VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Jan 20 2012 - 20:17:22 CST

On Fri, Jan 20, 2012 at 8:55 PM, Zumot, Elia Nabil <enz1_at_pitt.edu> wrote:
> Hi John,
>
> All my pdb and psf files were generated with VMD(1.8.7 or 1.9) and the AutoPSF plugin.
> Also, all my simulations were run by NAMD (2.7 or 2.8) (thus, dcd and restart.coor files).
> resnames here are SOD and CLA.

resname is irrelevant. out of the file formats that you list, VMD will
be able to recognize
the elements sodium and chlorine only correctly from a pdb file that
has the (mandated by
the standard but often omitted) columns with the element symbols.
try a simple .pdb file like this:

CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1
ATOM 1 SOD SOD X 0 -4.000 0.000 0.000 0.00 0.00 NA
ATOM 2 CLA CLA X 0 4.000 0.000 0.000 0.00 0.00 CL
END

and compare its visualization to the of this file:

CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1
ATOM 1 SOD SOD X 0 -4.000 0.000 0.000 0.00 0.00
ATOM 2 CLA CLA X 0 4.000 0.000 0.000 0.00 0.00
END

if you read a .psf file, you are missing the element information,
so VMD is in the dark about what elements you are actually looking at.

> I'm assuming the values that you will tell me about are the ones that will be multiplied by the scaling factor set by the user in the "sphere scale" in the "graphical representations" window for display?

yes.

> And if use the tcl command:
> $sel set radius 1.0
> Does this mean a radius of 1 Angstrom or a scaling of 1?

radius, of course. the scaling factor is a per-representation
property, while the radius is a per atom property.

axel.

> Thanks a lot
>
> Elia
>
>
> Elia Zomot, PhD
> Computational and Systems Biology Department
> School of Medicine, University of Pittsburgh
> 3083 BST3, 3501 Fifth Ave, Pittsburgh, PA 15213
> Voice: 412 624 8699 - Fax: 412 648 3163
> enz1_at_pitt.edu
> ________________________________________
> From: John Stone [johns_at_ks.uiuc.edu]
> Sent: Friday, January 20, 2012 3:05 PM
> To: Zumot, Elia Nabil
> Cc: Axel Kohlmeyer; vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: ionic radii of sodium and chloride
>
> Hi Elia,
>  The way VMD assigns atomic properties (e.g. radii, masses, etc) depends
> greatly upon what file formats you used when you loaded the structure into
> VMD.  Some file formats provide VMD with explicit values for all of the
> key atomic properties, other file formats provide nothing but the atom
> name and coordinates.  In the cases where the files loaded do not contain
> an atomic property such as the radius, VMD has to "guess" this information
> using some combination of the atomic properties that the file does specify.
> Some VMD molecule file reader plugins also contain their own atomic
> property lookup tables because they are able to do a better job at guessing
> than VMD can because they have access to file-format-specific details that
> VMD doesn't know about.  So, the particular strategy that is used for a given
> structure depends directly on the details of what files you loaded, what
> file formats they were stored in, and what information was contained therein.
>
> If you me us more about what files you're loading, I can tell you how the
> radii are getting assigned.
>
> Axel's suggestion is a simple way to address the immediate problem by
> overriding the auto-assigned radii with an atom selection command.
>
> Cheers,
>  John
>
>
> On Fri, Jan 20, 2012 at 11:57:19AM -0500, Zumot, Elia Nabil wrote:
>> Thank you Axel.
>>
>> Could you direct me to the file that contains the atomic radii that are displayed in VMD?
>>
>> (I have found the PeriodicTable.C file but it contains the correct ionic radii)
>>
>> Best
>>
>> Elia
>>
>>
>>
>>
>> Elia Zomot, PhD
>> Computational and Systems Biology Department
>> School of Medicine, University of Pittsburgh
>> 3083 BST3, 3501 Fifth Ave, Pittsburgh, PA 15213
>> Voice: 412 624 8699 - Fax: 412 648 3163
>> enz1_at_pitt.edu
>> ________________________________________
>> From: Axel Kohlmeyer [akohlmey_at_gmail.com]
>> Sent: Thursday, January 19, 2012 10:12 PM
>> To: Zumot, Elia Nabil
>> Cc: vmd-l_at_ks.uiuc.edu
>> Subject: Re: vmd-l: ionic radii of sodium and chloride
>>
>> On Jan 19, 2012, at 10:03 PM, "Zumot, Elia Nabil" <enz1_at_pitt.edu> wrote:
>>
>> > Dear VMDers,
>> >
>> > Any reason why VMD shows sodium ions to be bigger than chloride when it should be the other way around?
>> >
>> > In crystals the radius of Na+ is 0.095 nm and that of Cl-  0.181 nm.
>> >
>>
>> That is because VMD cannot tell the difference between an element and
>> an ion or a chlorine or chloride and a carbon.
>>
>> If you don't like VMD's choices you can always write a little script
>> that changes it or use a file format that does contain the radius
>> information in a way that VMD supports reading it.
>>
>> VMD is very deliberately a very dumb and ignorant software that relies
>> on you to provide it with the proper information. It does not even try
>> to be smart (for the most part, that is).
>>
>> Axel
>>
>>
>>
>> >
>> > Thanks
>> >
>> > Elia Zomot
>> >
>> >
>> >
>> > Elia Zomot, PhD
>> > Computational and Systems Biology Department
>> > School of Medicine, University of Pittsburgh
>> > 3083 BST3, 3501 Fifth Ave, Pittsburgh, PA 15213
>> > Voice: 412 624 8699 - Fax: 412 648 3163
>> > enz1_at_pitt.edu
>
> --
> 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 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.