Hi, Bob. Thanks a lot for the ideas! I'll try to test them in the next
days and report the results :)
El 14/01/2008, a las 23:57, [EMAIL PROTECTED] escribió:
>>
>> More testing:
>> Instead of loading some residues at once and then painting all of
>> them, I changed the script to select each residue individually and
>> then change its colour;
>>
>> select C1; color [0,0,0];
>> select N2; color [0,0,0];
>> select C3; color [0,0,0];
>> ...
>> select N100; color [0,10,0];
>> select C101; color [0,10,0];
>> ...
>>
>> Then, the running time of the full script is 42 seconds (2.5 times
>> slower). As the color commands are the same, I suppose that the issue
>> is related do the selects.
>
> the running time is related to parsing of the script. It's just a very
> long script.
>
>>
>>
>> Now for a bigger DNA (2000 bps)
>> -with the script split each 100 lines: 2min 26sec
>> -the full script (3000+ lines): i cancelled at 8 minutes...
>>
>>
>> So, clearly, there is an issue with the selects. I think that the
>> cost
>> of the function isn't lineal but more like exponential, as
>> multiplying
>> the residues number by four doesn't multiply the script running time
>> by four but by 12!
>>
>> How does jmol paint the molecule on load? Clearly it goes a different
>> way, because the initial load+paint is just 5-6 seconds
>
> Selecting is extremely fast. It must be the parsing of all those
> commands
> that is slowing the process. You could speed this several ways,
> depending
> upon where the data are coming from:
>
> 1) If you are creating these files yourself and you can assign group
> names
> to the atoms in the PDB file, then you could assign colors to those
> group
> names and be done with it.
>
> 2) If you can assign a number to the temperature column of the PDB
> file
> corresponding to a color, you can then use a color scheme to assign a
> given color to a given "temperature"
>
> 3) You don't need to select, then color. You can just
>
> color {N30} [0,0,0]
>
> 4) If you know exactly what atoms you want to color, not just their
> names,
> then you could use the (undocumented) color command:
>
> color ({0 4:10 13:15 18:30}) [0,0,0]
>
> The numbers in parentheses+braces are atom index numbers starting
> from 0.
> This feature is used by the state scripts Jmol generates.
>
> Bob Hanson
>
>>>
--
Carles Fenollosa Bielsa
Barcelona Supercomputing Center / Life Sciences
Nexus II / Jordi Girona, 29 / 08034 Barcelona
+34 93 413 76 02
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