How will hydrogen bonds be highlighted in the final rendering
Hello, when chimera software was used to analyze the interaction between small molecular ligands and proteins, the hydrogen bond width was set to 24, but the hydrogen bond in the rendered picture was very thin and difficult to distinguish. How can I solve this problem？ Looking forward to your reply 姜恩誉 2023111025@stu.njau.edu.cn
Hello, The FindHBond tool has a "Line width" option. If you want fatter lines, use a bigger number there. For explanations of all the options, click the "Help" button on the tool or see the copy at our website: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbo...> Or, if you are using the hbonds command, use the lineWidth option: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/hbonds.html> All the tools have Help buttons, you should check there first when you have a question. See also the general tips for making images, many topics are summarized there: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html#tips> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 7, 2024, at 11:47 PM, 姜恩誉 via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hello, when chimera software was used to analyze the interaction between small molecular ligands and proteins, the hydrogen bond width was set to 24, but the hydrogen bond in the rendered picture was very thin and difficult to distinguish. How can I solve this problem？
Looking forward to your reply
In the last email, I did not explain the situation I met clearly, so you did not understand the problem I met. I have set the display of hydrogen bond in the visualization window of chimera by means of tools to make it highlighted. However, when I saved the 800dpi picture required by the publication at the end, the hydrogen bond became very thin and it was difficult to see in the picture. I have attached the detailed comparison. looking forward to your reply. 姜恩誉 2023111025@stu.njau.edu.cn Original: From：Elaine Meng <meng@cgl.ucsf.edu>Date：2024-10-08 23:39:00(中国 (GMT+08:00))To：姜恩誉<2023111025@stu.njau.edu.cn>Cc：chimera-users <chimera-users@cgl.ucsf.edu>Subject：Re: [Chimera-users] How will hydrogen bonds be highlighted in the final renderingHello, The FindHBond tool has a "Line width" option. If you want fatter lines, use a bigger number there. For explanations of all the options, click the "Help" button on the tool or see the copy at our website: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbo...> Or, if you are using the hbonds command, use the lineWidth option: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/hbonds.html> All the tools have Help buttons, you should check there first when you have a question. See also the general tips for making images, many topics are summarized there: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html#tips> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 7, 2024, at 11:47 PM, 姜恩誉 via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hello, when chimera software was used to analyze the interaction between small molecular ligands and proteins, the hydrogen bond width was set to 24, but the hydrogen bond in the rendered picture was very thin and difficult to distinguish. How can I solve this problem？
Looking forward to your reply
Sorry, that is a limit of how fat the computer can draw the line, given the resolution. My only suggestion is when you use menu: File... Save Image, then in the "Image Options" try "Supersample: 1x1" instead of 3x3. This issue is discussed in the help page, under "Supersample": <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html> Still, at high resolution, it could be too thin. If so, you would need to use some other program like Gimp or Photoshop to thicken the line after you save the image file. Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 8, 2024, at 6:32 PM, 姜恩誉 via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
In the last email, I did not explain the situation I met clearly, so you did not understand the problem I met.
I have set the display of hydrogen bond in the visualization window of chimera by means of tools to make it highlighted. However, when I saved the 800dpi picture required by the publication at the end, the hydrogen bond became very thin and it was difficult to see in the picture. I have attached the detailed comparison.
looking forward to your reply.
姜恩誉 2023111025@stu.njau.edu.cn
Original: • From：Elaine Meng <meng@cgl.ucsf.edu> • Date：2024-10-08 23:39:00(中国 (GMT+08:00)) • To：姜恩誉<2023111025@stu.njau.edu.cn> • Cc：chimera-users <chimera-users@cgl.ucsf.edu> • Subject：Re: [Chimera-users] How will hydrogen bonds be highlighted in the final rendering Hello, The FindHBond tool has a "Line width" option. If you want fatter lines, use a bigger number there. For explanations of all the options, click the "Help" button on the tool or see the copy at our website: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbo...>
Or, if you are using the hbonds command, use the lineWidth option: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/hbonds.html>
All the tools have Help buttons, you should check there first when you have a question.
See also the general tips for making images, many topics are summarized there: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html#tips>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 7, 2024, at 11:47 PM, 姜恩誉 via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hello, when chimera software was used to analyze the interaction between small molecular ligands and proteins, the hydrogen bond width was set to 24, but the hydrogen bond in the rendered picture was very thin and difficult to distinguish. How can I solve this problem？
Looking forward to your reply
Another solution is use to sticks instead of wires for the hydrogen bonds. The stick width can scale indefinitely. To make the change, after the hydrogen bonds are made, bring up the PseudoBond Panel (in Tools / General Controls). Then select "hydrogen bonds" and click on "attributes...". In the resulting dialog, click on "Component PseudoBond Attritributes", and change the "bond style" from "wire" to "stick". And change the radius from 0.2 to 0.05 (or some other value that you like) to emphasis they are not regular bonds. Then save the image. HTH, Greg On 10/9/2024 7:37 AM, Elaine Meng via Chimera-users wrote:
Sorry, that is a limit of how fat the computer can draw the line, given the resolution. My only suggestion is when you use menu: File... Save Image, then in the "Image Options" try "Supersample: 1x1" instead of 3x3.
This issue is discussed in the help page, under "Supersample": <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html>
Still, at high resolution, it could be too thin. If so, you would need to use some other program like Gimp or Photoshop to thicken the line after you save the image file.
Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 8, 2024, at 6:32 PM, 姜恩誉 via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
In the last email, I did not explain the situation I met clearly, so you did not understand the problem I met.
I have set the display of hydrogen bond in the visualization window of chimera by means of tools to make it highlighted. However, when I saved the 800dpi picture required by the publication at the end, the hydrogen bond became very thin and it was difficult to see in the picture. I have attached the detailed comparison.
looking forward to your reply.
姜恩誉 2023111025@stu.njau.edu.cn
Original: • From：Elaine Meng <meng@cgl.ucsf.edu> • Date：2024-10-08 23:39:00(中国 (GMT+08:00)) • To：姜恩誉<2023111025@stu.njau.edu.cn> • Cc：chimera-users <chimera-users@cgl.ucsf.edu> • Subject：Re: [Chimera-users] How will hydrogen bonds be highlighted in the final rendering Hello, The FindHBond tool has a "Line width" option. If you want fatter lines, use a bigger number there. For explanations of all the options, click the "Help" button on the tool or see the copy at our website: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbo...>
Or, if you are using the hbonds command, use the lineWidth option: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/hbonds.html>
All the tools have Help buttons, you should check there first when you have a question.
See also the general tips for making images, many topics are summarized there: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html#tips>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 7, 2024, at 11:47 PM, 姜恩誉 via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hello, when chimera software was used to analyze the interaction between small molecular ligands and proteins, the hydrogen bond width was set to 24, but the hydrogen bond in the rendered picture was very thin and difficult to distinguish. How can I solve this problem？
Looking forward to your reply
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participants (3)
-
Elaine Meng -
Greg Couch -
姜恩誉