Jmol

Patrick wrote:

> 	I've noticed that Jmol draws space-filling models with what look like
> rather larger van der Waal's radii than you would expect. If you look
> at:
>
> 		http://macxray.chem.upenn.edu/tutorial/basepair.html
>
> and change all the atoms to 100% VDW, the H's are really totally buried
> in  the atoms to which they are hydrogen bonded.

The vdwRadius values that we are using are taken from OpenBabel.

Recently, there was some discussion on the OpenBabel list because someone
thought that some of the numbers were off.

> If I use the same PDB
> file in  rasmol, I get a more reasonable looking display.

I don't know what the RasMol numbers are.

I know that some of the RasMol radii are larger than they should be ...
because Roger is trying to make up for the fact that .PDB files do not
have hydrogen atoms.


NOTE!

It would be great if someone would volunteer to look up the VDW and
covalent bonding radii in an accepted reference text.

For the ionic radii we are using:
   * This data is from
   *  Handbook of Chemistry and Physics. 48th Ed, 1967-8, p. F143
   *  (scanned for Jmol by Phillip Barak, Jan 2004)
   ****************************************************************/

I can easily send the current values to someone ...


> The VDW radii
> displayed in  the "Atom Properties" item on the "edit" menu in the Jmol
> application up to  version 9 are reasonable, but the display looks
> "wrong".

I seriously doubt if those values are even being used in Jmol 9.

> BTW, that menu  item is "gone" from Jmol 10? (it would be nice
> to be able to adjust Atom  Properties).

Jmol will probably be able to support this kind of thing in the 'not near'
future ... through loading the values from a text file.

Then, someone can put a nice table display on top of it.


Miguel

Sarom wrote:
> Is it possible to take in a bunch of .xyz files and then convert them
> into .png files?

Jmol does not have a mechanism for doing this.

> This also also my first time posting - are there any etiquette for the
> group that I should be aware of?

The users list is relatively small. No special rules. Ask whatever you want.


Thank you for asking.


Miguel

On Mar 25, 2004, at 1:48 AM, Miguel wrote:

> Sarom wrote:
>> Is it possible to take in a bunch of .xyz files and then convert them
>> into .png files?
>
> Jmol does not have a mechanism for doing this.
>


Are you familiar with the program babel?  It is available for most 
platforms or can be compiled.  It's sole purpose in life is converting 
among different file formats for structure data.  I have  used it to 
convert among, for example, .mol, .pdb and .smi files.  It supports a 
long list of structure formats.


I thought .png was a generic graphics format like .tiff or .jpg.  
Therefore, could not one do a screen capture (on the Mac I would use 
grab) while using Jmol then save the screen capture and use another 
program to convert to .png (using photoshop or gimp or ?)?    But maybe 
you are thinking of another type of .png file.

Judith Cohn

--------------------------
Judith Cohn, Ph.D.
Bioscience Division
Mail Stop M888
Los Alamos National Lab
Los Alamos, NM 87545
Phone:  505-665-0999
Email:  jcohn@...

On Thu, 25 Mar 2004 02:19:12 -0500, Sarom @ George Mason University wrote
> Is it possible to take in a bunch of .xyz files and then convert 
> them into .png files?
> 

You can use PyMol to do this. Set up a script that'll give you the kind of
output image you want and then writea small shell script to loop through the
.xyz files to feed each to PyMol and write out the .png file.

Rich

Jan wrote:
> with the model structure 1uxf there is a strange cartoon-sheet-shape
> near ARG479A
> http://www.imb-jena.de/cgi-bin/SCOPlnk.exe?JMOL=1uxf

Yes, it looks strange.

I have logged a bug.


Miguel