Hello, I'm a first year graduate student and I am wondering what the differences are between Chimera and ChimeraX? I want to use the tools that are present in Chimera, but I don't know if those tools are also present in ChimeraX. Any feedback would be helpful. Best, Bon Ikwuagwu -- Bon Ikwuagwu PhD Student, Chemical and Biological Engineering Northwestern University
Advantages compared to Chimera: https://www.cgl.ucsf.edu/chimerax/docs/user/advantages.html See “Missing Features” here: http://www.rbvi.ucsf.edu/chimerax/download.html From: Chimera-users [mailto:chimera-users-bounces@cgl.ucsf.edu] On Behalf Of Bon Ikwuagwu Sent: Monday, June 26, 2017 8:53 AM To: chimera-users@cgl.ucsf.edu Subject: [Chimera-users] Difference between Chimera and ChimeraX Hello, I'm a first year graduate student and I am wondering what the differences are between Chimera and ChimeraX? I want to use the tools that are present in Chimera, but I don't know if those tools are also present in ChimeraX. Any feedback would be helpful. Best, Bon Ikwuagwu -- Bon Ikwuagwu PhD Student, Chemical and Biological Engineering Northwestern University
Thanks Markus, I was going to say exactly the same, at least for those who wanted a short summary. If anybody wants a little more detail, I recommend scanning through just the top index of the ChimeraX User Guide and seeing if your features of interest are listed: http://www.rbvi.ucsf.edu/chimerax/docs/user/index.html Of course, you can certainly use both programs. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 26, 2017, at 1:45 PM, Markus Heller <mheller@cdrd.ca> wrote:
Advantages compared to Chimera: https://www.cgl.ucsf.edu/chimerax/docs/user/advantages.html See “Missing Features” here: http://www.rbvi.ucsf.edu/chimerax/download.html
From: Chimera-users [mailto:chimera-users-bounces@cgl.ucsf.edu] On Behalf Of Bon Ikwuagwu Sent: Monday, June 26, 2017 8:53 AM To: chimera-users@cgl.ucsf.edu Subject: [Chimera-users] Difference between Chimera and ChimeraX
Hello, I'm a first year graduate student and I am wondering what the differences are between Chimera and ChimeraX? I want to use the tools that are present in Chimera, but I don't know if those tools are also present in ChimeraX. Any feedback would be helpful. Best, Bon Ikwuagwu
On 06/27/2017 05:45 AM, Markus Heller wrote:
Advantages compared to Chimera: https://www.cgl.ucsf.edu/chimerax/docs/user/advantages.html
Hello, In advantages: "Fast and robust solvent-excluded surfaces". What is the algorithm used to compute those? Regards, F.
See “Missing Features” here: http://www.rbvi.ucsf.edu/chimerax/download.html
*From:*Chimera-users [mailto:chimera-users-bounces@cgl.ucsf.edu] *On Behalf Of *Bon Ikwuagwu *Sent:* Monday, June 26, 2017 8:53 AM *To:* chimera-users@cgl.ucsf.edu *Subject:* [Chimera-users] Difference between Chimera and ChimeraX
Hello,
I'm a first year graduate student and I am wondering what the differences are between Chimera and ChimeraX? I want to use the tools that are present in Chimera, but I don't know if those tools are also present in ChimeraX. Any feedback would be helpful.
Best,
Bon Ikwuagwu --
Bon Ikwuagwu
PhD Student, Chemical and Biological Engineering
Northwestern University
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Francois, We wrote the ChimeraX solvent excluded surface code a few years ago using a distance grid-based calculation (by default using a grid spacing of 0.5 Angstroms). It is about the same speed as the Chimera surface calculation (MSMS from Michel Sanner) but the appearance is a bit smoother, and it works 100% reliably even on 100,000 or million atom structures. We also added separate code that does an analytic calculation of solvent accessible surface area. Tom
On Jun 26, 2017, at 4:18 PM, Francois BERENGER <berenger@bioreg.kyushu-u.ac.jp> wrote:
On 06/27/2017 05:45 AM, Markus Heller wrote:
Advantages compared to Chimera: https://www.cgl.ucsf.edu/chimerax/docs/user/advantages.html
Hello,
In advantages: "Fast and robust solvent-excluded surfaces". What is the algorithm used to compute those?
Regards, F.
See “Missing Features” here: http://www.rbvi.ucsf.edu/chimerax/download.html *From:*Chimera-users [mailto:chimera-users-bounces@cgl.ucsf.edu] *On Behalf Of *Bon Ikwuagwu *Sent:* Monday, June 26, 2017 8:53 AM *To:* chimera-users@cgl.ucsf.edu *Subject:* [Chimera-users] Difference between Chimera and ChimeraX Hello, I'm a first year graduate student and I am wondering what the differences are between Chimera and ChimeraX? I want to use the tools that are present in Chimera, but I don't know if those tools are also present in ChimeraX. Any feedback would be helpful. Best, Bon Ikwuagwu -- Bon Ikwuagwu PhD Student, Chemical and Biological Engineering Northwestern University _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (5)
-
Bon Ikwuagwu -
Elaine Meng -
Francois BERENGER -
Markus Heller -
Tom Goddard