[Chimera-users] coloring individual segments of a protein

Greg Couch gregc at cgl.ucsf.edu
Tue Apr 21 14:44:44 PDT 2015


Hi AGS,

After you type in the directory name, you need to press <Enter> or 
<Return> on your keyboard, then the files below will change to be the 
ones in the new directory, and the file will be saved in the new 
directory.  If not, it stays on the original directory.

     HTH,

     Greg

On 04/21/2015 09:22 AM, A G Szabo wrote:
> Elaine
>
> Thank you  once again. I sort of figured it out.
>
> Now one additional question.
>
> When I save the image the file location that comes up is
>
> C:\users\arthur\desktop
>
> And so not surprisingly the file gets saved to the desktop.
>
> I tried to change the location where I wanted the file saved, into
> libraries\documents\foldername
>
> I typed that in the bar where the save  location is listed.
>
> The image was not saved there but again went to the desktop!
>
> I can move it of course, but saving it directly to where I wanted to store
> it  is an extra step.
>
> Thanks again
>
> ags
>
> -----Original Message-----
> From: Elaine Meng [mailto:meng at cgl.ucsf.edu]
> Sent: April-21-15 11:46 AM
> To: A G Szabo
> Cc: 'Mailing List'
> Subject: Re: [Chimera-users] coloring individual segments of a protein
>
> Hello Prof. Szabo,
> Basically, if using the menu you will need to select the residue(s) of
> interest and then act upon them.  I don't know what happened when you were
> trying to hide the Phe.  Maybe it wasn't selected.   The selection should be
> outlined in green.  If atoms are selected and shown, they will be outlined
> in green, or if only the ribbon is shown, the ribbon segment representing
> the selected residue will be outlined.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html>
>
> So first, just try to correctly select the residue(s) that you want to act
> on.   The Sequence window is just one way.  As per your questions, another
> way is to select the residue from the screen, or "picking" as described
> here, Ctrl-click on an atom, bond, or ribbon segment, Shift-Ctrl-click to
> add to that selection without erasing the  previous:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html#pickselect>
>
> If you only selected an atom or bond, you may need to increase that to the
> whole residue. You can promote the selection up to the whole residue with
> keyboard up arrow or menu: Select. Broaden
>
> Once you have the desired item(s) selected, use the Actions menu to show or
> hide ribbon or sticks (Actions. Atoms/Bonds. show/hide, Actions. Ribbon.
> show/hide).
>
> If nothing is selected, the Actions menu will apply to everything.  For
> example, if you just want to hide ALL sticks, there is no need to select
> anything, just use menu: Actions. Atoms/Bonds. hide.
>
> I don't know of a video that specificially shows this general stuff.  It is
> covered somewhat in the Getting Started with the Menu written tutorial,
> which I've been updating recently:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/menutut.html>
>
> I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of
> Pharmaceutical Chemistry University of California, San Francisco
>
> On Apr 21, 2015, at 7:28 AM, A G Szabo <agszabo at bell.net> wrote:
>
>> Elaine
>>
>> I managed to figure out using your instructions and the menus how to
>> color different sse's of a protein ribonuclease (5RSA). The structure
>> that came up when I "fetched" it from the PDB had a few of the
>> residues as sticks. Using the sequence function I was able to select
>> one of the residues, then with the action menu could hide then sticks
>> of that residue. However, I am not sure that was the correct way to
>> proceed because when I tried to hide a Phe residue I was not able to
>> do so.  I have looked at the tutorials that are available on the site
>> and with due respect I found them to be difficult to learn from.
>>
>> Are there any you tube videos?
>>
>> So I have a couple of other simple! questions.
>>
>> If I click on a residue that is visible as sticks is it possible to
>> have the sticks disappear?
>>
>> If I click on a residue in the secondary structure, can I make the
>> stick structure appear?
>>
>> I will have another look at the tutorials and see if I can figure
>> things out. I  prefer to use the menu version rather than the command
>> version since I do not want to have to figure out what all the commands
> are.
>>
>> I  am  not really interested in the structure alignment or other
>> similar features of the program.  I will use the program primarily for
>> preparing images of secondary structures and highlight selected amino
> acids as sticks.
>> Thank you for your assistance.
>>
>> A. G.  Szabo
>> Professor Emeritus
>> Chemistry
>> Wilfrid Laurier University
>> Waterloo Ontario Canada.
>>
>> -----Original Message-----
>> From: Elaine Meng [mailto:meng at cgl.ucsf.edu]
>> Sent: April-17-15 4:33 PM
>> To: A G Szabo
>> Cc: chimera-users at cgl.ucsf.edu
>> Subject: Re: [Chimera-users] coloring individual segments of a protein
>>
>> Hello AG,
>> There are several ways.  I'll try to outline the main ones:
>>
>> (A) Use the "rainbow command  with the "sse" option to automatically
>> assign a different color for each secondary structure element (SSE,
>> e.g. helix and/or strand).
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rainbow.html>
>>
>> By "automatically" I mean that you don't name each color yourself.
>> Instead Chimera interpolates within the specified color range to give
>> each SSE a separate color.  It doesn't color the coil between SSEs.
>> Example commands (use Favorites menu to show Command Line):
>>
>> color gray coil
>> rainbow sse
>> rainbow sse orange,white,cyan #0
>>
>> . where the second example goes through orange, white, and cyan
>> instead of the default rainbow colors, and only affects model #0 (see
>> command-line specification
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec
>> .html> ).  As explained in the "rainbow" manual page linked above, you
>> could use "helix" or "strand" instead of "sse" to color only the
>> helices or strands, respectively. If you don't use any of those, the
>> color will be different for each residue and gradually change within
>> each SSE.
>>
>> (B) If you want to control the specific color for each SSE yourself,
>> you would have to do a separate coloring step for each SSE. You could
>> select the residues of the SSE and then use Actions. Color in the menu
>> or a command to color the selection, for example:
>>
>> color red sel
>> color purple,r sel
>> . where the second example ",r" means ribbon-only.
>>
>> A convenient way to select an individual SSE is by showing the protein
>> sequence (menu Favorites. Sequence) and then in the sequence window,
>> dragging a box to select an SSE.  The light yellow and light green
>> boxes in the sequence window show where each SSE starts and ends.
>>
>> However, if you already knew the residue numbers and were using
>> commands, you could specify the residues directly instead of selecting
>> them, for
>> example:
>>
>> color cyan,r :50-64.A
>> . to color ribbons-only of residues 50-64 in chain A
>>
>> Color command:
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/color.html>
>>
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.
>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department
>> of Pharmaceutical Chemistry University of California, San Francisco
>>
>> On Apr 14, 2015, at 7:47 AM, A G Szabo <agszabo at bell.net> wrote:
>>
>>> How do I use Chimera to color a protein in the following way: for
> example:
>>> Helix 1 -  red
>>> Helix 2 - yellow
>>> Helix 3 - magenta
>>> Strand 1 - dark blue
>>> Strand 2 - cyan
>>>
>>> Etc.
>>>
>>> A G Szabo
>>
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