[Chimera-users] about map split

[张雷]

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 at cgl.ucsf.edu>
> Sent Time: 2017-11-11 01:22:40 (Saturday)
> To: "张雷" <leizhang at hsc.pku.edu.cn>
> Cc: Chimera_mailing_list <chimera-users at 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 at 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 at cgl.ucsf.edu>
> >> 发送时间: 2017-11-10 01:50:43 (星期五)
> >> 收件人: "张雷" <leizhang at hsc.pku.edu.cn>
> >> 抄送: Chimera_mailing_list <chimera-users at 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 at 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
>