an image saved by ChimeraX on the Mac by double clicking it will show it in Preview, and using Preview menu entry Tools / Show Inspector reports the actual image size in pixels. This can help see if your images are the size you expect.
comment:3 by , 6 years ago
Hi, Thanks for your help. Just to answer your question, in both cases (laptop and PC) I use Windows and didn’t have any problems before, so I guess it’s not a display issue. Sent from my iPhone
follow-up: 3 comment:4 by , 6 years ago
Maybe this problem started for you because you got a new ChimeraX. I made ChimeraX start saving images at native screen resolution on retina displays on January 28. Before that it always saved at half resolution on retina displays. So in older ChimeraX all your images were the low quality ones. But once I gave you higher quality by default you probably noticed the difference.
At any rate, as I said you can specify the image width in pixels when saving. And the current behavior is to save an image that matches the screen resolution. If you are using remote desktop display the screen resolution may be different (lower) than if you are not using remote display. If this is not the behavior you see, ie saved image is lower resolution that what you see on-screen then that is a bug and please report it again.
Note:
See TracTickets
for help on using tickets.
Added by email2trac