Hi Abhinav,
Whitespace matters. In fact, the first two characters in the atom name field
of the pdb file are usually considered indicating the element type. Pymol
also does this. This means that " NA " will be considered of element type "
N", whereas "NA " will be interpreted as being of element "NA". Likewise "
CL " will give "C", while "CL " will give "CL". You can verify this
behaviour by issuing 'label (all),elem'.
Best,
Tsjerk
-- Forwarded message --
From: Abhinav Verma
Date: Nov 27, 2007 4:35 PM
Subject: Fwd: [PyMOL] sphere diameter
To: tsje...@gmail.com
Hi Tsjerk,
did you get this email. Ok I donot need this, but I am really confused.
Thanks for the help with changing ionic radii..
Abhi
-- Forwarded message --
From: Abhinav Verma
Date: Nov 26, 2007 6:36 PM
Subject: Re: [PyMOL] sphere diameter
To: "Mayer, Mark (NIH/NICHD) [E]" , Pymol
Okey, something wierd and I do not understand. I am attaching 2 pdb
files and 2 png's from pymol. 3.pdb, 4.pdb, 3.png and 4.png.
Now the only difference between 3 and 4 are in blank spaces. and the
sphere radius change between the two pdb files. In one Na is bigger
and in other Cl is ..
any ideas??.. bug or feature!!
On Nov 26, 2007 5:53 PM, Mayer, Mark (NIH/NICHD) [E]
wrote:
> Thanks Abhinav,
>
> No other posts yet; you are probably right that these are VDW values,
> but nice to know for sure, and also good to be able to change to ionic
> radii if desired.
>
>
>
> -Original Message-
> From: Abhinav Verma [mailto:abhinav1...@gmail.com]
> Sent: Mon 11/26/2007 7:35 PM
> To: Mayer, Mark (NIH/NICHD) [E]
> Cc: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] sphere diameter
>
> set sphere_scale should scale the spheres, but they should be
> proportionate and they are van der waal spheres I guess, so chlorine
> is smaller than soduim..
> http://pt.chemicalstore.com/
> 227 vs 175 pm for na and cl respecively.
>
>
>
> On Nov 26, 2007 4:15 PM, Dr. Mark Mayer wrote:
> > hello,
> >
> > Can't find anything about this in docs or in settings:
> >
> > Where are sphere diameter settings controlled for individual atomic
> > species: I'm trying to make fig with ions and the sizes don't seem
> > to be right - Cl too small and Na too big.
> >
> > Thanks
> >
> > --
> > Mark Mayer Ph.D.
> > LCMN NICHD NIH DHHS
> > Bldg 35, Room 3B 1002 MSC 3712
> > 35 Lincoln Drive
> > Bethesda MD 20892 3712
> > Phone: 301-496-9346 (office); 301-496-9347 (lab); FAX 301-496-2396
> > Lab web site: http://mayerlab.nichd.nih.gov
> >
> > Send packages, Fedex and anything requiring a signature to:
> >
> > Bldg 35, Room 3B 1004
> > 35 Lincoln Drive
> > Bethesda MD 20892
> >
> >
> >
-
> > This SF.net email is sponsored by: Microsoft
> > Defy all challenges. Microsoft(R) Visual Studio 2005.
> > http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/
> > ___
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> > PyMOL-users@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
>
>
>
> --
> Abhianv Verma
> Research Associate,
> Daggett Lab, Dept. of Medicinal Chemistry,
> University of Washington,
> Seattle, WA, 98195-7610 USA
>
>
--
Abhianv Verma
Research Associate,
Daggett Lab, Dept. of Medicinal Chemistry,
University of Washington,
Seattle, WA, 98195-7610 USA
--
Abhianv Verma
Research Associate,
Daggett Lab, Dept. of Medicinal Chemistry,
University of Washington,
Seattle, WA, 98195-7610 USA
--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
<><>
3.pdb
Description: Protein Databank data
4.pdb
Description: Protein Databank data
