VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Dec 16 2009 - 10:21:12 CST

Hi,
  The lone character z is a keyword in the VMD atom selection language,
as are x and y. In order to make the selection you've intended, you'll
need to quote the z character appropriately to prevent it from being
interpreted as the z keyword.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Dec 16, 2009 at 07:59:47AM -0800, Samuel Coulbourn Flores wrote:
> Hi Guys,
>
> I am trying to hide one chain in my molecule, chain z. However if I type
> "not chain z" in the "Selected Atoms" box, I get an error saying, "The
> atom selection you typed could not be understood." It seems to understand
> other chain ID's, even lowercase ones. I guess I could rename the chain
> in the input file, but it breaks up the nice scheme I had worked out for
> handling multiple ribosomes without running out of alphanumeric characters
> for chain IDs. Presumably this is a bug. Is there a workaround?
>
> Thanks
>
> Sam
>
>
> ----- Original Message -----
> From: "Berit Hinnemann" <behi_at_topsoe.dk>
> To: "VMD" <vmd-l_at_ks.uiuc.edu>
> Sent: Wednesday, December 16, 2009 7:16:14 AM GMT -06:00 US/Canada Central
> Subject: Re: vmd-l: Graphics card for VMD
>
> Dear all,
>
> Thank you very much for your input and recommendations. I am right now
> checking prices with our IT department, and you gave me good grounds for
> making a decision.
>
> Best regards, Berit
>
> ----------------------------------------------------------------------
>
> Berit Hinnemann
> Research Scientist | Characterization Department | Research and
> Development Division
> Haldor TopsA,e A/S
> Catalysing your business
> NymA,llevej 55, DK-2800 Kgs. Lyngby
> Phone: +45 4527 2130 (direct)
> Read more at www.topsoe.com
>
> Axel Kohlmeyer To Berit Hinnemann <behi_at_topsoe.dk>
> <akohlmey_at_gmail.com> cc VMD <vmd-l_at_ks.uiuc.edu>
> Sent by: owner-vmd-l_at_ks.uiuc.edu Subject Re: vmd-l: Graphics card for VMD
>
> 15-12-2009 21:19
>
> On Tue, 2009-12-15 at 18:25 +0100, Berit Hinnemann wrote:
> > Dear all,
> >
> > I am planning to buy a new computer, which is to be used for VMD
> > visualizations. I previously had an nvidia GeForce graphics card, and
> > I would like to choose that again. Which model would you recommend
> > that works well with vmd 1.8.7, and also can use the new acceleration
> > features? I am planning to run RHEL 5 on the machine. Other than that,
> > a quad core processor and 8GB memory I think.
>
> whatever you can afford. at GTX 285 is currently the top performing
> card and will also help a lot in the GPU accelerated computing modules.
>
> i would look for a model that doesn't aggressively overclock and
> has solid cooling and thus makes less noise, which i consider
> important in a desktop.
>
> the quadro cards are _much_ more expensive but required in case you
> need stereo. i am very happy with the GTX285 in my desktop which
> had replaced a mid-level (pre-CUDA) quadro card (which wasn't bad
> for visualization with GLSL either).
>
> the GTX 295 is the top model, but it is basically two GTX 260 cards
> rolled into one case. that would allow you to e.g. have one GPU
> dedicated for graphics and one for GPU computing. but then again,
> it depends on your typical usage patterns, how much you'd gain
> from it. if you want to spend less money, you can reduce your
> requirements to, say, a GTX 280, GTX 275, GTX 260 perhaps even
> a GTX 250.
> if you want to have a single slot card, there are 9800 series
> cards, which are also much less power hungry, but they are one
> compute architecture older (yet, the fastest 9800 series card
> is still at about 50% the speed of the fastest cards).
>
> HTH,
> axel.
>
> > I would appreciate any recommendations. Thanks!
> >
> > Best regards,
> > Berit
> >
> > ______________________________________________________________________
> >
> > Berit Hinnemann
> > Research Scientist | Characterization Department | Research and
> > Development Division
> >
> > Haldor TopsA,e A/S
> > Catalysing your business
> > NymA,llevej 55, DK-2800 Kgs. Lyngby
> > Phone: +45 4527 2130 (direct)
> >
> > Read more at www.topsoe.com
> >
> >
> > ______________________________________________________________________
> >
> >
> > This e-mail message (including attachments, if any) is confidential
> > and may be privileged. It is intended only for the addressee.
> > Any unauthorised distribution or disclosure is prohibited. Disclosure
> > to anyone other than the intended recipient does not constitute waiver
> > of privilege.
> > If you have received this e-mail in error, please notify the sender by
> > e-mail and delete it and any attachments from your computer system and
> > records.
> > HALDOR TOPSOE (www.topsoe.com)
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> Institute for Computational Molecular Science
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
>
> ----------------------------------------------------------------------
>
> This e-mail message (including attachments, if any) is confidential and
> may be privileged. It is intended only for the addressee.
> Any unauthorised distribution or disclosure is prohibited. Disclosure to
> anyone other than the intended recipient does not constitute waiver of
> privilege.
> If you have received this e-mail in error, please notify the sender by
> e-mail and delete it and any attachments from your computer system and
> records.
> HALDOR TOPSOE (www.topsoe.com) 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078