[Chimera-users] splitting and surfaces

A G Szabo agszabo at bell.net
Thu Aug 18 14:02:52 PDT 2016


Elaine

I too do not  know what was happening but I seem to have been able to sort things out. Your suggestion of using “vdwdefine +.01 #0.15" may prove useful in the future.

Thanks

arthur

-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: August-18-16 3:23 PM
To: A G Szabo
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] splitting and surfaces

Hi Arthur,
I really can’t tell what is going on.  I would just say that if you use command “vdwdefine” without specifying the model in the command, it will apply to all models.  It will not automatically use what is selected unless you enter “sel” as the specification.  Actually, don’t bother selecting for that purpose, just use a command like “vdwdefine +.01 #0.15"

“vdwdefine +0” does nothing, it adds zero to current radius.  If you want to back to defaults, command is “~vdwdefine”

As for coloring, I can’t tell what you mean by “attempted to change the color” … if you mean you used the menu Actions… Color, then I can only say to check on what the coloring is applying to, menu: Actions… Color… all options, see “Coloring applies to” on the right side of the resulting dialog.

Best,
Elaine


> On Aug 18, 2016, at 12:13 PM, A G Szabo <agszabo at bell.net> wrote:
> 
> Elaine
> 
> Thanks for your message.  I was able to find that page by typing the url into my browser.
> 
> There are six subunits that  I wish to show the surfaces in different colors. After splitting the model, I  was able  to visualize the surfaces of the first four of the subunits, #0.15 to #0.18. I at first was not able  to image the surface of #0.19, nor of #0.20
> 
> So in  the  case  of #0.19 I  changed 
> 
> vdwdefine +.01
> 
> and it worked.
> 
> I  selected #0.20, set my cursor after vdwdefine +.01 hit return and it did not work.  Eventually it did work with vbdwdefine .03
> 
> oK good so far.
> 
> I decided to change the color of the last C-terminal residues of #0.20 - success.
> 
> I went back to #0.16 and selected the last three residues and tried to change the color, nothing happened. So I selected the entire chain of #0.16 and attempted to change the color, and again nothing happened. I can tell  it  was selected because the sequence of#0.16 is highlighted in green, and I can see parts of the green outline under its surface. I changed the vdwdefine command to have +.00, nothing happened, deleted  vdwdefine from the command line, again nothing happened, even when I tried to hide the surface.
> 
> I am likely not doing something in the correct sequence, but cannot figure out what is the problem  As I indicated I was able to image the surface of #0.16 before without using vdwdefine.
> 
> Help!!!!
> 
> Thanks
> 
> arthur
> 




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