3 Selection Methods in Discovery Studio Visualizer
I have used PyMol for years and have done numerous posts related to it. However, that may soon come to an end. The reason being that Discovery Studio Visualizer 2.5 (DSV) is just better. I am still getting used to the program, but wanted to share with you three ways to ’select a region’ to get you pumped up!
1) Highlight amino acid sequence
You can display the amino acid sequence by Sequence -> Show Sequence
When you highlight on the sequence – the structure is also highlighted.
The structure can be viewed on the other tab (I really like having tabs instead of separate windows):
2) Lasso
Simply draw over the region you would like to be selected.
3) Clicking
An atom can simply be selected with the pointer and with a right click, pertinent information will be displayed. In this example, I have double clicked which highlights the residue.
Four clicks will select a chain.
Six will select the entire structure.
Once a selection is made you can then easily make adjustments using the display tab (I previously mentioned this here).
*Bonus*
4) Ligand
DSV has a ligand script so that can VERY quickly generate the following figure
Scripts -> Ligand Interactions -> Show Ligand Interactions with Atoms:
A couple of changes and you can have a publication quality figure in no time.
David
December 8th, 2009 at 6:48 PM #
Not sure if you know this already: You can drag a tab to place it in a side-by-side window. I really like this feature when I need to see the interaction between windows/tabs.
Shikha
December 9th, 2009 at 10:35 PM #
Hi Sean, I am so thrilled to see that you have been exploring all the cool features of the DVS! Thank you for sharing your notes with the community through your blog as well. It is a very rich product and I hope that more and more scientists start to take advantage of the capabilities.
Thanks to David for his pointer as well about moving the windows so you can see selections interactivity simultaneously in all windows. Moreover, you can detach the window and move it outside the application on a second monitor: it’s that little 2 boxes icon on the upper right hand corner.
Nat
December 11th, 2009 at 8:08 AM #
Sean, right-clicking on a structure to get a context menu is also a feature of PyMOL and has been for some time. It doesn’t work exactly as what you describe for DSV, but you can use it to perform actions on the atom, or the residue/chain/object that it belongs to.
Sean
December 11th, 2009 at 8:39 AM #
Hi Nat,
I didn’t mean to imply that these selection features are completely unique to DVS. Sorry for the confusion.
Gesa
December 18th, 2009 at 8:05 AM #
Can you tell me, how you selected the FAD as a ligand? When I load my structure, it says: Document does not contain both a receptor and a ligand molecule.
I tried label the FAD in the .pdb-file as ATOM and HETATM but both did not work.
Sean
December 18th, 2009 at 3:14 PM #
I am assuming you are loading your own pdb file. I loaded 3E6O, which contains a FAD without any problems. I was able to select only the ligand by using Scripts -> Selection -> Select Ligands. Here is a line from the pdb file that describes an atom from the FAD:
HETATM 6875 C10 H4B B1902 141.918 117.871 88.832 1.00 33.07 C
If you are still having problems, let me know (however, it maybe hard to trouble shoot the issue without seeing the pdb file) and I will track down the answer for you.
Shikha
December 18th, 2009 at 3:17 PM #
Hi Gesa,
I hope Sean’s instructions help. Otherwise, please feel free to contact Accelrys support: support-at-accelrys-dot-com to see a quick webex. Regards, Shikha