[Chimera-users] surface calculation

[Anton Vila Sanjurjo]

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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