Hi Vinu,
As far as I know there is no way to autmatically color a domain in
Jmol. To accomplish this you would need to select the residues in the
domain, and then use a color command. If the domain were from
residues 20-114 of chain B, it would look like this
select 20-114:B
color [r,g,b] or {xRRGGBB]
where the colors values r,g,b are red, green blue between 0 and 255,
or hexadecimal codes RRGGBB. There are also predefined colors
available at jmol.org.
Just this past weekend I saw that one can color by domain in CN3D,
the visualization program from NCBI (National Center for
Biotechnology Information). This is a great feature, but I am not
sure if they link to a database to do it, or what. But according to
the person I spoke to, it works off-line as well.
Frieda
On Mar 15, 2007, at 8:30 AM, vinu manikandan wrote:
hi..
every one.. i had small doubt..
i will input the sequence through a program in to the jmol
i want the domain sequence to be highlighted only ...
iam not able to figure that.
would any one able to give an hint for tht
loves vinu
On 3/15/07, [EMAIL PROTECTED] < jmol-users-
[EMAIL PROTECTED]> wrote:
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Today's Topics:
1. isosurfaces and the new translucency (Frieda Reichsman)
2. Re: isosurfaces and the new translucency (S?rgio Ceroni da
Silva)
3. Error message- Cannot invert matrix (Steven Vik)
4. Re: Translucency issue - black bonds (Bob Hanson)
5. Jmol 11.1.22 features (Bob Hanson)
6. Translucency issue - black bonds (Nick Greeves)
----------------------------------------------------------------------
Message: 1
Date: Wed, 14 Mar 2007 15:02:21 -0400
From: Frieda Reichsman <[EMAIL PROTECTED] >
Subject: [Jmol-users] isosurfaces and the new translucency
To: [email protected]
Message-ID: < [EMAIL PROTECTED]>
Content-Type: text/plain; charset="us-ascii"
I'm enjoying the beauty of the new translucency with surfaces. But I
find that In Jmol 11.1.21 , using the command
isosurface mysurface translucent on
the 'on' throws an error - invalid argument. Probably wants a number
for translucency, right?
But, in Jmol 11.1.18, the 'on' is required to show a surface (loaded
mysurface with a jvxl file) -- if I leave off the 'on' the command is
ineffective - no surface appears. So maybe a backward compatibility
issue?
The inconsistency between Jmol versions is the same using:
isosurface mysurface opaque on
Frieda
///////////////////////////////////////////
Frieda Reichsman, PhD
Molecules in Motion
Interactive Molecular Structures
http://www.moleculesinmotion.com
///////////////////////////////////////////
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Message: 2
Date: Wed, 14 Mar 2007 16:48:39 -0300
From: S?rgio Ceroni da Silva <[EMAIL PROTECTED]>
Subject: Re: [Jmol-users] isosurfaces and the new translucency
To: [email protected]
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Frieda Reichsman wrote:
> I'm enjoying the beauty of the new translucency with surfaces...
I also enjoyed the translucent beauty of Jmol, but after a "color
translucent X" commands like wireframe and spacefill cease to work
properly.
--
Dr. S?rgio Ceroni da Silva
Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul
Av. Bento Gon?alves, 9500 - Pr?dio 43421 - Campus do Vale - Caixa
Postal 15005
Porto Alegre, RS - Brasil - 91501-970
==================================================
Tel.: +55 (51) 3316-6091 | Fax: +55 (51) 3316-7309
http://www6.ufrgs.br/bioquimica
------------------------------
Message: 3
Date: Wed, 14 Mar 2007 16:04:34 -0500
From: Steven Vik <[EMAIL PROTECTED]>
Subject: [Jmol-users] Error message- Cannot invert matrix
To: < [email protected]>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset="US-ASCII"
Using both the applet and the application ( jmol-11.0.RC4), I get the
following error message when using the pdb file 6LDH:
ScriptException:javax.vecmath.SingularMatrixException: cannot
invert matrix
Presumably there is something unusual about this pdb file, but I can't
figure out what it is.
-Steve
*****************************************************************
Steven B. Vik
Professor
Department of Biological Sciences
Southern Methodist University
Dallas, TX 75275-0376
Phone (214) 768-4228
Fax (214) 768-3955
E-mail [EMAIL PROTECTED]
WWW http://faculty.smu.edu/svik or http://www.smu.edu/biology/
*****************************************************************
------------------------------
Message: 4
Date: Wed, 14 Mar 2007 18:32:40 -0500
From: Bob Hanson < [EMAIL PROTECTED]>
Subject: Re: [Jmol-users] Translucency issue - black bonds
To: Nick Greeves <[EMAIL PROTECTED]>
Cc: [email protected]
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Thank you! I had seen that and then couldn't reproduce it. This is
easily fixable. I'm onto it. Should be fixed in 11.1.22
Bob
Nick Greeves wrote:
> Hi Bob,
> I like this new feature but I've noticed an odd aretefact. If I
select
> oxygen in say binaphthol.pdb and make them translucent the bonds to
> oxygen go black.
> I used select oxygen: color translucent .4 in console.
>
> All the best
>
> Nick
>
> --
>
> WWW Pages: http://www.liv.ac.uk/Chemistrywww/Staff/greeves.html
>
> Tel: +44 (0)151-794-3506 (3500 secretary)
>
>
> =
>
----------------------------------------------------------------------
--
>
>
>
>
----------------------------------------------------------------------
--
>
>
> On 13 Mar 2007, at 20:00, [EMAIL PROTECTED]
> <mailto:[EMAIL PROTECTED] > wrote:
>
>> Date: Tue, 13 Mar 2007 09:58:53 -0500
>>
>> From: Bob Hanson <[EMAIL PROTECTED] <mailto: [EMAIL PROTECTED]>>
>>
>> Subject: [Jmol-users] 11.1.21 dial-a-tranlucency
>>
>> To: [EMAIL PROTECTED] <mailto: [EMAIL PROTECTED]>,
>> [email protected]
>> <mailto:[email protected] >
>>
>> Message-ID: <[EMAIL PROTECTED]
>> <mailto:[EMAIL PROTECTED] >>
>>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>>
>> 11.1.21 is ready for release. This version contains one new item:
>>
>> adjustable translucency.
>>
>
> =
------------------------------
Message: 5
Date: Thu, 15 Mar 2007 02:44:21 -0500
From: Bob Hanson <[EMAIL PROTECTED] >
Subject: [Jmol-users] Jmol 11.1.22 features
To: [email protected]
Message-ID: <[EMAIL PROTECTED] >
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Q: What do you get when you combine?
- isosurface WITHIN x.xx [some point or atom] # just now added
- translucent surfaces
- navigation
A: A guided tour of a protein binding site.
The key commands are:
isosurface s1 within 10.0 (atomno=185) sasurface colorscheme rwb color
absolute 0 20 map property temperature translucent 0.2;# ({0:2180})
({1749:1758 1760:2180})
isosurface s2 within 8.0 (atomno=433) sasurface colorscheme rwb color
absolute 0 20 map property temperature translucent 0.2;# ({0:2180})
({1749:1758 1760:2180})
draw arrow1 ARROW {18.50816 -5.9783783 6.6065865} {22.577888 2.2955093
17.283516} {36.745804 12.123276 29.579498} {37.168575 15.102219
37.04515};
draw off;
navigate 10 PATH $arrow1
The arrow was set up just be using
draw arrow1 arrow {0 0 0} {10 10 10} {20 20 20} {30 30 30}
set picking draw
and then moving it around by hand until it fit the cavity.
Bob
------------------------------
Message: 6
Date: Wed, 14 Mar 2007 22:42:41 +0000
From: Nick Greeves <[EMAIL PROTECTED]>
Subject: [Jmol-users] Translucency issue - black bonds
To: [email protected]
Cc: Bob Hanson <[EMAIL PROTECTED]>
Message-ID: < [EMAIL PROTECTED]>
Content-Type: text/plain; charset="utf-8"
Hi Bob,
I like this new feature but I've noticed an odd aretefact. If I
select oxygen in say binaphthol.pdb and make them translucent the
bonds to oxygen go black.
I used select oxygen: color translucent .4 in console.
All the best
Nick
--
WWW Pages: http://www.liv.ac.uk/Chemistrywww/Staff/greeves.html
Tel: +44 (0)151-794-3506 (3500 secretary)
?
On 13 Mar 2007, at 20:00, [EMAIL PROTECTED]
wrote:
> Date: Tue, 13 Mar 2007 09:58:53 -0500
> From: Bob Hanson <[EMAIL PROTECTED]>
> Subject: [Jmol-users] 11.1.21 dial-a-tranlucency
> To: [EMAIL PROTECTED], [email protected]
> Message-ID: <[EMAIL PROTECTED] >
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> 11.1.21 is ready for release. This version contains one new item:
> adjustable translucency.
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