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@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])

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Message: 1 Date: Tue, 4 Mar 2014 12:31:46 +0100 From: Julian Marzi <julian.marzi@googlemail.com> To: chimera-users@cgl.ucsf.edu Subject: [Chimera-users] surface failures Message-ID: <F372C2E9-7034-47D3-B94A-CBE2D6DEF470@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

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Message: 2 Date: Thu, 6 Mar 2014 10:20:22 -0800 From: Elaine Meng <meng@cgl.ucsf.edu> To: Julian Marzi <julian.marzi@googlemail.com> Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] surface failures Message-ID: <E468C80B-D21F-40B7-A569-B66126212530@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@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

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Message: 3 Date: Thu, 6 Mar 2014 19:48:26 +0000 From: "Hurt, Darrell (NIH/NIAID) [E]" <darrellh@niaid.nih.gov> To: "chimera-users@cgl.ucsf.edu BB" <chimera-users@cgl.ucsf.edu> Subject: [Chimera-users] Area/Volume from Web not working Message-ID: <CF3E3B45.E956%darrellh@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.a...> Twitter: @niaidbioit<https://twitter.com/niaidbioit>

Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

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End of Chimera-users Digest, Vol 131, Issue 5 *********************************************

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