[Molvis-list] FirstGlance 0.99 Pre-Release

Frieda Reichsman friedar at nsm.umass.edu
Fri Apr 14 12:48:04 EDT 2006


On Apr 14, 2006, at 12:01 PM, A. Malcolm Campbell wrote:

> I just tried out 0.99 using OS 10.4.6 using Safari 2.03. Find  
> worked perfectly and I like it a lot.
>
> I tried contacts and the first time, it crashed when I made my  
> display selections and then clicked on the molecule.

Hi Malcolm,

I am also on OSX 10.4.6 and Safari 2.03, and I'd like to try to  
reproduce this - Can you clarify what you mean by 'display  
selections' ? Do you mean using Find to select a Target for contacts?

Frieda

> I tried a second time when I clicked on my molecule first and then  
> made my display choices and clicked on the link that said show  
> contacts and it worked fine. Very nice display with good support text.
>
> I like both of these features a lot. Very powerful in combination,  
> too.
>
> Malcolm
>
>
> On Apr 13, 2006, at 9:09 PM, Eric Martz wrote:
>
>> I have put a pre-release of FirstGlance in Jmol 0.99 at
>>
>> http://bioinformatics.org/firstglance/fgij
>>
>> Please try this new version and let me know of any unexpected  
>> results, bugs, or suggestions. I anticipate that after a settling/ 
>> debugging period of about a week, 0.99 will supercede the present  
>> public version 0.98 (at firstglance.jmol.org). I have tested  
>> Windows IE/Firefox, and Mac OSX 10.3.9 Safari/Firefox. (I don't  
>> have OSX 10.4.)
>>
>> MAJOR NEW FEATURES IN 0.99
>>
>> -- A "Find.." dialog that highlights residues specified with  
>> sequence numbers or ranges. Something along this line was  
>> requested by NSMB before Evelyn Jabri departed. A link, with  
>> explanation, to Dunbrack's S2C listing -- available from "Find.."  
>> or "More Views..". S2C reveals gaps in the structural coordinates,  
>> typically due to crystallographic disorder.
>>
>> -- A "Contacts.." dialog that shows non-covalent bonds between any  
>> "target" you select (usually by clicking on it) and the remainder  
>> of the model. Non-covalent bonds are divided into five types, and  
>> each type can be shown or hidden. "Contacts.." required by far the  
>> largest amount of code among all the features of FirstGlance, but  
>> I thought it well worth the effort.
>>
>> -- All salt bridges or cation-pi interactions can be shown from a  
>> new link under More Views..
>>
>> List of all changes in this version:
>> http://bioinformatics.org/firstglance/fgij/versions.htm
>>
>> The main enhancement planned between version 0.99 and future  
>> version 1.0 is support for translations to Spanish and other  
>> languages.
>>
>> -Eric
>>
>> /* - - - - - - - - - - - - - - - - - - - - - - - - - - -
>> Eric Martz, Professor Emeritus, Dept Microbiology
>> U Mass, Amherst -- http://www.umass.edu/molvis/martz
>>
>> Biochem 3D Education Resources http://MolviZ.org
>> See 3D Molecules, Install Nothing! - http://firstglance.jmol.org
>> Protein Explorer - 3D Visualization: http://proteinexplorer.org
>> Workshops: http://workshops.proteinexplorer.org
>> World Index of Molecular Visualization Resources: http:// 
>> molvisindex.org
>> ConSurf - Find Conserved Patches in Proteins: http:// 
>> consurf.tau.ac.il
>> Atlas of Macromolecules: http://atlas.proteinexplorer.org
>> PDB Lite Macromolecule Finder: http://pdblite.org
>> Molecular Visualization EMail List (molvis-list):
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>
>
> ________________________________________________________
> A. Malcolm Campbell, Ph.D.
> Associate Professor of Biology
> Davidson College
> Director of GCAT (www.bio.davidson.edu/GCAT)
>
> Box 7118 (US Mail)
> 209 Ridge Road (shipping)
> Davidson, NC  28036
> 704-894-2692 (phone)
> 704-894-2512 (fax)
> www.bio.davidson.edu/campbell
>
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///////////////////////////////////////////

Frieda Reichsman, PhD
Molecules in Motion
Interactive Molecular Structures
http://www.moleculesinmotion.com

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