VMD-L Mailing List

From: Wagener, M. (Markus) (markus.wagener_at_organon.com)
Date: Fri Feb 27 2004 - 04:39:48 CST

Hi John,

thank you very much for your kind answer.

In the meantime the problems has been solved. While porting
some protocols from charmm to namd/vmd we got confused
and were comparing slightly different pdb files in charmm
and vmd. So, there are no issues with distance based
selections in charmm/vmd, respectively.

Markus

> -----Original Message-----
> From: John Stone [mailto:johns_at_ks.uiuc.edu]
> Sent: Wednesday, February 25, 2004 8:29 PM
> To: Wagener, M. (Markus)
> Cc: 'vmd-l_at_ks.uiuc.edu'
> Subject: Re: vmd-l: atomselect within
>
>
>
> Markus,
> There could be several reasons for the differences you mention.
> One could implement distance based atom selections a number of ways,
> but they aren't actually the same thing. For example, do you only
> return the atoms for which the atom centers fall within the distance
> cutoff, or do you also return atoms for which any part of the atom
> (i.e. based on its radius) falls within the cutoff distance, or do you
> only return atoms that are entirely within the cutoff distance?
>
> Since I don't know anything about how Charmm implements its ".around"
> command, I can't really say what the differences are, but I
> suspect that
> VMD and Charmm are doing a slightly different type of cutoff
> calculation.
>
> Keep in mind that if you make a selection such as "within 5
> of (xxxx)"
> if VMD and Charmm implement 'xxxx' differently, then you'll also get
> differing results. Since you didn't mention what selections
> you actually
> tried, I don't have any other suggestions for you to try.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, Feb 25, 2004 at 03:23:37PM +0100, Wagener, M. (Markus) wrote:
> > Hi,
> >
> > while comparing distance based atomselections made with
> > charmm (using ".around.") and with vmd (using "within")
> > I noticed some small differences. Are there any issues known?
> >
> > BTW, I am using vmd V1.8.1 on IRIX and CHARMm V29.1
> >
> > Cheers,
> > Markus
> >
> >
> > --
> > -----------------------------------------------------------
> > Dr. Markus Wagener
> > NV Organon
> > MDI-CMC RK2330 phone: +31-412-661380
> > P.O. Box 20 FAX: +31-412-662539
> > 5340 BH Oss Email: markus.wagener_at_organon.com
> > The Netherlands
> > -----------------------------------------------------------
> >
> > --------------------------------------------------------------------
> > This message, including attached files, may contain confidential
> > information and is intended only for the use by the individual
> > and/or the entity to which it is addressed. Any unauthorized use,
> > dissemination of, or copying of the information contained herein is
> > not allowed and may lead to irreparable harm and damage for which
> > you may be held liable. If you receive this message in error or if
> > it is intended for someone else please notify the sender by
> > returning this e-mail immediately and delete the message.
> > --------------------------------------------------------------------
>
> --
> 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

> -----Original Message-----
> From: John Stone [mailto:johns_at_ks.uiuc.edu]
> Sent: Wednesday, February 25, 2004 8:29 PM
> To: Wagener, M. (Markus)
> Cc: 'vmd-l_at_ks.uiuc.edu'
> Subject: Re: vmd-l: atomselect within
>
>
>
> Markus,
> There could be several reasons for the differences you mention.
> One could implement distance based atom selections a number of ways,
> but they aren't actually the same thing. For example, do you only
> return the atoms for which the atom centers fall within the distance
> cutoff, or do you also return atoms for which any part of the atom
> (i.e. based on its radius) falls within the cutoff distance, or do you
> only return atoms that are entirely within the cutoff distance?
>
> Since I don't know anything about how Charmm implements its ".around"
> command, I can't really say what the differences are, but I
> suspect that
> VMD and Charmm are doing a slightly different type of cutoff
> calculation.
>
> Keep in mind that if you make a selection such as "within 5
> of (xxxx)"
> if VMD and Charmm implement 'xxxx' differently, then you'll also get
> differing results. Since you didn't mention what selections
> you actually
> tried, I don't have any other suggestions for you to try.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, Feb 25, 2004 at 03:23:37PM +0100, Wagener, M. (Markus) wrote:
> > Hi,
> >
> > while comparing distance based atomselections made with
> > charmm (using ".around.") and with vmd (using "within")
> > I noticed some small differences. Are there any issues known?
> >
> > BTW, I am using vmd V1.8.1 on IRIX and CHARMm V29.1
> >
> > Cheers,
> > Markus
> >
> >
> > --
> > -----------------------------------------------------------
> > Dr. Markus Wagener
> > NV Organon
> > MDI-CMC RK2330 phone: +31-412-661380
> > P.O. Box 20 FAX: +31-412-662539
> > 5340 BH Oss Email: markus.wagener_at_organon.com
> > The Netherlands
> > -----------------------------------------------------------
> >
> > --------------------------------------------------------------------
> > This message, including attached files, may contain confidential
> > information and is intended only for the use by the individual
> > and/or the entity to which it is addressed. Any unauthorized use,
> > dissemination of, or copying of the information contained herein is
> > not allowed and may lead to irreparable harm and damage for which
> > you may be held liable. If you receive this message in error or if
> > it is intended for someone else please notify the sender by
> > returning this e-mail immediately and delete the message.
> > --------------------------------------------------------------------
>
> --
> 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
>
--------------------------------------------------------------------
This message, including attached files, may contain confidential
information and is intended only for the use by the individual
and/or the entity to which it is addressed. Any unauthorized use,
dissemination of, or copying of the information contained herein is
not allowed and may lead to irreparable harm and damage for which
you may be held liable. If you receive this message in error or if
it is intended for someone else please notify the sender by
returning this e-mail immediately and delete the message.
--------------------------------------------------------------------