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Regarding selection of leucine residues
Respected Mam, 
Greetings of the day.
Firstly I would like to thank you for making Chimera so easy to be dealt even by beginners like me.

I had a query about the selection made. Here at 3.14 min you had made a selection for leucine residue and coloured it yellow. but once the preset was changed to ribbon the selection was not visible in that color. So is it possible to continue the selection i.e. to see it in same color or whether it changes every time we change the appearance of protein molecule?

Secondly, once you selected preset interactive 1 the molecule which was earlier appearing grey now is appearing in blue and red so is there any specific reason to this? What changes took place which lead to change in color of the chain A and B from grey to red and blue respectively?

Also, these presets must be havng some set of rules for each of them. Kindly help me to understand these.

Yours Sincerely 
Manisha Gurnani
Research Scholar
Amity University

UCSF-Chimera Picking-and-Selection 03-04 min 10-20 sec 04-05-20, 8:37 p.m. manishagurnani


  Hello Manisha,

   Thank you for your kind words of appreciation. We are happy that the tutorials are helping you to learn and use UCSF Chimera.

Regarding your 1st query:

The steps for selecting and highlighting particular amino acid residues in a protein sequence are demonstrated in the video from 2.06 to 3.14, here I have selected leucine and changed their color to highlight them.

But once you change to another display using "Presets" menu, the earlier selections will be canceled and on the screen you will only see the current selection, that is, we chose "Interactive 1" ribbons display. You can save the previous action of highlighting leucines in the "Interactive 2" display (ball and stick model, atoms display) using theFile menu and save using "Save Session As"  or "Save Image" option.

Regarding your 2nd query:

To begin with, when you load the PDB file in Chimera, here we have taken the example of the Leucine zipper (1zik), the default color is grey ribbons, these are default settings in the program.

Next when you use "Presets" menu and choose "Interactive1" option the two chains of the zipper (A&B) are colored differently for clarity,the default colors for the two chains are red and blue. You can change the color of these chains according to your choice of colors.

We can change the color of these ribbon display by selecting each chain at a time using "Select" menu (Select>>Chain>>A/B) and change the color using "Actions" menu (Action>>Color>>choose any color from the dropdown).

Regarding Presets menu:

We select an option from "Presets" menu so as to avoid using many steps to get the desired display.

A detailed explanation about "Presets" menu is given in the link below, kindly go through the document.

"A preset is a predefined combination of display settings. Choosing an entry in the Presets menu applies its settings and is much easier than adjusting the many settings individually. Presets are provided for a handful of usage scenarios; of course, many more combinations of settings are possible."

Hope this helps.

Best Wishes

05-05-20, 11:57 a.m. snehalathak

Thank you mam. 
05-05-20, 9:50 p.m. manishagurnani

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