Paul or anyone who can help,
I am trying to automate the selection and coloring of residues in JMol
using the following script:
*******************************************************************
<script type="text/javascript">
function residues()
{
var x = prompt("Enter Residues")
var y = prompt("Enter Color")
if (!x)return
else if (!y)return
jmolScript(""select "+x; "color "+y")
}
</script>
<button style='width:250' onclick="residues()">Select Residues</button>
*******************************************************************
It does NOT work! What am I doing wrong?!
Thank you SO MUCH!
Amjad
On Fri, Aug 9, 2013 at 10:51 AM, Amjad Farooq <am...@farooqlab.net> wrote:
> Hi Rolf,
>
> Thanks very much for your advice. I will look into your suggestions and
> get back to you.
>
> Amjad
>
>
> *AMJAD FAROOQ PhD DIC | Associate Professor
> Dept of Biochemistry & Molecular Biology | Miller School of Medicine |
> University of Miami | Miami | FL 33136
> Located @ Gautier Building #217 | Mail @ 1011 NW 15th Street #217, Miami ,
> FL 33136
> am...@farooqlab.net | off 305-243-2429 | lab 305-243-9799 | fax
> 305-243-3955 | www.farooqlab.net*
>
>
>
>
> On Fri, Aug 9, 2013 at 5:43 AM, Rolf Huehne <rhue...@fli-leibniz.de>wrote:
>
>> On 08/08/2013 08:31 PM, Amjad Farooq wrote:
>> > Paul,
>> >
>> > Thanks for your input. But, I do not believe Chimera is a web-based
>> > application. I am looking for a web-based application to perform
>> mutations.
>> >
>> Although an external program might not be web-based you could still use
>> it for doing the mutation.
>>
>> With the Jena3D viewer (http://jena3d.fli-leibniz.de) we do something
>> similar with Jmol in combination with the 'scap' program from the
>> 'jackal' program package for visualizing known variants (SNPs) in
>> protein structures (e.g. for PDB code 1DEH).
>> Although the amino acid exchanges are usually known beforehand and the
>> mutations are precomputed we also do it on-the-fly if no precomputed
>> mutants are available.
>>
>> Since there might be up to several hundred variants known for a single
>> structure we only load each mutated residue as a separate model and not
>> the whole modeled structure provided by 'scap'.
>>
>> I currently don't have time to go into more detail but if you are
>> interested I could tell you more in about a week.
>>
>> Regards,
>> Rolf
>>
>> --
>>
>> Rolf Huehne
>> Postdoc
>>
>> Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI)
>> Beutenbergstrasse 11
>> 07745 Jena, Germany
>>
>> Phone: +49 3641 65 6205
>> Fax: +49 3641 65 6210
>> E-Mail: rhue...@fli-leibniz.de
>> Website: http://www.fli-leibniz.de
>>
>> Scientific Director: Prof. Dr. K. Lenhard Rudolph
>> Head of Administration: Dr. Daniele Barthel
>> Chairman of Board of Trustees: Dennys Klein
>>
>> VAT No: DE 153 925 464
>> Register of Associations: No. 230296, Amtsgericht Jena
>> Tax Number: 162/141/08228
>>
>>
>>
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