VMD-L Mailing List

From: matziast_at_med.uth.gr
Date: Mon Oct 31 2011 - 16:23:38 CDT

Hi,
you are right, sorry. Both of the two ways:
(proteinback or nucleicback) and not within 12 of resname X and
backbone and not (within 12 of resname X) gave the same result, all atoms were
fixed. I checked VMD, it recognizes correctly the structure.
Thank you in advance,
Maria.

Quoting John Stone <johns_at_ks.uiuc.edu>:

>
> Hi,
> Are you sure that VMD is correctly recognizing your structure
> in the first place? Do you see what you expect to see if you
> just select "protein", or "not protein", "backbone", and "not backbone"
> for example? If you expect people to help you, you'll have to give
> more feedback on what results you got than simply "it was not the solution".
> What remained incorrect after you tried the suggestions people gave you?
> Be specific.
>
> Cheers,
> John
>
> On Mon, Oct 31, 2011 at 10:57:03PM +0200, matziast_at_med.uth.gr wrote:
>> Unfortunately it was not the solution.
>>
>>
>> Quoting Chris Harrison <charris5_at_gmail.com>:
>>
>> >backbone and not (within 12 of resname X))
>> >
>> >Best,
>> >Chris
>> >
>> >
>> >--
>> >Chris Harrison, Ph.D.
>> >Theoretical and Computational Biophysics Group
>> >NIH Resource for Macromolecular Modeling and Bioinformatics
>> >Beckman Institute for Advanced Science and Technology
>> >University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
>> >
>> >char_at_ks.uiuc.edu Voice: 773-570-0329
>> >http://www.ks.uiuc.edu/~char Fax: 217-244-6078
>> >
>> >
>> >matziast_at_med.uth.gr writes:
>> >>Date: Mon, 31 Oct 2011 19:45:50 +0200
>> >>From: matziast_at_med.uth.gr
>> >>To: vmd-l_at_ks.uiuc.edu
>> >>Subject: vmd-l: selection
>> >>User-Agent: Internet Messaging Program (IMP) H3 (4.0.3)
>> >>
>> >>Hi,
>> >>I want to select only the protein backbone and the nucleic backbone and
>> >>not
>> >>within 12 or resname X.
>> >>For that reason I type "proteinback or nucleicback and not within 12
>> >>of resname
>> >>X"
>> >>but the final selection included all proteins and backbone. Why?
>> >>I would appreciate if anyone could help me.
>> >>Thank you in advance.
>> >
>>
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078
>

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