[Chimera-users] Problem in Surface depiction

[Elaine Meng]

Hi Yongjun,
Again, we do not recommend sending bug reports to chimera-users at cgl.ucsf.edu 
  -- instead you should use "Help... Report a Bug" in the Chimera menu.

However, there is no need to do that in this case, it is the common  
problem previously discussed in many messages.  Please see this  
previous post for possible workarounds:
<http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-January/004713.html 
 >

Elaine

On Mar 31, 2010, at 9:40 AM, Yongjun Dang wrote:

> This is error report when I try to run this program.
> Thanks.
> Yongjun
>
>
> You are now running Chimera version 1.4.1 (build 30333).
> Your previous version was 1.4.1 (build 30226).
> Check the release notes for new features and other info.
> (To access the release notes, use the Help menu to bring up the User's
> Guide.
> Then click the 'Documentation index' link and you will then see a link
> for the release notes.)
> /Applications/Chimera.app/Contents/Resources/bin/mscalc 1.400000  
> 2.000000 1
> MSMSLIB 1.3 started on wirelessjhmi144-10-237-144-73.ebalto.jhmi.edu
> Copyright M.F. Sanner (March 2000)
> Compilation flags
>
> Surface 2otl, category ligand, probe radius 1.4, vertex density 2
>  1 connected surface components
>  Total solvent excluded surface area = 171.512
>  Total solvent accessible surface area = 345.462
> /Applications/Chimera.app/Contents/Resources/bin/mscalc 1.400000  
> 2.000000 1
> MSMSLIB 1.3 started on wirelessjhmi144-10-237-144-73.ebalto.jhmi.edu
> Copyright M.F. Sanner (March 2000)
> Compilation flags
> ERROR: add_rs_component: Too many RS components
> Calculation of some surface components failed.
> Falling back to single-component calculation.
> /Applications/Chimera.app/Contents/Resources/bin/mscalc 1.400000  
> 2.000000 0
> MSMSLIB 1.3 started on wirelessjhmi144-10-237-144-73.ebalto.jhmi.edu
> Copyright M.F. Sanner (March 2000)
> Compilation flags
> Surface calculation failed, mscalc returned code -11
>
>
> On 3/31/10 12:04 PM, "Elaine Meng" <meng at cgl.ucsf.edu> wrote:
>
>> Hi Kshatresh,
>> Although we are aware of problems calculating some surfaces, this
>> sounds like a different problem because the others would not stop
>> Chimera, and they only happen for some fraction of structures, not  
>> all
>> the time as you suggest.
>>
>> Your problem is more likely with the graphics driver on your machine.
>> It is better to use "Help... Report a Bug" in the Chimera menu to
>> report these problems (not sending mail to chimera-
>> users at cgl.ucsf.edu), because that would send us details about your
>> machine.
>>
>> However, some things you could try are
>> - updating your graphics driver
>> - in Chimera, set Preferences (under Favorites), General category,
>> "Debug OpenGL on startup" to "true", click Save.  Exit Chimera and
>> restart, and then in the debug dialog, turn off "VertexBufferObject"
>>
>> Although it doesn't sound like you are having the other surface
>> problems I mentioned, they and some workarounds are discussed here:
>> <http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-January/004713.html
>>>
>>
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.
>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>>
>> On Mar 31, 2010, at 4:18 AM, Kshatresh Dutta Dubey wrote:
>>
>>> Dear All,
>>> I am using chimera 1.41 and  1.4 on a 3 GB Core 2 duo machine. When
>>> i draw surface for any ligand or residue then suddenly it get
>>> closed. This problem occurs in both versions 1.4 and 1.4.1. Kindly
>>> suggest me to fix this problem.
>>> Regards
>>> Kshatresh Dutta Dubey
>>>
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>
>
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