[Chimera-users] Difference between Chimera and ChimeraX

Tom Goddard goddard at sonic.net
Mon Jun 26 16:58:50 PDT 2017


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 at 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 at cgl.ucsf.edu] *On Behalf Of *Bon Ikwuagwu
>> *Sent:* Monday, June 26, 2017 8:53 AM
>> *To:* chimera-users at 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
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