[Chimera-users] surface calculation

Elaine Meng meng at cgl.ucsf.edu
Fri Nov 30 10:06:12 PST 2012 

We have not changed the default atomic radii since deciding on the original values, as far as I know.  That was long before 2008. 
Elaine

On Nov 30, 2012, at 9:55 AM, Tom Goddard wrote:

> Hi Antón,
> 
>   The molecular surface calculation code in Chimera (MSMS from Michel Sanner) has not been changed since 2008 (prior to Chimera 1.3).  So I am not sure why it would fail more often now.  Possibly  we have changed our standard atom radii in recent years, but I would not expect that to cause more failures.
> 
> 	Tom
> 
> 
>> From: Anton Vila Sanjurjo 
>> Subject: Re: [Chimera-users] surface calculation
>> Date: November 30, 2012 1:00:50 AM PST
>> To: Tom Goddard 
>> 
>> Hi Tom,
>> 
>> I had the same problem in Linux with the newer versions as well. 
>> 
>> thanks,
>> 
>> Antón
> 
> On Nov 30, 2012, at 3:27 AM, Anton Vila Sanjurjo <antonvila.s at gmail.com> wrote:
> 
>> 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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