[Chimera-users] surface calculation

[Anton Vila Sanjurjo]

Hi Eric,

I have finally found some time to play with a Linux machine and you are
perfectly right in that RNA surface computation works much better than on
Windows.

thanks,

anton

On Fri, Nov 30, 2012 at 9:17 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> Hi Anton,
> Yeah, on Windows machines it seems the RNA surface computation fails.  Do
> you have any ability to use a Linux or Mac machine?  The surfaces all work
> there.  Sorry about this.  On Windows, you can at least show the protein
> surfaces and RNA as ribbons by doing Actions->Ribbons->show after the
> Multiscale Models thing.
>
> --Eric
>
> On Nov 30, 2012, at 3:27 AM, Anton Vila Sanjurjo 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
>
>
>


-- 
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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20121211/863c908b/attachment.html>