[Chimera-users] Chimera-users Digest, Vol 131, Issue 5

Fri Mar 7 09:17:12 PST 2014

Dear Chimera,

We recently got a mail on instruction to install correct parameters to  
get VMD-L to work:

"vmd-l: help with stereo viz on new samsung "3D" LCD and quadro card"

Now we ask, do you have any suggestion how to get "Samsung "3D" LCD  
and quadro card not to work - not only for:

1. Linux (Ubuntu) with "quadro card"

but also and on:

2. MacPro/Mavericks with "a quadro card"

We thank you in advance

Cheers
Peter et al.

Quoting chimera-users-request at cgl.ucsf.edu:

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> Today's Topics:
>
>    1.  surface failures (Julian Marzi)
>    2. Re: surface failures (Elaine Meng)
>    3. Area/Volume from Web not working (Hurt, Darrell (NIH/NIAID) [E])
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 4 Mar 2014 12:31:46 +0100
> From: Julian Marzi <julian.marzi at googlemail.com>
> To: chimera-users at cgl.ucsf.edu
> Subject: [Chimera-users]  surface failures
> Message-ID: <F372C2E9-7034-47D3-B94A-CBE2D6DEF470 at googlemail.com>
> Content-Type: text/plain; charset=us-ascii
>
> Dear Chimera,
>
> I try to show the surface of the 60S in yeast (PDB: 3O5H), but it  
> doesn't work. Mscalc returned code 11 is shown. If I split the 60S  
> every chain show the surface except the first strain (25S). How can  
> I show the surface from the first chain?
>
> Thank you very much
>
> Best regards
>
> Julian Marzi
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 6 Mar 2014 10:20:22 -0800
> From: Elaine Meng <meng at cgl.ucsf.edu>
> To: Julian Marzi <julian.marzi at googlemail.com>
> Cc: chimera-users at cgl.ucsf.edu
> Subject: Re: [Chimera-users] surface failures
> Message-ID: <E468C80B-D21F-40B7-A569-B66126212530 at cgl.ucsf.edu>
> Content-Type: text/plain; charset=us-ascii
>
> Dear Julian,
> The surface failure is a numerical thing that may differ on  
> different machines, and there is not a consistent recipe for how to  
> solve the problem.  Please see this page on possible solutions,  
> including showing some alternative types of surface instead of a  
> "molecular" surface:
>
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfprobs.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 4, 2014, at 3:31 AM, Julian Marzi <julian.marzi at googlemail.com> wrote:
>
>> Dear Chimera,
>> I try to show the surface of the 60S in yeast (PDB: 3O5H), but it  
>> doesn't work. Mscalc returned code 11 is shown. If I split the 60S  
>> every chain show the surface except the first strain (25S). How can  
>> I show the surface from the first chain?
>> Thank you very much
>> Best regards
>> Julian Marzi
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 6 Mar 2014 19:48:26 +0000
> From: "Hurt, Darrell (NIH/NIAID) [E]" <darrellh at niaid.nih.gov>
> To: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
> Subject: [Chimera-users] Area/Volume from Web not working
> Message-ID: <CF3E3B45.E956%darrellh at niaid.nih.gov>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi Chimera friends,
>
> I'm trying to use "Area/Volume from Web", but I keep getting an  
> error about how the server is not giving the expected output.
>
> I'm using build 39297.
>
> Any hints?
>
> Thanks,
> Darrell
>
> --
> Darrell Hurt, Ph.D.
> Section Head, Computational Biology
> Bioinformatics and Computational Biosciences Branch (BCBB)
> OCICB/OSMO/OD/NIAID/NIH
>
> 31 Center Drive, Room 3B62B, MSC 2135
> Bethesda, MD 20892-2135
> Office: 301-402-0095
> Mobile: 301-758-3559
> Web: BCBB Home  
> Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.aspx#niaid_inlineNav_Anchor>
> Twitter: @niaidbioit<https://twitter.com/niaidbioit>
>
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>
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> End of Chimera-users Digest, Vol 131, Issue 5
> *********************************************

-- 
___________________________________________________________
Peter Engelhardt, PhD, docent
Adjunct Professor in Molecular Genetics
Unit of Molecular Electron Tomography
Department of Pathology
Haartman Institute
P.O.Box 21 (Haartmaninkatu 3)
FIN-00014 University of Helsinki,
Finland

Email: Peter.Engelhardt at Helsinki.Fi
URL: http://www.lce.hut.fi/~engelhar/

Department of Pathology lab. tel: (+358-9)-19126729, 19126442
EM-lab, Tel: (+358-9)-19126261
Fax: (+358-9)-19126700 (Dept. of Pathology)

Nanomicroscopy Center,
Department of Applied Physics
Aalto University, School of Science and Technology,
Puumiehenkuja 2, FI02150 Espoo
Finland

Mobil: +358-400193342
Home address:
Lindstedstvägen 1 B 7
FIN-02700 Grankulla,
Finland
Home Tel: +358400193342