Re: [Jmol-users] rotateSelected and translateSelected does not work in 12.0.RC[34]
I do wish I hadn't missed this one Sorry Daniel -- it went under my
radar. This is what we just fixed. Oy, April!
On Thu, Apr 8, 2010 at 9:42 AM, Daniel Lundin wrote:
> Hi,
>
> I am using rotateSelected and translateSelected to superpose two protein
> molecules. My code works in recent 11.9 (currently, I'm using 11.9.17)
> versions of Jmol, but not in 12.0.RC3 nor .RC4.
>
> In 12.0.RC3 the below script fails silently, while in 12.0.RC4 I get an
> error message: "script-FEL: unrecognized command
> line 18 command 18 of
>
> file:///home/dl/projects/r2_evolution/structural_alignment/c.7.1.d/test.spt:
> >> rotateSelected << molecular {0.17656176 -0.4046893 0.745402
> 0.49942806}"
>
> ..and similar for translateSelected.
>
> Here's the script, which requires the 1l1l.pdb and 1xjj.pdb files in the
> same directory as the script:
>
> load 1l1l.pdb
> load append 1xjj.pdb
> frame *
> select *
> wireframe off
> cpk off
> select :A/1
> cartoon
> color group
> select :A/2
> cartoon
> color [x00]
> # 1l1lA - 1xjjA
> r = [[ -0.43879509947, -0.88745464558, -0.14100749175 ],\
> [0.60164401412,-0.17359627068, -0.7796722485 ], [ 0.66744538425,\
> -0.42695267519, 0.61010496818 ]]
> rq = quaternion(r)
> t = { -54.380571529, 78.315030918, 80.097824409 }
> rotateSelected MOLECULAR @rq
> translateSelected @t
>
> /D
>
>
> --
> Daniel Lundin
>
> Department of Molecular Biology & Functional Genomics
> Arrhenius Laboratories for Natural Sciences
> Stockholm University, SE-106 91 Stockholm, Sweden
>
> tel. +46 (0)8 16 41 95, mobile: +46 (0)708 123 922, fax. +46 (0)8 16 64 88
>
> Email: daniel.lun...@molbio.su.se
>
>
> --
> Download Intel® Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> ___
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>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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[Jmol-users] rotateSelected and translateSelected does not work in 12.0.RC[34]
Hi,
I am using rotateSelected and translateSelected to superpose two protein
molecules. My code works in recent 11.9 (currently, I'm using 11.9.17)
versions of Jmol, but not in 12.0.RC3 nor .RC4.
In 12.0.RC3 the below script fails silently, while in 12.0.RC4 I get an
error message: "script-FEL: unrecognized command
line 18 command 18 of
file:///home/dl/projects/r2_evolution/structural_alignment/c.7.1.d/test.spt:
>> rotateSelected << molecular {0.17656176 -0.4046893 0.745402
0.49942806}"
..and similar for translateSelected.
Here's the script, which requires the 1l1l.pdb and 1xjj.pdb files in the
same directory as the script:
load 1l1l.pdb
load append 1xjj.pdb
frame *
select *
wireframe off
cpk off
select :A/1
cartoon
color group
select :A/2
cartoon
color [x00]
# 1l1lA - 1xjjA
r = [[ -0.43879509947, -0.88745464558, -0.14100749175 ],\
[0.60164401412,-0.17359627068, -0.7796722485 ], [ 0.66744538425,\
-0.42695267519, 0.61010496818 ]]
rq = quaternion(r)
t = { -54.380571529, 78.315030918, 80.097824409 }
rotateSelected MOLECULAR @rq
translateSelected @t
/D
--
Daniel Lundin
Department of Molecular Biology & Functional Genomics
Arrhenius Laboratories for Natural Sciences
Stockholm University, SE-106 91 Stockholm, Sweden
tel. +46 (0)8 16 41 95, mobile: +46 (0)708 123 922, fax. +46 (0)8 16 64 88
Email: daniel.lun...@molbio.su.se
--
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
___
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Re: [Jmol-users] RotateSelected
Michael, We are within days of releasing 11.2, and that is why the documentation got a bit ahead of us. Just go to the download page and select 11.1.48 Bob Hanson [EMAIL PROTECTED] wrote: >Hello, > >I tried to use the RotateSelected function, but it doesn't work. In the >documentation I found a remark "V. 11.2 - new", but the newest stable >version to download is 11.0.3, and I cannot believe that the documentation >ist earlier online than the program. > >So my questions : Can I get version 11.2 from somewhere, or if not, when >will it be ready ? Or may there be other reasons that the use of the >RotateSelected command failed ? > >Thanks >Michael Schmidt > > >- >This SF.net email is sponsored by DB2 Express >Download DB2 Express C - the FREE version of DB2 express and take >control of your XML. No limits. Just data. Click to get it now. >http://sourceforge.net/powerbar/db2/ >___ >Jmol-users mailing list >Jmol-users@lists.sourceforge.net >https://lists.sourceforge.net/lists/listinfo/jmol-users > > - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] RotateSelected
I think that Bob puts the documentation online the moment a functionality is in the newest code. Actually, all software documentation should be like this, don't you think? Therefore, try to get the prerelease (at 11.1.48 now so still to old) or get the code via SVN and build it, that should surely have the latest updates there. http://jmol.sourceforge.net/download/#Subversion%20Access On 6/13/07, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote: > Hello, > > I tried to use the RotateSelected function, but it doesn't work. In the > documentation I found a remark "V. 11.2 - new", but the newest stable > version to download is 11.0.3, and I cannot believe that the documentation > ist earlier online than the program. > > So my questions : Can I get version 11.2 from somewhere, or if not, when > will it be ready ? Or may there be other reasons that the use of the > RotateSelected command failed ? > > Thanks > Michael Schmidt > > > - > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- greetings, Pim - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] RotateSelected
Hello, I tried to use the RotateSelected function, but it doesn't work. In the documentation I found a remark "V. 11.2 - new", but the newest stable version to download is 11.0.3, and I cannot believe that the documentation ist earlier online than the program. So my questions : Can I get version 11.2 from somewhere, or if not, when will it be ready ? Or may there be other reasons that the use of the RotateSelected command failed ? Thanks Michael Schmidt - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
