[Chimera-users] difficulty in using chimera for large PDB files

[Tom Goddard]

Hi Shruti,

 This is certainly a graphics limitation so upgrading the graphics is the way to go.  Moving molecules is all done by the graphics not the CPU (unless you have no graphics processor and so the CPU does the graphics).

 Any current generation graphics will work.  To get an idea what people use with Chimera look at the Chimera graphics benchmarks

	http://plato.cgl.ucsf.edu/trac/chimera/wiki/benchmarks

You don’t need a high-end card, the most basic graphics designed for video games will be much faster than no graphics.  Most computers from recent years with an Intel processor have an Intel graphics processor (GPU) integrated with the CPU.  You didn’t say what you have now so many you already have that.

 In terms of rotating molecules at say 5-10 frames/sec minimum Chimera can handle 1 million atoms with a good graphics card.  But in terms of everything, else, like changing colors, hiding some atoms or chains, stuff done by the CPU, things get slow around a few hundred thousand atom.  Chimera is not know for its speed.  You should try PyMol or VMD for handling larger molecules.

	Tom

> On Dec 2, 2016, at 2:45 AM, Shruti Khare <shrutikhare at mbu.iisc.ernet.in> wrote:
> 
> Dear Sir/Madam,
> 
> When we use chimera to visualize PDB files with ~18,000 atoms (PDB ID 5FUU) even
> rotating the molecule is slow in chimera.
> The computer has 6GB RAM. Would upgrading RAM help or we need to get a graphics
> card installed?
> Graphics card capacity should be 2GB or higher?
> 
> Could you please tell me the minimum computer configuration required by chimera
> to handle large PDB files?
> Also what is chimera's maximum limit for handling PDB files given a computer
> with very good configuration?
> 
> 
> Thank you.
> 
> -- 
> Shruti Khare
> Graduate Student
> Prof. Raghavan Varadarajan Lab
> Molecular Biophysics Unit
> Indian Institute of Science
> Bangalore
> +91-80-2293-2612
> 
> 
> -- 
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