[Chimera-users] surface calculation

[Anton Vila Sanjurjo]

Hi Eric,

thanks for the help. I've tried the Multiscale Models tool with a couple of
models of ribosomal subunits (2I2P and 3CPW) and, in both cases, it fails
to render the RNA but not the proteins at resolution = 0. I have also tried
a smaller RNA (tRNA, 1TRA) and it renders it fine. It also fails when I try
a pdb file containing 23S rRNA from 3CPW.

Antón

On Thu, Nov 29, 2012 at 8:14 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> 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
>
>
>
>


-- 
Antón Vila-Sanjurjo, PhD
Marie Curie fellow
Grupo QOSBIOS, Dept. Química Fundamental
Facultade de Ciencias
Universidade de A Coruña (UDC)
Campus Zapateira, s/n
15.071 - A Coruña - España (Spain).

tlf: (34) 981-167000 ext:2659
e-mail: antonvila.s at gmail.com
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