[Chimera-users] Higher Order

hsosa at aecom.yu.edu hsosa at aecom.yu.edu
Wed Jan 21 10:02:30 PST 2009

Dear Tom , Elaine David

   Thanks a lot for the help.  As suggested we placed helical symmetry 
information in the BIOMT entries of the  PDB file  (3EDL). A 
representation of the molecule made with chimera using the Higher Order 
Structures tool and PovRay is attached.
As mentioned making these type of figures in my computer was relatively 
slow.  What would be the best graphic card choice to accelerate the 
display and manipulation of surfaces ? (I need to replace the graphic 
card anyway).  A graphic card  with the  biggest amount of graphics  
memory   ?.  From your benchmark scores it seems that memory is not the 
most important parameter, right ?.  Would the Quadro FX 1700 be the best 
choice to display  many surfaces ?.

Thanks again


Tom Goddard wrote:
> 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.
>    Tom
> 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

Hernando Sosa
Dept. of Physiology and Biophysics
Albert Einstein College of Medicine
1300 Morris Park Av.
Bronx NY 10461
phone	(718) 430-3456
FAX	(718) 430-8819
email	hsosa at aecom.yu.edu

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