about select and label a residul with another different from the color of the whole model
Hi the experts of Chimera,
Good noon! I had selected a residul and labeled it with the commands
sel #0:500 rlabel #0:500.
Then, the label can be displayed on the selected residul. How could I change the color of the label and display the label in a different color different from the color of the whole model? Thank a lot!
Sincerely,
Lei Zhang Peking University, Beijing, China
Hi Lei Zhang, You can use the “color” command to color labels separately from the other things. For example, commands like these to change all residue labels or only a specific residue label:
color cyan,lr color yellow,lr #0:500
… the “,lr” part means residue label. You could also use “,l” (these are the letter L, not number 1) for all kinds of labels, atom and/or residue. There is no space after the comma. You can also color ribbons, surfaces, etc. separately from the atoms. This is explained in the “color” help page: http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/color.html
You could also do these things with the menu, Actions… Color… all options… to open a coloring dialog, in which you could change the choice under “Coloring applies to”
For a figure, however, you may want the fancier “2D Labels” (menu: Tools… Depiction… 2D Labels): http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.html
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 8, 2017, at 7:32 PM, 张雷 leizhang@hsc.pku.edu.cn wrote:
Hi the experts of Chimera, Good noon! I had selected a residul and labeled it with the commands
sel #0:500 rlabel #0:500.
Then, the label can be displayed on the selected residul. How could I change the color of the label and display the label in a different color different from the color of the whole model? Thank a lot! Sincerely, Lei Zhang Peking University, Beijing, China
Hi Elaine,
Thank for your kindly help! I have tried the command "color red,lr #0:500", but this is a chimera error "color 'red,'is undefined". Therefore, I defined the red color by command "colordef red 1 0 0" and "colordef transparent_red 1 0 0". When I carried out the command "color red,lr#0:500", there was a chimera error "mangled atom specifier". The color of the label can not be changed. I didn't know why. However, the color dialog can work very well. Thanks a lot!
Sincerely,
Lei Zhang
-----原始邮件----- 发件人: "Elaine Meng" meng@cgl.ucsf.edu 发送时间: 2017-11-10 01:50:43 (星期五) 收件人: "张雷" leizhang@hsc.pku.edu.cn 抄送: Chimera_mailing_list chimera-users@cgl.ucsf.edu 主题: Re: [Chimera-users] about select and label a residul with another different from the color of the whole model
Hi Lei Zhang, You can use the “color” command to color labels separately from the other things. For example, commands like these to change all residue labels or only a specific residue label:
color cyan,lr color yellow,lr #0:500
… the “,lr” part means residue label. You could also use “,l” (these are the letter L, not number 1) for all kinds of labels, atom and/or residue. There is no space after the comma. You can also color ribbons, surfaces, etc. separately from the atoms. This is explained in the “color” help page: http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/color.html
You could also do these things with the menu, Actions… Color… all options… to open a coloring dialog, in which you could change the choice under “Coloring applies to”
For a figure, however, you may want the fancier “2D Labels” (menu: Tools… Depiction… 2D Labels): http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.html
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 8, 2017, at 7:32 PM, 张雷 leizhang@hsc.pku.edu.cn wrote:
Hi the experts of Chimera, Good noon! I had selected a residul and labeled it with the commands
sel #0:500 rlabel #0:500.
Then, the label can be displayed on the selected residul. How could I change the color of the label and display the label in a different color different from the color of the whole model? Thank a lot! Sincerely, Lei Zhang Peking University, Beijing, China
Dear Lei Zhang, You are putting spaces in the wrong places. Your first try probably had one space after the comma, giving message color is undefined. Your second try needs to have a space after the lr and before #0.
Type exactly like this and it will work:
color red,lr #0:500
There are only two spaces. One space is after “color” and the other space is before “#”
Also as mentioned in my previous message, another way is to select the residue and then use the menu to color only its label.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 9, 2017, at 10:20 PM, 张雷 leizhang@hsc.pku.edu.cn wrote:
Hi Elaine, Thank for your kindly help! I have tried the command "color red,lr #0:500", but this is a chimera error "color 'red,'is undefined". Therefore, I defined the red color by command "colordef red 1 0 0" and "colordef transparent_red 1 0 0". When I carried out the command "color red,lr#0:500", there was a chimera error "mangled atom specifier". The color of the label can not be changed. I didn't know why. However, the color dialog can work very well. Thanks a lot! Sincerely, Lei Zhang
-----原始邮件----- 发件人: "Elaine Meng" meng@cgl.ucsf.edu 发送时间: 2017-11-10 01:50:43 (星期五) 收件人: "张雷" leizhang@hsc.pku.edu.cn 抄送: Chimera_mailing_list chimera-users@cgl.ucsf.edu 主题: Re: [Chimera-users] about select and label a residul with another different from the color of the whole model
Hi Lei Zhang, You can use the “color” command to color labels separately from the other things. For example, commands like these to change all residue labels or only a specific residue label:
color cyan,lr color yellow,lr #0:500
… the “,lr” part means residue label. You could also use “,l” (these are the letter L, not number 1) for all kinds of labels, atom and/or residue. There is no space after the comma. You can also color ribbons, surfaces, etc. separately from the atoms. This is explained in the “color” help page: http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/color.html
You could also do these things with the menu, Actions… Color… all options… to open a coloring dialog, in which you could change the choice under “Coloring applies to”
For a figure, however, you may want the fancier “2D Labels” (menu: Tools… Depiction… 2D Labels): http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.html
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 8, 2017, at 7:32 PM, 张雷 leizhang@hsc.pku.edu.cn wrote:
Hi the experts of Chimera, Good noon! I had selected a residul and labeled it with the commands
sel #0:500 rlabel #0:500.
Then, the label can be displayed on the selected residul. How could I change the color of the label and display the label in a different color different from the color of the whole model? Thank a lot! Sincerely, Lei Zhang Peking University, Beijing, China
Dear Dr. Meng,
Thanks for your previous kindly help. Now, I have tried to split a special part from a whole map with the methods of surface zone (done) and vop multiply (still trying), but I found that the effect was not satisfactory. Is there some way to split a map much more real ，accurate and pricise as possible. Thank your very much!
Sincerely,
Lei
-----Original Messages----- From: "Elaine Meng" meng@cgl.ucsf.edu Sent Time: 2017-11-11 01:22:40 (Saturday) To: "张雷" leizhang@hsc.pku.edu.cn Cc: Chimera_mailing_list chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] about select and label a residul with another different from the color of the whole model
Dear Lei Zhang, You are putting spaces in the wrong places. Your first try probably had one space after the comma, giving message color is undefined. Your second try needs to have a space after the lr and before #0.
Type exactly like this and it will work:
color red,lr #0:500
There are only two spaces. One space is after “color” and the other space is before “#”
Also as mentioned in my previous message, another way is to select the residue and then use the menu to color only its label.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 9, 2017, at 10:20 PM, 张雷 leizhang@hsc.pku.edu.cn wrote:
Hi Elaine, Thank for your kindly help! I have tried the command "color red,lr #0:500", but this is a chimera error "color 'red,'is undefined". Therefore, I defined the red color by command "colordef red 1 0 0" and "colordef transparent_red 1 0 0". When I carried out the command "color red,lr#0:500", there was a chimera error "mangled atom specifier". The color of the label can not be changed. I didn't know why. However, the color dialog can work very well. Thanks a lot! Sincerely, Lei Zhang
-----原始邮件----- 发件人: "Elaine Meng" meng@cgl.ucsf.edu 发送时间: 2017-11-10 01:50:43 (星期五) 收件人: "张雷" leizhang@hsc.pku.edu.cn 抄送: Chimera_mailing_list chimera-users@cgl.ucsf.edu 主题: Re: [Chimera-users] about select and label a residul with another different from the color of the whole model
Hi Lei Zhang, You can use the “color” command to color labels separately from the other things. For example, commands like these to change all residue labels or only a specific residue label:
color cyan,lr color yellow,lr #0:500
… the “,lr” part means residue label. You could also use “,l” (these are the letter L, not number 1) for all kinds of labels, atom and/or residue. There is no space after the comma. You can also color ribbons, surfaces, etc. separately from the atoms. This is explained in the “color” help page: http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/color.html
You could also do these things with the menu, Actions… Color… all options… to open a coloring dialog, in which you could change the choice under “Coloring applies to”
For a figure, however, you may want the fancier “2D Labels” (menu: Tools… Depiction… 2D Labels): http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.html
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 8, 2017, at 7:32 PM, 张雷 leizhang@hsc.pku.edu.cn wrote:
Hi the experts of Chimera, Good noon! I had selected a residul and labeled it with the commands
sel #0:500 rlabel #0:500.
Then, the label can be displayed on the selected residul. How could I change the color of the label and display the label in a different color different from the color of the whole model? Thank a lot! Sincerely, Lei Zhang Peking University, Beijing, China
Dear Dr. Meng,
Thanks for your previous kindly help. Now, I have tried to split a special part from a whole map with the methods of surface zone (done) and vop multiply (still trying), but I found that the effect was not satisfactory. Is there some way to split a map much more real ，accurate and pricise as possible. Thank your very much!
Sincerely,
Lei
-----Original Messages----- From: "Elaine Meng" meng@cgl.ucsf.edu Sent Time: 2017-11-11 01:22:40 (Saturday) To: "张雷" leizhang@hsc.pku.edu.cn Cc: Chimera_mailing_list chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] about select and label a residul with another different from the color of the whole model
Dear Lei Zhang, You are putting spaces in the wrong places. Your first try probably had one space after the comma, giving message color is undefined. Your second try needs to have a space after the lr and before #0.
Type exactly like this and it will work:
color red,lr #0:500
There are only two spaces. One space is after “color” and the other space is before “#”
Also as mentioned in my previous message, another way is to select the residue and then use the menu to color only its label.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 9, 2017, at 10:20 PM, 张雷 leizhang@hsc.pku.edu.cn wrote:
Hi Elaine, Thank for your kindly help! I have tried the command "color red,lr #0:500", but this is a chimera error "color 'red,'is undefined". Therefore, I defined the red color by command "colordef red 1 0 0" and "colordef transparent_red 1 0 0". When I carried out the command "color red,lr#0:500", there was a chimera error "mangled atom specifier". The color of the label can not be changed. I didn't know why. However, the color dialog can work very well. Thanks a lot! Sincerely, Lei Zhang
-----原始邮件----- 发件人: "Elaine Meng" meng@cgl.ucsf.edu 发送时间: 2017-11-10 01:50:43 (星期五) 收件人: "张雷" leizhang@hsc.pku.edu.cn 抄送: Chimera_mailing_list chimera-users@cgl.ucsf.edu 主题: Re: [Chimera-users] about select and label a residul with another different from the color of the whole model
Hi Lei Zhang, You can use the “color” command to color labels separately from the other things. For example, commands like these to change all residue labels or only a specific residue label:
color cyan,lr color yellow,lr #0:500
… the “,lr” part means residue label. You could also use “,l” (these are the letter L, not number 1) for all kinds of labels, atom and/or residue. There is no space after the comma. You can also color ribbons, surfaces, etc. separately from the atoms. This is explained in the “color” help page: http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/color.html
You could also do these things with the menu, Actions… Color… all options… to open a coloring dialog, in which you could change the choice under “Coloring applies to”
For a figure, however, you may want the fancier “2D Labels” (menu: Tools… Depiction… 2D Labels): http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.html
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 8, 2017, at 7:32 PM, 张雷 leizhang@hsc.pku.edu.cn wrote:
Hi the experts of Chimera, Good noon! I had selected a residul and labeled it with the commands
sel #0:500 rlabel #0:500.
Then, the label can be displayed on the selected residul. How could I change the color of the label and display the label in a different color different from the color of the whole model? Thank a lot! Sincerely, Lei Zhang Peking University, Beijing, China
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