How to change transparency of ladder mode of nucleic acids
Dear ChimeraX Team, I hope this email finds you well. My name is Zhang Yan, and I am a beginner of ChimeraX. I am writing to seek assistance regarding how to change transparency of ladder mode of nucleic acids in ChimeraX. Despite trying the command 'trans #1 60 all', I have been unable to achieve the desired effect. Could you please suggest an alternative solution or provide guidance on how to accomplish this task? Thank you for your attention to this matter. Best regards, Zhang Yan
Dear Zhang Yan, I can see this problem -- unfortunately, it is a current limitation of the "transparency" command. It applies to the cartoon (ribbons) but not the nucleotide representations: ladder, stubs, ellipsoids, etc. I will make a ticket for this problem in our bug database and include your email so that you will be notified if the problem is fixed. There is a workaround but it is not convenient. The "color" command has a "target f" option that does apply to the nucleotide representation of each residue. So you can use "color" with its "transparency" option instead of the "transparency" command, but you have to give a color in the command. So if your ladders have several different colors you would have to know which residues are which colors, and then use several different color commands. Here is an example of making the ladder transparent tan: color #1 tan transparency 60 target f Or for a specific residue, residue number 5 in chain A, with yellow ladder: color #1/A:5 yellow transparency 60 target f Info about "color" command: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#simple> I hope this helps, and sorry for the inconvenience! Sincerely, 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 Mar 14, 2024, at 1:27 AM, Yan ZHANG 张艳 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX Team, I hope this email finds you well.
My name is Zhang Yan, and I am a beginner of ChimeraX. I am writing to seek assistance regarding how to change transparency of ladder mode of nucleic acids in ChimeraX. Despite trying the command 'trans #1 60 all', I have been unable to achieve the desired effect. Could you please suggest an alternative solution or provide guidance on how to accomplish this task?
Thank you for your attention to this matter. Best regards, Zhang Yan
Dear UCSF Chimera(X) team, Thank you very much for your prompt response to my email. The command you mentioned in your message is very helpful to me. Meanwhile, I also tried the command 'transparency #1/A:5 60 target f', but the transparency failed to change. It's possible that the selection mechanism here differs from independent selection, but it's truly remarkable. Thank you once again for your constructive advice. Wishing you a wonderful day ahead! Sincerely, Zhang Yan ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Friday, March 15, 2024 8:35 AM To: Yan ZHANG 张艳 <zhangyan30@westlake.edu.cn> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] How to change transparency of ladder mode of nucleic acids [You don't often get email from meng@cgl.ucsf.edu. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ] Dear Zhang Yan, I can see this problem -- unfortunately, it is a current limitation of the "transparency" command. It applies to the cartoon (ribbons) but not the nucleotide representations: ladder, stubs, ellipsoids, etc. I will make a ticket for this problem in our bug database and include your email so that you will be notified if the problem is fixed. There is a workaround but it is not convenient. The "color" command has a "target f" option that does apply to the nucleotide representation of each residue. So you can use "color" with its "transparency" option instead of the "transparency" command, but you have to give a color in the command. So if your ladders have several different colors you would have to know which residues are which colors, and then use several different color commands. Here is an example of making the ladder transparent tan: color #1 tan transparency 60 target f Or for a specific residue, residue number 5 in chain A, with yellow ladder: color #1/A:5 yellow transparency 60 target f Info about "color" command: <https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fcolor.html%23simple&data=05%7C02%7Czhangyan30%40westlake.edu.cn%7C34b9b0a2c778490d663108dc4487cf99%7C7e82de2f7ef644169b9644c1457be81b%7C1%7C0%7C638460597343408668%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=zvyUrc%2BOpPvukGopP2VhSQbz8uujMMrjywCLjBH%2Fy%2Fs%3D&reserved=0<https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#simple>> I hope this helps, and sorry for the inconvenience! Sincerely, 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 Mar 14, 2024, at 1:27 AM, Yan ZHANG 张艳 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX Team, I hope this email finds you well.
My name is Zhang Yan, and I am a beginner of ChimeraX. I am writing to seek assistance regarding how to change transparency of ladder mode of nucleic acids in ChimeraX. Despite trying the command 'trans #1 60 all', I have been unable to achieve the desired effect. Could you please suggest an alternative solution or provide guidance on how to accomplish this task?
Thank you for your attention to this matter. Best regards, Zhang Yan
Yes, as we both confirmed, the "transparency" command does not have a "target f" option currently... that is the problem! I'm glad you were able to use "color" instead. Elaine
On Mar 14, 2024, at 7:58 PM, Yan ZHANG 张艳 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear UCSF Chimera(X) team, Thank you very much for your prompt response to my email. The command you mentioned in your message is very helpful to me. Meanwhile, I also tried the command 'transparency #1/A:5 60 target f', but the transparency failed to change. It's possible that the selection mechanism here differs from independent selection, but it's truly remarkable. Thank you once again for your constructive advice.
Wishing you a wonderful day ahead! Sincerely, Zhang Yan
From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Friday, March 15, 2024 8:35 AM To: Yan ZHANG 张艳 <zhangyan30@westlake.edu.cn> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] How to change transparency of ladder mode of nucleic acids
[You don't often get email from meng@cgl.ucsf.edu. Learn why this is important athttps://aka.ms/LearnAboutSenderIdentification ]
Dear Zhang Yan, I can see this problem -- unfortunately, it is a current limitation of the "transparency" command. It applies to the cartoon (ribbons) but not the nucleotide representations: ladder, stubs, ellipsoids, etc.
I will make a ticket for this problem in our bug database and include your email so that you will be notified if the problem is fixed.
There is a workaround but it is not convenient. The "color" command has a "target f" option that does apply to the nucleotide representation of each residue. So you can use "color" with its "transparency" option instead of the "transparency" command, but you have to give a color in the command. So if your ladders have several different colors you would have to know which residues are which colors, and then use several different color commands.
Here is an example of making the ladder transparent tan:
color #1 tan transparency 60 target f
Or for a specific residue, residue number 5 in chain A, with yellow ladder:
color #1/A:5 yellow transparency 60 target f
Info about "color" command: <https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf....>
I hope this helps, and sorry for the inconvenience! Sincerely, 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 Mar 14, 2024, at 1:27 AM, Yan ZHANG 张艳 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX Team, I hope this email finds you well.
My name is Zhang Yan, and I am a beginner of ChimeraX. I am writing to seek assistance regarding how to change transparency of ladder mode of nucleic acids in ChimeraX. Despite trying the command 'trans #1 60 all', I have been unable to achieve the desired effect. Could you please suggest an alternative solution or provide guidance on how to accomplish this task?
Thank you for your attention to this matter. Best regards, Zhang Yan
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participants (2)
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Elaine Meng -
Yan ZHANG 张艳