[Chimera-users] Coloring higher ordered structures

Elaine Meng meng at cgl.ucsf.edu
Thu Oct 19 12:57:17 PDT 2017

Hi Frances,
Well, “in theory” yes, but in practice, that many atoms will kill the usability of the program.  I’ll say how but at the same time, I  don’t recommend trying!  (I started to do it but then had to force quit about 10% of the way through).  How is to select “All” chains in the Multiscale Models dialog and then in the “Act on selected chains” section, choose Style Show… Sphere (or anything except surface, really).  If it were possible to handle all those atoms, you could change back to showing surface afterward.

Our newer program ChimeraX is far, far better with large numbers of atoms.  It is freely available for any noncommercial use.  It's in alpha release now with not many GUIs (mostly commands), but if you just wanted to make a nice figure or movie showing all the atoms of the 3iyu capsid with the same coloring on all copies, it’s perfectly capable.

Here’s an example:

(1) start ChimeraX
(2) enter command: open 3iyu
(3) …some tables automatically appear in the Log listing the chains and the assemblies.  In the Assemblies table I clicked the “1” to show the complete icosahedral assembly, only takes a couple of seconds on my machine. Default coloring uses a different color for each chain, but same color for copies of the same chain.
(4) then to color all copies of chain N cyan, command: color /N cyan
(5) then to color all copies of chain N residues 100-200 white, command: color /N:100-200 white

Screenshot of the result is attached.  Of course, you could color each chain however you like, have white background (click white square icon up top), different kinds of lighting, black outlines (click seahorse icon up top) etc.  This assumes all the copies of a given chain will be colored the same.  To allow different coloring of different copies of the same chain of the asymmetric unit (e.g. chain N) you’d have to use a command to make the assembly instead of clicking in the Log and it would be more complicated, although still doable.


ChimeraX download (I tested the above in both the alpha3 and current daily) 
list of color names

On Oct 19, 2017, at 9:40 AM, Frances Shepherd <sheph085 at umn.edu> wrote:
> Hi Elaine,
> Thank you also for that information!  Is there a way to load the atomic structure to the entire capsid protein so I could, for example, color residues 100-200 with red on all N chains?  
> Thanks,
> Frances
>> On Oct 18, 2017, at 4:08 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> Hello Frances,
>> I see Tom also answered, but we came at the answers from some different angles, so I’m sending my reply too in case it adds anything…
>> There is no need to do any splitting.  You could just open 3iyu and then use Multiscale Models “Make models”. In the result, you can select and color individual chain surfaces.  Select with the mouse is Ctrl-click, and there are several buttons in the Multiscale Models dialog  “Select chains” section (top part) to control which ones are selected, as indicated with green outlines. The “Act on selected chains” section of Multiscale Models (middle) includes a color well and other options.  Clicking the square color well shows the Color Editor, in which you can interactively choose a color for the selected chain(s).  That colors a whole chain’s surface one color.  As Tom mentioned you can select and color all the symmetry copies the same if you want, or color individual chains different colors.
>> By default, Multiscale Models shows a low-resolution surface for all the copies that were added to create the overall assembly, and only has atomic detail for the original copy of 3iyu. If you want to see low-res surfaces for all, including the original copy, you would use Select chains “With loaded atoms” (in the Multiscale Models dialog) and then in Act on selected chains, “Show” selected chains.
>> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemulti.html>
>> To color individual residues, you need to have atomic detail loaded. The original copy of the structure is already loaded, so if you only wanted to do it in one copy you might as well use that one.  Detailed coloring can be done in the ribbon or atomic representations (stick, sphere, etc.); if you want to color the surface by specific atoms/residues, however, you may want to increase the resolution of that surface first.  For example, select the chains with loaded atoms as described above, change resolution in the Act on selected chains section to some lower number (default is 8, I tried 3… setting it to 0 would calculate the standard high-resolution molecular surface, but that gives a lot of errors on structure 3iyu)
>> Next you would color the atoms as desired, for example, command:
>> color red :100-200.N
>> … to color residues 100-200 in chain N red.  Then select them and use Color Zone, commands:
>> select :100-200.N
>> start Color Zone
>> … click Color button and adjust the zone distance.  I have trouble controlling the slider so I just enter a number directly.  I attached an image of the result at that point.
>> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/colorzone.html>
>> I hope this helps,
>> Elaine
>> ----------
>> Elaine C. Meng, Ph.D. 
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> <redzone.png>
>>> On Oct 18, 2017, at 11:00 AM, Frances Shepherd <sheph085 at umn.edu> wrote:
>>> Hello,
>>> I’m working with a rotavirus capsid structure and I’d like to highlight individual residues on it if possible.  I’m using PDB #3IYU which I split into individual chains, and used the multiscale model function to create the capsid structure.  I’m able to color different surfaces, but it applies the color to each spot where the chain is on the entire capsid, rather than just one subunit.  I’d like to recreate the kind of figure from a paper by Zeller et al (2012), attached below.  Additionally, is it possible to color individual residues on a capsid structure? 
>>> Thanks in advance!
>>> -Frances Shepherd
>>> <Screen Shot 2017-10-18 at 12.58.29 PM.png>
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