Discovery Studio Visualizer 2.5
The developers at Accelrys are behind Discovery Studio Visualizer 2.5 (DSV) are really pushing the molecular visualization field along. You can download DSV for FREE after a quick registration.
I actually tried to use this program a couple of months ago, but ran into problems because my computer did not meet the minimum system requirements.
I dropped Accelrys a quick note on their blog and they were able to connect with someone who was able to give me a hand (thanks again, Luke).
My reason for wanting to play around with this program is my need to find a simple and efficient way to create figures for presentations and publications. The program contains many other capabilities related to small molecule libraries and pharmacophore modeling, but those will have to wait.
A couple of items that I like right from the start:
1) I love that the program runs from one window and utilizes tabs
2) The layout can be customized by a simple drag and drop (ie. you can have your tools on the top, to the left or right, on the side bar, etc.)
3) You have the option for a full screen view that saves some squinting
4) I am fan of GUIs and not typing commands – DSV has really come through in that department
5) The Display Style window is really easy to use and check out the number of options, awesome.
One suggest is to add the ability to move the protein while the Display Style window is open
6) Check this one out called Line ribbons
I don’t think I would ever use it in a presentation or paper, but still think it looks cool.
The reason that I am such a fan of Pymol is its capability of producing high quality images. I selected the Ultra high resolution in DSV and exported it as a png file.
Here are two pictures side (left Pymol) by side (right DSV) both are 564×507 pixels.
I found it strange how the program displayed bonds such as the double bonds from carbon to oxygen. The reason being that this is usually not shown in other visual programs. I am guessing there is some way to turn it off, but by initial reaction was wow – look at all these dual conformers 
Overall, definitely worth downloading. I would love hear your thoughts on how the DSV compares to your favorite visualization program.
Sili
November 5th, 2009 at 11:17 AM #
Haven’t worked with proteins, but this looks good, for sure.
I fell in love with X-seed for small molecule work (rendering in POV-Ray). Really nice for ‘growing’ and exploring structures, too.
Shikha
November 6th, 2009 at 7:10 PM #
Great post, Sean! Nice to see that you are exploring the DSV functionality. Color by Property is probably one of the most favorite tools which our customers like. On the small molecule side, pharmacophore perception is also very nice.
Keep me posted on any enhancement requests!
Sean
November 8th, 2009 at 11:08 PM #
Well requesting is easy
How about a place to enter the four digit PDB ID to automatically load a structure and the option to load the maps from the electron density server?
An option to take into account crystal packing during the solvent accessibility calculation? As far as I can tell it does not, but don’t have another method to verify it.
The ability to scroll the slab (add and remove the amount of surface shown) under the scripts -> ligand interactions -> Create surface around ligand. I would like a more ‘zoomed out view’ which is different from the default script so it would be awesome to adjust that by scrolling.
Shikha
November 10th, 2009 at 5:40 PM #
Hi Sean,
You can actually download PDBs automatically from File -> Open URL, type in the 4 digit code and voila!
For the surface calculation, it’s currently a little cumbersome but an option has been added in an upcoming release. The user still have to create the crystal symmetry mates before the solvent accessible surface is calculated though. For the final point, The script mentioned does not create a slab, (if it did, you would be able to move the structure or the slab to get a zoom effect). The
amount of surface shown depends on the cavity and the radius of atoms selected, you can change the radius in the script.
Sean
November 24th, 2009 at 4:53 PM #
Hi Shikha,
Thanks for the reply! I can’t believe I missed that simply download feature, thanks. I played around with DSV for a couple of days before writing this post. I have been putting some more time getting familiar with the program and now believe overall it is the best program out there.
I am unsure if you have a method to compare the rendering (image quality) between DSV and PyMol, but to me DSV looks slightly worse. However, I am assuming that the image quality from DSV is fine for publication.
sri
December 17th, 2009 at 12:14 PM #
hey can u suggest me way to download this software
Sean
December 17th, 2009 at 12:26 PM #
The sentence from the post “You can download DSV for FREE after a quick registration.”
You need to click on the underlined/highlighted section which represents a link.
Megan
January 15th, 2010 at 4:49 PM #
I want to use this software but am a Mac user. Any suggestions for similar software or a way to use this software without buying Windows?
Sean
January 17th, 2010 at 1:32 AM #
Hi Megan,
PyMOL is able to run on Mac OS X, which is a great program. I would say that it is has a bit of a learning curve so if you haven’t used it and get stuck feel free to drop me a line.
Shikha
January 19th, 2010 at 2:07 PM #
Hi Megan,
A number of users have reported successfully installing and running the Discovery Studio Visualizer on MacOS X under Windows emulators such as VMWare and Parallels. While the DS team does not extensively test the software on these emulators, we know of no reason why the software would not run. Regards.
Sanjay Kamat
June 11th, 2010 at 9:00 AM #
Can you please tell me how you insert missing residues in a pdb file without affecting the co ordinates of the existing residues??
Thanx!!