[Jmol-users] frame range not working?
Hi I have a file with 40 models/frames. I am trying to restrict animation to the first 5 frames: frame range 1.1 1.5 anim mode palindrome anim on I think this agrees with the scripting doc, but what I get is an animation spanning the 40 frames. Same using frame 1.1 1.5, or with the hyphen Am I doing wrong, or it's a bug? - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Applying chemical group definitions
Hi, I'm a newcomer trying to produce web pages with embebed molecular views using jmolApplet. Data are loaded from a .cif file. I've tried to apply a set of chemical group definitions to the current model. When explicitely included in the same load instruction, it does wok. but I do not manage to read all thouse definitions from an external text file similar to that kindly provided by Bob Hanson (~groups.txt or ~groups.scr). Should it work as a defaultLoadScript? And if so, how can it be applied to the loaded molecule? Thanks in advance for any help or advice - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] frame range not working?
Oops I should read my own notes carefully.
Answering my own question:
After defining a frame range, anim on resets the range to all
models/frames.
One must use anim play, not anim on
The documentation also says it clearly (why didn't I see it before?):
http://chemapps.stolaf.edu/jmol/docs/?ver=11.4#animation
animation ON/OFF{default: ON}
Turns on or off animation. With animation ON, the frame range is
also reset to all frames. (An implicit frame range ALL command is
executed. This functionality is for backward compatibility with
Chime.) If this resetting is not desired because the frame range has
been set, then frame PLAY or frame PLAYREV should be used instead of
animation ON.
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[Jmol-users] labels bug?
Hi Bob, In Jmol 11.4.RC4a (and RC2, for what it's worth) I am finding that labels are not working properly. Commands that are issued after a specific atom is selected then overrule global label settings. select none# (or select all) font label 20 sans bold color label black select atomno=230 label Arg194 select atomno=100 font label 12 sans bold color label blue label Ala324 above works fine, atom 230 label is black and 20 point font. But when it is followed by select atomno=230 label Arg194 the Arg194 label is blue and in 12 point font. I don't think that's the intended behavior for labels. Frieda // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Applying chemical group definitions
Hi [EMAIL PROTECTED] You should be able to use any of these methods: 1. Script commands in the jmolApplet() call, as you have tried. 2. Apply the commands using jmolScript() in the web page [or any equivalent, like jmolButton()] 3. Read an external script file, either from jmolApplet() or jmolScript() 4. Use set defaultLoadScript, but of course this will apply to all models loaded If any doesn't work for you, it must be some different problem, I'd guess related to the javascript, or the file locations and paths. Send me your example off-list if you want and I'll take a look. · Dr. Angel Herráez Dep. Bioquímica y Biología Molecular, Universidad de Alcalá 28871 Alcalá de Henares (Madrid) · · · · · · · · · · · · · · · · · · · · · · · · · · · Cómo utilizar Jmol para estudiar y presentar estructuras moleculares. Angel Herráez. ISBN 978-1-84753-710-2 Publicado en septiembre de 2007. http://stores.lulu.com/angel_herraez . - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] labels bug?
OK, this is a bit tricky. It IS the way it is designed to work, but that is not well described. Generally, you can do this: select atomno=100 font label 12 sans bold color label blue label Ala324 And the label will go in as size 12, blue. But, if you have defined a default font and color and you do the same thing, the label command picks up the defaults instead. So in that case, if you are using defaults, you have to change the font and color AFTER the label command: select atomno=100 label Ala324 font label 12 sans bold color label blue I don't know if this is reasonable or not. But that is the way Jmol is configured. (And always has been, I think.) Bob Frieda Reichsman wrote: Hi Bob, In Jmol 11.4.RC4a (and RC2, for what it's worth) I am finding that labels are not working properly. Commands that are issued after a specific atom is selected then overrule global label settings. select none# (or select all) font label 20 sans bold color label black select atomno=230 label Arg194 select atomno=100 font label 12 sans bold color label blue label Ala324 above works fine, atom 230 label is black and 20 point font. But when it is followed by select atomno=230 label Arg194 the Arg194 label is blue and in 12 point font. I don't think that's the intended behavior for labels. Frieda // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson 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. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] pdb file format and electrostatic molecular potential surface
Hello to all, I just joined this list, because I currently try to convert a website from using the old MDL Chime to jmol. (jmol 11.2.14). The molecules are represented by a bunch of PDB files, where the columns 61-66 usually holding the temperature factor have been filled instead with partial charges of the atoms which where computed with MOPAC. This arrangement made it possible in Chime to generate an isosurface with a coloring scheme according to the partial charges. If I laod the same pdb files in jmol, the menu option Surfaces - Molecular Electrostatic Potential is not accessible, and a script using the command color atoms temperature gives an image of red an blue atom colorings bearing no relation to the temperature factors (which are actually partial charges). Even if I change some of the these values in the pdb file by hand, this has no effect on the given coloration of the manipulated atoms. Maybe Jmol does not support this trick to visualize molecular electrostatic potentials from pdb files? So if I have to convert the pdb files to some other format, what would it be? (I still need the pdb columns for the residue name to be conserved in that other format, because some other coloration scheme depends on that.) Dr. Reinhold Störmann Bioorganic Chemistry Center for Environmental Research Technology (UFT) Leobener Str. D-28359 Bremen - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Bug in Jmol menu - Select Element ?
I just noticed in the Jmol application that if I pick Select - Element - (some element) from the pop-up menu, nothing gets selected. The console history shows that Jmol just sent the element name, not a select (element) command. For example, loading a structure and then trying to select iron from the menu gives the following in the history: vector 3 vector scale 1.0 vibration scale 0.5 vibration 0.5 load /home/djohnston/Structures and Plots/ferrocene.mol console iron#?? $ Should I submit a bug report on this? Dean Johnston - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Bug in Jmol menu - Select Element ?
oops! Dean Johnston wrote: I just noticed in the Jmol application that if I pick Select - Element - (some element) from the pop-up menu, nothing gets selected. The console history shows that Jmol just sent the element name, not a select (element) command. For example, loading a structure and then trying to select iron from the menu gives the following in the history: vector 3 vector scale 1.0 vibration scale 0.5 vibration 0.5 load /home/djohnston/Structures and Plots/ferrocene.mol console iron#?? $ Should I submit a bug report on this? Dean Johnston - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson 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. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] pdb file format and electrostatic molecular potential surface
Reinhold,
Jmol won't assume those temperature values are partial charges. So what
you have to do is assign the partial charges yourself based on that
data. The way this is done is really quite easy in 11.4 (not 11.2):
{*}.partialCharge = {*}.temperature.all
That assigns the partial charges based on the list of temperature
values. Then, after that, you can use
isosurface sasurface map mep
for example. I notice that the popup menu doesn't reconfigure to show
the MEP option, but that will be fixed.
Bob
Reinhold Stoermann wrote:
Hello to all,
I just joined this list, because I currently try to convert a website
from using the old MDL Chime to jmol.
(jmol 11.2.14).
The molecules are represented by a bunch of PDB files, where the columns
61-66 usually holding the temperature factor have been filled instead
with partial charges of the atoms which where computed with MOPAC.
This arrangement made it possible in Chime to generate an isosurface
with a coloring scheme according to the partial charges.
If I laod the same pdb files in jmol, the menu option
Surfaces - Molecular Electrostatic Potential
is not accessible, and a script using the command
color atoms temperature
gives an image of red an blue atom colorings bearing no relation to the
temperature factors (which are actually partial charges). Even if I
change some of the these values in the pdb file by hand, this has no
effect on the given coloration of the manipulated atoms.
Maybe Jmol does not support this trick to visualize molecular
electrostatic potentials from pdb files?
So if I have to convert the pdb files to some other format, what would
it be?
(I still need the pdb columns for the residue name to be conserved in
that other format, because some other coloration scheme depends on that.)
Dr. Reinhold Störmann
Bioorganic Chemistry
Center for Environmental Research Technology (UFT)
Leobener Str.
D-28359 Bremen
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--
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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.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
-
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Re: [Jmol-users] Bug in Jmol menu - Select Element ?
thanks, Dean. That's fixed for the next release. Dean Johnston wrote: I just noticed in the Jmol application that if I pick Select - Element - (some element) from the pop-up menu, nothing gets selected. The console history shows that Jmol just sent the element name, not a select (element) command. For example, loading a structure and then trying to select iron from the menu gives the following in the history: vector 3 vector scale 1.0 vibration scale 0.5 vibration 0.5 load /home/djohnston/Structures and Plots/ferrocene.mol console iron#?? $ Should I submit a bug report on this? Dean Johnston - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson 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. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] pdb file format and electrostatic molecular potential surface
The trick to updating the menu is to use the frame command. If you only have one frame, just add this: frame 0 and the menu will be updated to enable isosurface mapping of MEP Bob frame Reinhold Stoermann wrote: Hello to all, I just joined this list, because I currently try to convert a website from using the old MDL Chime to jmol. (jmol 11.2.14). The molecules are represented by a bunch of PDB files, where the columns 61-66 usually holding the temperature factor have been filled instead with partial charges of the atoms which where computed with MOPAC. This arrangement made it possible in Chime to generate an isosurface with a coloring scheme according to the partial charges. If I laod the same pdb files in jmol, the menu option Surfaces - Molecular Electrostatic Potential is not accessible, and a script using the command color atoms temperature gives an image of red an blue atom colorings bearing no relation to the temperature factors (which are actually partial charges). Even if I change some of the these values in the pdb file by hand, this has no effect on the given coloration of the manipulated atoms. Maybe Jmol does not support this trick to visualize molecular electrostatic potentials from pdb files? So if I have to convert the pdb files to some other format, what would it be? (I still need the pdb columns for the residue name to be conserved in that other format, because some other coloration scheme depends on that.) Dr. Reinhold Störmann Bioorganic Chemistry Center for Environmental Research Technology (UFT) Leobener Str. D-28359 Bremen - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson 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. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] labels bug?
Nope, that's not what I am saying. At least, I don't think so. I think I just wasn't watching the order of commands in my example. Here's the real code: In the initialization script, I set the default for labels: select none font label 20 sans bold color label black in the label script, first I create a label that should pick up the defaults, and follow with a label that I want to be different: select 179:A.CA label Hsp90-N set labeloffset 0 -20 select 377:G.CA label catalytic|loop set labeloffset 0 -50 color label [xf701f7] #magenta font label 12 sans bold Everything works the first time the script is triggered. But if I send the label script again (which happens if someone turns off the labels and then turns them on again), the label on 179:A.CA is magenta and 12 point. In each case, I am labeling before I set the color and font. The same thing happens with label pointers, etc. Frieda On Feb 13, 2008, at 12:20 PM, Bob Hanson wrote: OK, this is a bit tricky. It IS the way it is designed to work, but that is not well described. Generally, you can do this: select atomno=100 font label 12 sans bold color label blue label Ala324 And the label will go in as size 12, blue. But, if you have defined a default font and color and you do the same thing, the label command picks up the defaults instead. So in that case, if you are using defaults, you have to change the font and color AFTER the label command: select atomno=100 label Ala324 font label 12 sans bold color label blue I don't know if this is reasonable or not. But that is the way Jmol is configured. (And always has been, I think.) Bob Frieda Reichsman wrote: Hi Bob, In Jmol 11.4.RC4a (and RC2, for what it's worth) I am finding that labels are not working properly. Commands that are issued after a specific atom is selected then overrule global label settings. select none# (or select all) font label 20 sans bold color label black select atomno=230 label Arg194 select atomno=100 font label 12 sans bold color label blue label Ala324 above works fine, atom 230 label is black and 20 point font. But when it is followed by select atomno=230 label Arg194 the Arg194 label is blue and in 12 point font. I don't think that's the intended behavior for labels. Frieda // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson 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. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] jmol applet export image
Thanks for the info, I'll put in practice, although I would also like to know how to implement the hack for MSIE, could you share that too (or some example pages) please. Mauricio Carrillo Tripp wrote: I'm sorry, I couldn't find an answer for this: can the applet export an image (jpg, png, etc) of the current view? The applet can export a JPG in an ASCII-encoded base64 way that can be read by some browsers (Firefox, but not MSIE). See http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htmhttp://chemapps.stolaf.edu/jmol/docs/examples-11/new.htmand click on image under the applet. This does not work with Microsoft Explorer unless you have your page send that back to your server and have the server repackage it and send it back as a file. Some sites do this. The command that gets the job done is: var image = opener.jmolGetPropertyAsString(image) and the way to put this in a page is: var image = jmolGetPropertyAsString(image) document.getElementById(imageDiv).innerHTML ='img src=data:image/jpeg;base64,'+image+'' where there is div id=imageDiv/div somewhere on that page. - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] labels bug?
Hmmm, maybe I have something else going on that's interfering. I'll look at it again... On Feb 13, 2008, at 4:52 PM, Bob Hanson wrote: Frieda, I'm not able to reproduce the problem. Frieda Reichsman wrote: Nope, that's not what I am saying. At least, I don't think so. I think I just wasn't watching the order of commands in my example. Here's the real code: In the initialization script, I set the default for labels: select none font label 20 sans bold color label black works in the label script, first I create a label that should pick up the defaults, and follow with a label that I want to be different: select 179:A.CA label Hsp90-N set labeloffset 0 -20 works select 377:G.CA label catalytic|loop set labeloffset 0 -50 color label [xf701f7] #magenta font label 12 sans bold works Everything works the first time the script is triggered. But if I send the label script again (which happens if someone turns off the labels and then turns them on again), the label on 179:A.CA is magenta and 12 point. I'm not seeing that. Please send a history so we can see what exactly was sent. What exactly is in that label script you send again? My GUESS is that later, after a LABELS OFF, you are sending the LABEL command without again giving the desired font/offset/color information after. But maybe I'm still missing something. Bob In each case, I am labeling before I set the color and font. The same thing happens with label pointers, etc. Frieda On Feb 13, 2008, at 12:20 PM, Bob Hanson wrote: OK, this is a bit tricky. It IS the way it is designed to work, but that is not well described. Generally, you can do this: select atomno=100 font label 12 sans bold color label blue label Ala324 And the label will go in as size 12, blue. But, if you have defined a default font and color and you do the same thing, the label command picks up the defaults instead. So in that case, if you are using defaults, you have to change the font and color AFTER the label command: select atomno=100 label Ala324 font label 12 sans bold color label blue I don't know if this is reasonable or not. But that is the way Jmol is configured. (And always has been, I think.) Bob Frieda Reichsman wrote: Hi Bob, In Jmol 11.4.RC4a (and RC2, for what it's worth) I am finding that labels are not working properly. Commands that are issued after a specific atom is selected then overrule global label settings. select none# (or select all) font label 20 sans bold color label black select atomno=230 label Arg194 select atomno=100 font label 12 sans bold color label blue label Ala324 above works fine, atom 230 label is black and 20 point font. But when it is followed by select atomno=230 label Arg194 the Arg194 label is blue and in 12 point font. I don't think that's the intended behavior for labels. Frieda // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson 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. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson 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. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
