Re: [Jmol-users] Jmol/JSmol 3.2.4 and 3.3.4 released
Bob,
Just updated to 13.2.4, and I'm having a couple of problems.
First, loading PDBs using "load =" doesn't seem to work on Safari or Google
Chrome (OS X 10.8.4). Try File > Load PDB Structure on this page:
http://www.metallacycle.com/play/netmol/jmol/. Looking at it, I think I've
traced the problem…my page is trying to use jsmol.php on your server. How do I
set JSmol up to use jsmol.php in my own copy of JSmol? If it's any help,
loading up compounds by name works fine.
I see a weird error in the JS console when the page loads: "GET
http://www.metallacycle.com/lib/jquery.min.map 404 (Not Found)"--maybe a .map
where a .js should be?
Cheers, Mike
Michael Evans
Freshman Chemistry Lab Coordinator
Georgia Institute of Technology
(502) 439-2540 | mevan...@gmail.com
On Aug 23, 2013, at 1:44 PM, Robert Hanson wrote:
> Jmol users ---
>
> Ah, for those 258 people who downloaded 13.2.4 or 13.3.4, just to let you
> know, the SELECT command is broken for proteins:
>
> select 1-3 // (with no chain identifier)
>
> will return 0 atoms selected
>
>
> 13.2.4 and 13.3.4 have been uploaded. Check for a date of 23-8-2013 under
> ...about on the pop-up menu.
>
> Sorry about that. This bug was introduced June 27, I believe, when I added
> support for multi-character chains in mmCIF files.
>
> Thanks very much to Shannon Colton at Milwaukee School of Engineering for
> tipping me off to this.
>
> Bob
>
>
>
> On Thu, Aug 22, 2013 at 3:15 PM, Robert Hanson wrote:
> See https://sourceforge.net/projects/jmol/files/
>
> There is a feature change:
>
> FEATURE CHANGE: set wireframeRotation expanded to include bioshapes and
> isosurfaces
>
> Bug fixes in 3.2.4 and 3.3.4:
>
> bug fix: set wireframeRotation not working ("inMotion" flag not properly read
> in Viewer).
> bug fix: CIF reader not processing _ccdc_geom_bond_order records
> bug fix: File dialog problems with paths having space
> bug fix: GAMESS reader not reading energies
> bug fix: TRY failure in a load command followed by a successful load
> having a loadScript will pop past the second TRY and crash Jmol
>
> bug fix: translation not read from state
> bug fix: CIF reader does not find Hall name for space groups
> bug fix: binding names not included in SHOW MOUSE
> bug fix: "single" touch can fire double-click
> bug fix: {x}.tensor() command fails when no atom tensors
> bug fix: screen repaints were being requested far too frequently
> bug fix: set loglevel 6 (debugHigh) not working
> bug fix: {*}.tensor("", "id") not implemented
> bug fix: {*}.tensor("") not implemented
> bug fix: {*}.tensor("adp") fails
> bug fix: {*}.symmetry fails when space group is P1
> bug fix: atom tensors lost when merging
> bug fix: float parser broken in dev_2013.08.07
> bug fix: zoom setting lost in state
> bug fix: shapeInfo not reporting visibility of isosurface
> bug fix: filter lost after CENTROID or PACKED load option
> bug fix: set rangeSelected not functional
> bug fix: minimization can fail after MMFF switches to UFF.
> bug fix: CIF reader fix for no element given "phenyl1" in ZjzxlegN.cif
>
> New Features in 3.3.4:
>
>
> new feature: set platformSpeed [0 to 10]
> -- basically an expanded "set wireframe OFF" with more options
> -- only effected during model rotation
> (including mouse dragging, spin, vibration, and animation)
> -- default value is 10 (all features; no compromises)
> --value >= enables
> 8 antialiasDisplay (and thus, all features)
> 7 translucency
> 6 meshes (contact, draw, isosurface, MO, pmesh,
> lcaocartoon, CGO)
> 5 cartoons, rockets, trace, ribbon
> 4 geosurfaces
> 3 ellipsoids
> 2 wireframe and balls
> 1 none of the above (same as "set wireframeRotation
> off")
> 0 [reserved for "auto"]
>
> new feature: rotate BEST
> new feature: rotate SELECTED BEST
>
> new feature: quaternion("best")
> -- delivers actual quaternion
>
> new feature: pop-up menu selection "view...best"
>
> new feature: show ROTATION BEST
> -- operates on currently selected atoms
> -- reports "{quaternion}"
>
> new feature: show ROTATION VOLUME
> -- calculates approximate best box (from 1495 quaternion-based alternatives)
> -- reports " {dx dy dz}"
> -- where is the volume,
> -- and {dx dy dz} are the dimensions, where dx > dy > dz
>
> new feature: COMPARE {atoms} [coords]
> new feature: COMPARE {atoms} ATOMS {subset1} [coords1] {subset2} [coords2] ...
>
> new feature: _logfile holds full path to logfile
>
> new feature: reading of incommensurate modulated crystal structures:
> new feature: Jana2006 M40/M50 file reading
> new feature: MODULATION command -- for modulated structures
> -- operates on currently selected set of atoms
> -- MODULATION ON
> -- MODULATION OFF
>
Re: [Jmol-users] Help please (Tiqing Liu)
Hi Angel,
Thank you for the reply.
In http://bdb4.ucsd.edu/bind/surflex.jsp?PDB=1GSI&HET=TMP, the multi layer
means one protein (as model=1.1), one crystal ligand (as model=2.1), and the
other ligands (as model=3).
var jmolcmds = [ "load http://bdb4.ucsd.edu${hmap.url}.pdb";,
"set appendNew true",
"load APPEND http://bdb4.ucsd.edu${hmap.url}_ligand0.mol2";,
"load APPEND http://bdb4.ucsd.edu${hmap.url}-results.mol2";,
"set frank off",
"model 0",
"select model=1.1; spacefill off; cpk off; wireframe off;
cartoon; color cartoon translucent; zoom 200",
"select model=2.1; wireframe 80; spacefill 0.35; center
hetero; color translucent; zoom 200",
"select model=3; wireframe off; cpk off; spacefill off",
"background white",
"display all"
];
jmolInitialize("/bind/jmol-13.0.18/",true);
jmolApplet( 600, jmolcmds.join(";"), "${pdb}" );
jmolBr();
I agree that single protein behaves nicely at
http://bdb4.ucsd.edu/bind/jmol_pdb.jsp?pdbid=1GSI&monomerid=50332929&polymerid=p5494&seq=100&title=pound34Thymidylate%20kinasepound34%20AND%20pound34CHEMBL394429pound34.
But did you try http://bdb4.ucsd.edu/bind/surflex.jsp?PDB=1GSI&HET=TMP. I
would like jmol show the protein in
http://bdb4.ucsd.edu/bind/surflex.jsp?PDB=1GSI&HET=TMP as protein displayed in
http://bdb4.ucsd.edu/bind/jmol_pdb.jsp?pdbid=1GSI&monomerid=50332929&polymerid=p5494&seq=100&title=pound34Thymidylate%20kinasepound34%20AND%20pound34CHEMBL394429pound34
Thank you in advance.
PS. the two are posted again
http://bdb4.ucsd.edu/bind/jmol_pdb.jsp?pdbid=1GSI&monomerid=50332929&polymerid=p5494&seq=100&title=pound34Thymidylate%20kinasepound34%20AND%20pound34CHEMBL394429pound34
http://bdb4.ucsd.edu/bind/surflex.jsp?PDB=1GSI&HET=TMP
---
All the best to you,
Tiqing Liu, Ph. D.
Message: 1
Date: Thu, 22 Aug 2013 20:22:55 +0200
From: Angel Herr?ez
Subject: Re: [Jmol-users] Help please
To:
Message-ID: <521656ff.6419.f3faf...@angel.herraez.uah.es>
Content-Type: text/plain; charset="US-ASCII"
Hello Liu
Can you be more specific? That would help.
By "multiple layer", do you mean several models (frames) are loaded
together? Or something else?
> http://bdb4.ucsd.edu/bind/surflex.jsp?PDB=1GSI&HET=TMP does not
behave where not all the atoms and bonds in protein are cartooned.
Which parts of the protein are not displayed? I just loaded the pdb into Jmol
and I see no problem in the cartoon.
Finally, this will not affect, but for your information
you do not need to repeat "set appendNew true",
and "zoom" applies to all models at the same time, so no need to repeat it.
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Re: [Jmol-users] Jmol/JSmol 3.2.4 and 3.3.4 released
Jmol users ---
Ah, for those 258 people who downloaded 13.2.4 or 13.3.4, just to let you
know, the SELECT command is broken for proteins:
select 1-3 // (with no chain identifier)
will return 0 atoms selected
13.2.4 and 13.3.4 have been uploaded. Check for a date of 23-8-2013 under
...about on the pop-up menu.
Sorry about that. This bug was introduced June 27, I believe, when I added
support for multi-character chains in mmCIF files.
Thanks very much to Shannon Colton at Milwaukee School of Engineering for
tipping me off to this.
Bob
On Thu, Aug 22, 2013 at 3:15 PM, Robert Hanson wrote:
> See https://sourceforge.net/projects/jmol/files/
>
> There is a feature change:
>
> FEATURE CHANGE: set wireframeRotation expanded to include bioshapes and
> isosurfaces
>
> Bug fixes in 3.2.4 and 3.3.4:
>
> bug fix: set wireframeRotation not working ("inMotion" flag not properly
> read in Viewer).
> bug fix: CIF reader not processing _ccdc_geom_bond_order records
> bug fix: File dialog problems with paths having space
> bug fix: GAMESS reader not reading energies
> bug fix: TRY failure in a load command followed by a successful load
> having a loadScript will pop past the second TRY and crash
> Jmol
> bug fix: translation not read from state
> bug fix: CIF reader does not find Hall name for space groups
> bug fix: binding names not included in SHOW MOUSE
> bug fix: "single" touch can fire double-click
> bug fix: {x}.tensor() command fails when no atom tensors
> bug fix: screen repaints were being requested far too frequently
> bug fix: set loglevel 6 (debugHigh) not working
> bug fix: {*}.tensor("", "id") not implemented
> bug fix: {*}.tensor("") not implemented
> bug fix: {*}.tensor("adp") fails
> bug fix: {*}.symmetry fails when space group is P1
> bug fix: atom tensors lost when merging
> bug fix: float parser broken in dev_2013.08.07
> bug fix: zoom setting lost in state
> bug fix: shapeInfo not reporting visibility of isosurface
> bug fix: filter lost after CENTROID or PACKED load option
> bug fix: set rangeSelected not functional
> bug fix: minimization can fail after MMFF switches to UFF.
> bug fix: CIF reader fix for no element given "phenyl1" in ZjzxlegN.cif
>
> New Features in 3.3.4:
>
>
> new feature: set platformSpeed [0 to 10]
> -- basically an expanded "set wireframe OFF" with more options
> -- only effected during model rotation
> (including mouse dragging, spin, vibration, and animation)
> -- default value is 10 (all features; no compromises)
> --value >= enables
> 8 antialiasDisplay (and thus, all features)
> 7 translucency
> 6 meshes (contact, draw, isosurface, MO, pmesh,
> lcaocartoon, CGO)
> 5 cartoons, rockets, trace, ribbon
> 4 geosurfaces
> 3 ellipsoids
> 2 wireframe and balls
> 1 none of the above (same as "set wireframeRotation
> off")
> 0 [reserved for "auto"]
>
> new feature: rotate BEST
> new feature: rotate SELECTED BEST
>
> new feature: quaternion("best")
> -- delivers actual quaternion
>
> new feature: pop-up menu selection "view...best"
>
> new feature: show ROTATION BEST
> -- operates on currently selected atoms
> -- reports "{quaternion}"
>
> new feature: show ROTATION VOLUME
> -- calculates approximate best box (from 1495 quaternion-based
> alternatives)
> -- reports " {dx dy dz}"
> -- where is the volume,
> -- and {dx dy dz} are the dimensions, where dx > dy > dz
>
> new feature: COMPARE {atoms} [coords]
> new feature: COMPARE {atoms} ATOMS {subset1} [coords1] {subset2} [coords2]
> ...
>
> new feature: _logfile holds full path to logfile
>
> new feature: reading of incommensurate modulated crystal structures:
> new feature: Jana2006 M40/M50 file reading
> new feature: MODULATION command -- for modulated structures
> -- operates on currently selected set of atoms
> -- MODULATION ON
> -- MODULATION OFF
> -- MODULATION t
> -- sets modulation "t" of selected atoms
> -- MODULATION PLAY t1 t2
> -- animates a once-through sequence of t from t1 to t2
> -- MODULATION FPS x.x // may be < 1
> -- sets speed of animation
> new feature: Jana2006 reader -- reader for http://jana.fzu.cz/
> new feature: CIF reader reads incommensurate modulated structures
> -- FILTER options include:
> -- NOSPECIAL (include special atoms for debugging
> -- MODAVERAGE (do not read modulation
> -- MODAXES=xyz (select only specific axes -- x, y, and/or z)
> -- MODVIB (set positions to average, but enable modulation as if
> vibration
> -- NOSYM (no symmetry read)
>
>
>
>
>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> --
