[Chimera-users] Higher order

Tom Goddard goddard at cgl.ucsf.edu
Tue Jan 13 12:18:15 PST 2009

Hi Hernando,

  If you make multiscale surfaces totaling millions of triangles it can 
take a while to create the surfaces and it can be slow rotating them.  
To see how many triangles you've got press the select "All" button on 
the multiscale dialog and then use Actions / Inspect, set the Inspect 
menu to Surface (probably already set that way) and the last line says 
"triangles 522960" when I try with the biological unit of 1uf2 and 
default surface resolution 8 Angstroms.  That rotates fast but took 
several seconds to create the surfaces on my Mac laptop.  If you get 
into millions of triangles it can be quite slow.  To speed it up you can 
set the resolution to a larger value in the multiscale dialog, select 
all chains and press Resurface.  Or set the resolution value larger 
before you make the model in the first place.  With resolution 15 
Angstroms I get 121000 triangles for 1uf2.


hsosa at aecom.yu.edu wrote:
> Thanks Tom, Now I can change the colors on each chain.
> Another issue is that after displaying the surfaces of a big complex (33 
> copies as BIOMT entries) chimera seems to freeze for very long periods 
> of time.  It may be related to not having enough computer power (Dual 
> Xeon 1.4 GHz,, 1GB RAM,  Windows XP,  Graphics ATI Radeon 9550, Chimera 
> 1.3) ?.
> Hernando
> Tom Goddard wrote:
>> Hi Hernando,
>>  Multiscale models assigns colors by chain by default.  All copies of 
>> chain B will initially get the same color.  All copies of chain C get 
>> another color.  If you wish to change those colors, select a chain 
>> surface, click the select Copies button, then use the Color button or 
>> the Actions / Color menu (in Chimera 1.3 or newer).
>>  Maybe the case you are thinking of is where chains B and C are really 
>> copies of the same protein with different conformations.  If you 
>> select the surface for chain B you can then select all chains which 
>> have identical amino acid sequences with shortcut xc, then color 
>> those.  Now if you have several chains that are the same protein but 
>> have different sequences (maybe some residues not observed in some of 
>> the copies) then they are not identical.  Then you'd just have to 
>> hand-select one copy of each chains known to be the same, press the 
>> Copies button and color.  This is the situation with rice dwarf virus 
>> 1uf2.  Might be nice to have the ability to extend selection to all 
>> chains that have the same chain name (given in PDB file though not 
>> currently used in Chimera).
>>    Tom
>> hsosa at aecom.yu.edu wrote:
>>> Is it possible to assign colors by chain  to the surfaces created my 
>>> the multiscale models tool ?
>>> Thanks
>>> Hernando

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