[Chimera-users] surface calculation

[Tom Goddard]

Hi Anton,

   The molecular surface calculation (Actions / Surface / show) fails 
much more often with 64-bit Windows Chimera.  The 32-bit Windows Chimera 
fails less often, and Linux and Mac versions fail in even fewer cases.  
Maybe Chimera 1.5 worked for you because it was 32-bit.

   Eric's trick of using the Multiscale dialog with resolution 0 
computes the molecular surface for each chain separately.  It should 
give the same result as splitting the molecule into chains with the 
"split" command and then surfacing.

     Tom


-------- Original Message --------
Subject: Re: [Chimera-users] surface calculation
From: Eric Pettersen
To: Anton Vila Sanjurjo
Date: 11/29/12 11:14 AM
> Hi Anton,
> I'm not certain why you don't want to split the chains, but it is 
> possible to get Chimera to compute the per-chain surfaces without 
> splitting the model.  The simplest way is to use the Multiscale Models 
> tool (in the Higher-Order Structure category).  With that dialog up, 
> click its "Make models" button.  Then in the "Select chains" section 
> at the top, click the "All" button.  Then in the "Resolution" entry 
> field near the center of the dialog type "0" (zero) and then click the 
> "Resurface" button near that field.  You will get some complaints 
> about multiple-component surfaces failing, but since all the 
> single-component surfaces work the entire structure will be surfaced.
>
> --Eric
>
>                         Eric Pettersen
>                         UCSF Computer Graphics Lab
> http://www.cgl.ucsf.edu
>
> On Nov 29, 2012, at 3:00 AM, Anton Vila Sanjurjo wrote:
>
>> Hi,
>>
>> I have seen posts regarding this problem before. Here is the log I 
>> got after attempting to render a surface representation of the 50S 
>> ribosomal subunit (rcsb ID: 3CPW).
>>
>> #0, chain 0: 23S ribosomal rna
>> #0, chain 1: L35E
>> #0, chain 2: 50S ribosomal protein L44E
>> #0, chain 4: 5'-R(*cp*cp*ap*(phe)*(aca))-3'
>> #0, chain 9: 5S ribosomal rna
>> #0, chain A: 50S ribosomal protein L2P
>> #0, chain B: 50S ribosomal protein L3P
>> #0, chain C: 50S ribosomal protein L4P
>> #0, chain D: 50S ribosomal protein L5P
>> #0, chain E: 50S ribosomal protein L6P
>> #0, chain F: 50S ribosomal protein L7AE
>> #0, chain G: HS6
>> #0, chain H: 50S ribosomal protein L10E
>> #0, chain I: 50S ribosomal protein L13P
>> #0, chain J: HMAL13
>> #0, chain K: 50S ribosomal protein L15P
>> #0, chain L: 50S ribosomal protein L15E
>> #0, chain M: 50S ribosomal protein LC12
>> #0, chain N: 50S ribosomal protein L18E
>> #0, chain O: 50S ribosomal protein L19E
>> #0, chain P: 50S ribosomal protein L21E
>> #0, chain Q: HL31
>> #0, chain R: 50S ribosomal protein L23P
>> #0, chain S: 50S ribosomal protein L24P
>> #0, chain T: 50S ribosomal protein L24E
>> #0, chain U: HL21/HL22
>> #0, chain V: 50S ribosomal protein L30P
>> #0, chain W: 50S ribosomal protein L31E
>> #0, chain X: 50S ribosomal protein L32E
>> #0, chain Y: HL5
>> #0, chain Z: 50S ribosomal protein L37E
>> C:\Program Files\Chimera 1.7s\bin\mscalc.exe 1.400000 2.000000 1
>> MSMSLIB 1.3 started on Local PC
>> Copyright M.F. Sanner (March 2000)
>> Compilation flags
>> C:\Program Files\Chimera 1.7s\bin\mscalc.exe 1.400000 2.000000 0
>> MSMSLIB 1.3 started on Local PC
>> Copyright M.F. Sanner (March 2000)
>> Compilation flags
>> Surface calculation failed, mscalc returned code 5.
>>
>> Surface calculation frequently fails for large, multi-chain 
>> structures. The calculation may be successful if the chains are 
>> treated individually, by using the "split" command before generating 
>> a surface.  If splitting is not desired or the structure is already a 
>> single chain, changing molecular surface parameters in the Selection 
>> Inspector or (before surface creation) the New Surfaces category of 
>> Preferences may allow the calculation to succeed.
>>
>> C:\Program Files\Chimera 1.7s\bin\mscalc.exe 1.400000 2.000000 1
>> MSMSLIB 1.3 started on Local PC
>> Copyright M.F. Sanner (March 2000)
>> Compilation flags
>>
>> Surface 3CPW.pdb, category ligand, probe radius 1.4, vertex density 2
>>   1 connected surface components
>>   Total solvent excluded surface area = 989.35
>>   Total solvent accessible surface area = 1473.85
>>
>> In this case, I am not interested in splitting the file into its 
>> individual chains. I have also unsuccessfully played with the 
>> probe-radius and vertex parameters.  I should mention that I was able 
>> to get this to work with previous versions of Chimera (1.5.something) 
>> and that small proteins can be successfully rendered with the latest 
>> versions.
>>
>> best,
>>
>> Antón
>
>
>
>
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20121129/ba6414f7/attachment.html>