[Jmol-users] Question about JavaScript reader.readAsText(buFile, "UTF-8")

Bob or Anyone Else Who Might Know, I'm reading the HTML in a local text file directly into a page JavaScript variable using reader.readAsText(buFile, "UTF-8"). When this process reads an html SMILES (e.g. C(=C\C)/C), it sure looks like the back slashes are automatically escaped for the JavaScri

Re: [Jmol-users] Question

Thank you so much!! Stan On Thu, 11/5/15, Angel Herráez wrote: Subject: Re: [Jmol-users] Question To: jmol-users@lists.sourceforge.net Date: Thursday, November 5, 2015, 12:08 PM Hello Stanley The state saves information about the

Re: [Jmol-users] Question

Hello Stanley The state saves information about the molecule, not the window. Usually, the window size of the Jmol application is remembered, but that is in the hands of the operating system. If you are in Windows, try to locate the users folder (in C) and inside your user there will be a fol

[Jmol-users] Question

Hello, I am trying to open Jmol in a specific window size. Is there a way to set window size. When I "Save state" it doesn't work. -- ___ Jmol-users mailing list Jmol-users@lis

Re: [Jmol-users] Question about 'data' command

To follow up on this, a separate message introduced http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.11_2014.12.04.zip with new functionality that allows reading tab-separated and CSV file data back into Jmol as atom properties. Bob On Wed, Dec 3, 2014 at 8:45 AM, Marc Chakiachvili < marc.chakiachv

Re: [Jmol-users] Question about 'data' command

On 12/03/2014 03:32 PM, Robert Hanson wrote: > I'm missing something. ".all" where? You mean for .label()? Labels are > strings; it wouldn't make sense to average them. > I agree that averaging label strings wouldn't make sense. But in other cases it also doesn't make sense but still it is require

Re: [Jmol-users] Question about 'data' command

I Successfully saved my data in file, using Robert method, thanks again, now in order to retrieve data, just have to load it with the data command this time ? or do I need to parse saved file to set property_qresno / property_qsimil to my atoms ? In a perfect world, I would like to do as in doc :

Re: [Jmol-users] Question about 'data' command

On Wed, Dec 3, 2014 at 5:28 AM, Rolf Huehne wrote: > Before you run the script you > should restore the original lines. Each line should either end with a > semicolon (';') or a brace ('{' or '}'). If this is not the case for a > line you see you must combine it with the next line. > > I note t

Re: [Jmol-users] Question about 'data' command

I'm missing something. ".all" where? You mean for .label()? Labels are strings; it wouldn't make sense to average them. On Wed, Dec 3, 2014 at 7:45 AM, Rolf Huehne wrote: > On 12/03/2014 01:53 PM, Robert Hanson wrote: > > It's actually easier than that: > > > > var tsv_data = > > > {selected}.la

Re: [Jmol-users] Question about 'data' command

Hi, Rolf, Robert, Many thanks for your answer, I will try your solutions and let you know if it fixes my problem. Regards, Marc Le Wed Dec 03 2014 at 14:45:56, Rolf Huehne a écrit : > On 12/03/2014 01:53 PM, Robert Hanson wrote: > > It's actually easier than that: > > > > var tsv_data = > > {

Re: [Jmol-users] Question about 'data' command

On 12/03/2014 01:53 PM, Robert Hanson wrote: > It's actually easier than that: > > var tsv_data = > {selected}.label("%[resno]\t%[chain]\t%[model]\t%[property_seqresno]\t%[property_qsimil]") > write VAR tsv_data "atom_properties.txt"; > > Using %[...] allows you also to format the lines any way you

Re: [Jmol-users] Question about 'data' command

It's actually easier than that: var tsv_data = {selected}.label("%[resno]\t%[chain]\t%[model]\t%[property_seqresno]\t%[property_qsimil]") write VAR tsv_data "atom_properties.txt"; Using %[...] allows you also to format the lines any way you want -- in fixed columns, left/right justified, etc. ---

Re: [Jmol-users] Question about 'data' command

On 12/03/2014 10:38 AM, Marc Chakiachvili wrote: > Hi, > > > Newbie question about using the command "data", I currently set new > properties for atoms, a sequence number generated for my project, and > properties about alignements values returned by BLAST. > > As I have many file to process, I cur

[Jmol-users] Question about 'data' command

Hi, Newbie question about using the command "data", I currently set new properties for atoms, a sequence number generated for my project, and properties about alignements values returned by BLAST. As I have many file to process, I currently load BLAST aligned models, set my propreties, then load

Re: [Jmol-users] Question re filetype

nope. You have to load it and check the variable "_modeltype" On Thu, Apr 10, 2014 at 1:37 PM, Otis Rothenberger wrote: > Bob, > > If I do > > var x= load "filePath" > > is there a quick way to determine the fileType of the file in x? > > I'm trying to make pre-load load script decisions. > > O

[Jmol-users] Question re filetype

Bob, If I do var x= load "filePath" is there a quick way to determine the fileType of the file in x? I'm trying to make pre-load load script decisions. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com -

Re: [Jmol-users] Question: Does "zap;" stop rotation?

[not exactly a typical jmol-users list discussion -- moving off line] -- Flow-based real-time traffic analytics software. Cisco certified tool. Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow Analyzer Customize

Re: [Jmol-users] Question: Does "zap;" stop rotation?

Hi Bob, I'm now set up to do some investigating about this issue. in the "interrupt" function in jsmol/j2s/core/core.z.js (which I replaced with jsmol/js/core.js) where this.stopped = true;, I've added the ability to write to window._sb_debugging (an array that I can push information for later

Re: [Jmol-users] Question: Does "zap;" stop rotation?

Thanks, Bob! Great timing, I was just setting up to go poking around. I'm using HTML5. I'll see if I can figure out what is happening. Thanks, --Chuck On Feb 25, 2014, at 12:27 PM, Robert Hanson mailto:hans...@stolaf.edu>> wrote: First question: Java or HTML5? If Java, I'm quite surprised

Re: [Jmol-users] Question: Does "zap;" stop rotation?

First question: Java or HTML5? If Java, I'm quite surprised. Java is multi-threaded. So I would need to have a very specific example to try myself. If HTML5, the problem is in the way we are emulating multi-threading. To debug: 1) replace jsmol/j2s/core/core.z.js with jsmol/js/core.js 2) add

Re: [Jmol-users] Question: Does "zap;" stop rotation?

Hi Bob, This is helpful as I wasn’t sure if I understood the intent. I’ll do some more testing with my app in the next day or so to make sure that I can reproduce what I’m seeing and create a generic example. There is still a pretty good possibility that the bug is in my code. The first larger

Re: [Jmol-users] Question: Does "zap;" stop rotation?

It's definitely supposed to stop. The rotation is a separate process, so it is supposed to be continuing after the script is "finished". I'm not able to reproduce your problem. -- Can you put up a page that illustrates that? On Mon, Feb 24, 2014 at 3:35 PM, Charles Harrison Shubert wrote: > JSm

[Jmol-users] Question: Does "zap;" stop rotation?

JSmol.min.js ___JmolDate="$Date: 2014-02-14 13:28:43 -0600 (Fri, 14 Feb 2014) $";___fullJmolProperties="src/org/jmol/viewer/Jmol.properties";___JmolVersion="14.0.8"; Issue: zap does not seem to stop the rotation of a molecule that has been zapped. Here's what I do and see: My app load a large

Re: [Jmol-users] Question

Nothing elegant. I've started to implement structureModifyCallback, but it's not done yet. On Mon, Feb 17, 2014 at 11:01 AM, Otis Rothenberger wrote: > Bob, > > I hate to bug you while you're chasing bugs (ouch), but a quick question: > > I currently load only JSmol.min.js on page load. Is there

[Jmol-users] Question

Bob, I hate to bug you while you're chasing bugs (ouch), but a quick question: I currently load only JSmol.min.js on page load. Is there any file or files that could be loaded to immediately cache model kit activity, specifically bond and atom change? Otis -- Otis Rothenberger o...@chemagic.c

Re: [Jmol-users] Question: What is the preferred way to save JSmol state and orientation?

Hi Bob, I guess I would have been surprised if a backdoor existed. Thanks for thinking about this. —Chuck On Feb 5, 2014, at 4:45 PM, Robert Hanson mailto:hans...@stolaf.edu>> wrote: PNGJ is not designed to save any settings other than those that are specifically necessary to define a state

Re: [Jmol-users] Question: What is the preferred way to save JSmol state and orientation?

PNGJ is not designed to save any settings other than those that are specifically necessary to define a state. So no user variables, no overall preferences. You could save a "message" in the state by using the message command, I suppose, but that would have to be a message that was visible to the us

Re: [Jmol-users] Question: What is the preferred way to save JSmol state and orientation?

Hi, I am also quite interested in that. > Can I save my app’s private UI state (preferences, etc) as a variable > or static function in JSmol so that PNGJ will write it to the .png > file? As far as I know user defined variables or functions (from jmolscript) are not saved within the Jmol state

Re: [Jmol-users] Question: What is the preferred way to save JSmol state and orientation?

Hi Bob and Paul, Thanks for your replies (both are very helpful). The PNGJ functionality looks great! Can I save my app’s private UI state (preferences, etc) as a variable or static function in JSmol so that PNGJ will write it to the .png file? (I can imagine the user saving the PNGJ .png file

Re: [Jmol-users] Question: What is the preferred way to save JSmol state and orientation?

very best way is to have the user save a PNGJ file -- write PNGJ "?.png" and then have them drag-drop it back into Jmol when they want to restore it. On Fri, Jan 31, 2014 at 3:41 PM, Paul Pillot < paul.pil...@ac-orleans-tours.fr> wrote: > Hi Chuck, > have you tried << get property stateInfo

Re: [Jmol-users] Question: What is the preferred way to save JSmol state and orientation?

Hi Chuck, have you tried « get property stateInfo » ? It should restore everything including orientation, zoom, etc… Paul Le 31 janv. 2014 à 16:32, Charles Harrison Shubert a écrit : > Hi, > > When my users open my app, I'd like for JSmol to be in the same state that > they left it in. My use

[Jmol-users] Question: What is the preferred way to save JSmol state and orientation?

Hi, When my users open my app, I'd like for JSmol to be in the same state that they left it in. My users can generate quite a bit of JSmol script. Currently, I'm using the browser's localStorage to store app state in a JSON object. What would be the preferred way to extract JSmol state includin

Re: [Jmol-users] Question: How is Info intended to be used?

j2sPath could be anywhere, including on another server. It doesn't have to be ./j2s, but that is the default, and that is why it doesn't "seem" to need it. On Wed, Jan 29, 2014 at 2:21 PM, Charles Harrison Shubert wrote: > Thanks, Bob! JSmol is really amazing. > > Info is now pretty minimali

Re: [Jmol-users] Question: How is Info intended to be used?

Thanks, Bob! JSmol is really amazing. Info is now pretty minimalist and I am not reusing it. I was wondering why Info needs to specify j2sPath given that Jmol seems to locate the js path without an explicit path name in Info. I think I'm missing something here that may be important when I dep

Re: [Jmol-users] Question: How is Info intended to be used?

On Wed, Jan 29, 2014 at 10:42 AM, Charles Harrison Shubert wrote: > Here's a follow on question: Assuming that I've created a Jmol Object > using an Info variable, what happens when I change (say) Info.script > instead of calling the script() function? > > The Info object is only used at applet

Re: [Jmol-users] Question: How is Info intended to be used?

Wow! Thanks, guys! I've been a lurker on this list for quite a while and have picked up a lot of interesting technique for using Jmol from you. Angel's response is very helpful for my particular issue. The point is that I must treat the Info variable in my javascript as belonging to the Jmol

Re: [Jmol-users] Question: How is Info intended to be used?

Chuck, I'm sorry. I misunderstood. I thought you were trying to write Info variable data to Jmol.setInfo. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Jan 28, 2014, at 12:54 PM, Otis Rothenberger wrote: > Chuck and Angle, > > I think I'm in basic agreement with Angle

Re: [Jmol-users] Question: How is Info intended to be used?

Chuck, the Info variable you pass is supplemented with default values. .Partially so that doing exactly what you are doing you can see what more options are. On Tue, Jan 28, 2014 at 10:35 AM, Charles Harrison Shubert wrote: > Hi, > > Yesterday, I was experimenting with localStorage. My inten

Re: [Jmol-users] Question: How is Info intended to be used?

Did I send you the article about the moss in Northern Canada? On Jan 28, 2014, at 12:54 PM, Otis Rothenberger wrote: > Chuck and Angle, > > I think I'm in basic agreement with Angle. I look at this as a scratch pad > per the following JS function: > > function scratchPad(header, conten

Re: [Jmol-users] Question: How is Info intended to be used?

Chuck and Angle, I think I'm in basic agreement with Angle. I look at this as a scratch pad per the following JS function: function scratchPad(header, content) { header = (!header) ? "" : header; content = (!content) ? "" : content; if (hea

Re: [Jmol-users] Question: How is Info intended to be used?

Hi, Chuck this is how I see it (but I may not be right) There is not "your" variable and "Jmol's" variable. The single Info variable belongs to the Jmol Object once you invoke getApplet. What you do is initialize some values/parameters that are part of the Info variable (which is more properly

[Jmol-users] Question: How is Info intended to be used?

Hi, Yesterday, I was experimenting with localStorage. My intent is to save my local javascript state so that the next time the user goes to my web site, they'll start up from where they left off. Part of the state that I saved is my Info for Jmol. I was surprised to find that Jmol had writte

Re: [Jmol-users] Question: How do I turn tracking off?

Thanks, Bob! We wind up running in some restricted network environments and anything that is not on the designated server will either be really slow or won’t work. I guess some faculty and academic IT folks are really serious about classroom management. I did notice in poking around that the late

Re: [Jmol-users] Question: How do I turn tracking off?

Sure. I'd love to have all stats, but feel free to turn that off. Just add delete Jmol._tracker somewhere after loading JSmol.min.js On Mon, Jan 20, 2014 at 10:53 AM, Charles Harrison Shubert wrote: > Hi, > > When running JSmol, I noticed that there was a network message sent to > http:

[Jmol-users] Question: How do I turn tracking off?

Hi, When running JSmol, I noticed that there was a network message sent to http://chemapps.stolaf.edu/jmol/JmolTracker.htm?id=UA-45940799-1' and some google analytics activity. I’d like to turn this tracking off. On searching around JSmol I found the following: Jmol._track = function(applet) {

Re: [Jmol-users] question about conversion of Jmol to JSmol with Java2Script

This was a major task. Consider Google Web Toolkit instead. That was used for JSME. On Tue, Oct 8, 2013 at 10:19 AM, Grossman, Robert B wrote: > Hi folks, > > Your development of JSmol has inspired me to try to convert one of my > own applets into JavaScript. However, my applet imports javax

[Jmol-users] question about conversion of Jmol to JSmol with Java2Script

Hi folks, Your development of JSmol has inspired me to try to convert one of my own applets into JavaScript. However, my applet imports javax.swing.* and java.awt.* classes, and the developer of Java2Script says that it does not provide a Swing library. Did you encounter this problem when dev

Re: [Jmol-users] Question Jmol / CGI response

That's not possible, Angel. They will run sequentially. Period. On Thu, Jun 21, 2012 at 2:47 PM, Angel Herráez wrote: > More important than the time needed, the scripts may end up running in > parallel, not sequentially (maybe not, but you better be sure). Send them > all > in one go as Paul sa

Re: [Jmol-users] Question Jmol / CGI response

More important than the time needed, the scripts may end up running in parallel, not sequentially (maybe not, but you better be sure). Send them all in one go as Paul says. On 21 Jun 2012 at 20:56, Paul Pillot wrote: > You should reduce the successive jmolScript calls to a single one, with > d

Re: [Jmol-users] Question Jmol / CGI response

That's probably not related to the issue you reported, but this part of the js might have performance issues : function build_interface(resp) { /* Handling of Q_tot coming from bio_rho.cgi. Json does not work right now, probably problem on

[Jmol-users] Question Jmol / CGI response

Dear Jmol Developers The next version of our application is almost ready. http://www.biofetsim.org/ku_prototype.html All features we want are in place, now we're basically debugging it and cleaning it up. One bug which is difficult for me to track down is the following: you'll notice a "pH Respo

Re: [Jmol-users] Question about rotation matrix

Well, that's an idea, anyway. How common do you think it is to have the actual matrix and not other information? On Wed, Mar 21, 2012 at 6:30 AM, Nikolay Bogdanov wrote: > Thanks! Thus I do a proper rotation (which is my matrix multiplied by (-1) > ) and then INVERTSELECTED, and that gives me wha

Re: [Jmol-users] Question about rotation matrix

Thanks! Thus I do a proper rotation (which is my matrix multiplied by (-1) ) and then INVERTSELECTED, and that gives me what I want. Shouldn't this be a default action for the left-handed matrix rotation? Because now Jmol does something strange when one tries to apply a rotation/reflection matr

Re: [Jmol-users] Question about rotation matrix

Well, it's not a valid matrix for rotation. What you have right now in rot2 is an improper rotation -- a rotation/reflection. As interesting as that might be, it's not a rotation, doesn't correspond to a quaternion (which is what Jmol turns that matrix into), and therefore shouldn't be used with th

Re: [Jmol-users] Question about rotation matrix

But they are not identical: Point (1.0, 1.0, 1.0) goes into (0.0016, 0., -1.7320) with my left-handed matrix, and to (1.4393, -0.1442, -0.9527) with Jmol's rotation. If I multiply the rotation matrix with (-1) and thus make it right-handed. This is fine for me now, because I need only axes o

Re: [Jmol-users] Question about rotation matrix

Your rot2 matrix is a left-handed axis system, not a right-handed one. That matrix has a determinant of -1, not 1. Jmol is considering your left-handed matrix [-0.430167-0.384841020.816611] [0.693676-0.7198110.0261867] [-0.57772803-0.57772905-0.57659] ] and the prop

[Jmol-users] Question about rotation matrix

Hi, I try to find out how to apply a rotation matrix to the model with jmol. I have a matrix to be applied to coordinates this way: matrix [[a1,b1,c1],[a2,b2,c2],[a3,b3,c3]] xnew=a1*x+b1*y+c1*z, ynew=a2*x+b2*y+c2*z etc It looks like I need just to do $ rotate selected @matrix. But it works for o

Re: [Jmol-users] question

Hans, Congratulations on achieving all this on just your second day. Many good days to come, I think. Right, we refer to cell 555 as all atoms that are within or on the edges/faces/vertices of cell 555. Same with 556. so some atoms are, for example "cell 555 and cell 556". Hope that sounds reason

Re: [Jmol-users] question

Bob, thx for the clarifications about "REMARK 290". Btw., I'm able to hide the atom at (0,0,17.59) (which is equivalent by translational symmetry to the atom at (0,0,0)) by issuing: $ display remove cell=556 (or cell={1 1 2}) (1 atoms hidden) but *NOT* by issuing: $ display cell=555 (0 ato

Re: [Jmol-users] question

On Wed, Nov 30, 2011 at 2:09 PM, Hans Horn wrote: > Bob, > > $ display cell=555 > 0 atoms hidden > (all 10 atoms shown) > > $ display cell=556 > 9 atoms hidden > > exactly. So you would use display cell=555 and not cell=556 if you want to remove that particular atom. > > Would you mind reit

Re: [Jmol-users] question

Bob, $ display cell=555 0 atoms hidden (all 10 atoms shown) $ display cell=556 9 atoms hidden Would you mind reiterating about what I should do about "REMARK 290". thx, H. On 11/30/2011 10:41 AM, Robert Hanson wrote: > BTW -- to remove that atom, use > > display cell=555 and not cell=556 >

Re: [Jmol-users] question

BTW -- to remove that atom, use display cell=555 and not cell=556 On Wed, Nov 30, 2011 at 12:31 PM, Robert Hanson wrote: > {1 1 1} replicates the symmetry operations, and some of those might bring > an atom into another unit cell. Particularly with molecular compounds, we > see this all the

Re: [Jmol-users] question

{1 1 1} replicates the symmetry operations, and some of those might bring an atom into another unit cell. Particularly with molecular compounds, we see this all the time, and it is what people want. You can specify PACKED to get only atoms within one unit cell, although then atoms that are at vert

Re: [Jmol-users] question

Bob, whatever magic you did - it fixed the atom duplication. However, I think the unit cell should have only 9 atoms, not 10. The Mg atom (0.0  0.0  17.59) pointed to by the arrow should be in the next cell, shouldn't it?. I'm afraid that I di

Re: [Jmol-users] question

Hans, OK, I got it. Very simple fix. See http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip By the way, Jmol is guessing at the origin and setting of that unit cell. Jmol can read the Jones-Faithful data in the PDB record REMARK 290: REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMM

Re: [Jmol-users] question

Oh, I guess I did not actually try it with your file. I didn't realize it was a complete model! Ah, that's a problem! Well, I can tell you why that is. Jmol presumes that a PDB file is a protein and saves hugely on processing by assuming that there are no special positions. Therefore it does not c

Re: [Jmol-users] question

Robert, neat! when I do that with the pdb file posted, I see 10 atoms in the unit cell. However, when I write it out (e.g. as xyz) I get 72 atoms. Why's that? Is there a way to save the unit cell as 3*3 matrix? thx, H. On 11/29/2011 1:45 PM, Robert Hanson wrote: sure. load xxx.pdb {1 1 1} g

Re: [Jmol-users] question

sure. load xxx.pdb {1 1 1} gives you a full unit cell. unitcell on gets you the unit cell axes on gets you a,b,c axes for the unit cell. On Tue, Nov 29, 2011 at 3:03 PM, Hans Horn wrote: > Folks, > > I have a pdb file : > > # > HEADER > 09-NOV-11 > TITLE Structure > 1 >

[Jmol-users] question

Folks, I have a pdb file : # HEADER 09-NOV-11 TITLE Structure 1 REVDAT 1 09-NOV-11 0 REMARK 4 REMARK 4 COMPLIES WITH FORMAT V. 2.1, 25-OCT-1996 HETUNK A 1 2 FORMUL 1 UNKMg3 Cl6 CRYST13.5963

Re: [Jmol-users] Question to "Load Append" in Jmol

Just go to http://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm On Fri, May 13, 2011 at 5:00 PM, Robert Hanson wrote: > Just go to > > in the command box type > > set debug > > and press ENTER. Then do your tests with menu opening. See what the Java > console reports. If you can, monitor t

Re: [Jmol-users] Question to "Load Append" in Jmol

Just go to in the command box type set debug and press ENTER. Then do your tests with menu opening. See what the Java console reports. If you can, monitor the Java console while you manipulate the mouse. You should see a whole stream of info, and if you press the mouse button, you should see s

Re: [Jmol-users] Question to "Load Append" in Jmol

Am 13.05.2011 19:03, schrieb Robert Hanson: right-click problem: We could put some debugging lines in if you want, but it will have to be for 12.1, not 12.0. Do you want me to do that? -- Achieve unprecedented app pe

Re: [Jmol-users] Question to "Load Append" in Jmol

right-click problem: We could put some debugging lines in if you want, but it will have to be for 12.1, not 12.0. Do you want me to do that? -- Achieve unprecedented app performance and reliability What every C/C++ and For

Re: [Jmol-users] Question to "Load Append" in Jmol

Am 11.05.2011 19:08, schrieb Robert Hanson: 2011/5/11 Reinhold Störmann > But I still get some strange behavior of the jmol Applet that doesn't necessarily have to be caused by my script: After opening the jmol menue (right mouse button), a small wa

Re: [Jmol-users] Question to "Load Append" in Jmol

2011/5/11 Reinhold Störmann > > But I still get some strange behavior of the jmol Applet that doesn't > necessarily have to be caused by my script: > > After opening the jmol menue (right mouse button), a small warning symbol > appears to the right of the first menu entry ("all molecules") and >

Re: [Jmol-users] Question to "Load Append" in Jmol

Hi, first of all a lot of thanks to all of you for the help provided. Hi, http://chemapps.stolaf.edu/jmol/docs/?ver=12.0#setmisc There is a command for rotation and translation each: set allowRotateSelected FALSE When set TRUE, this parameter allows user rotation of the molecule c

Re: [Jmol-users] Question to "Load Append" in Jmol

Well, let's see... On Tue, May 10, 2011 at 2:16 PM, Paul Pillot < paul.pil...@ac-orleans-tours.fr> wrote: > I've tested set picking dragSelected. > - when the atoms that are part of the selections are clicked and dragged, > the selection can be rotated and dragged, which is the expected behavior

Re: [Jmol-users] Question to "Load Append" in Jmol

I've tested set picking dragSelected. - when the atoms that are part of the selections are clicked and dragged, the selection can be rotated and dragged, which is the expected behavior - when an atom that is not part of the selection is clicked and dragged, the selection is rotated and dragged ac

Re: [Jmol-users] Question to "Load Append" in Jmol

I think we would need a flag like "set picking dragSelected". We have set pickingStyle select drag, but it really doesn't do much, and it it doesn't allow for rotation, which I think is a nice feature of set picking dragMolecule (with SHIFT). OK, I have added for Jmol 12.1.46 set picking dragSele

Re: [Jmol-users] Question to "Load Append" in Jmol

Yes ! I'm finally on Jmol's cutting edge ! Here is my report : - no more gliding spiders with Bob's last version ! - when a chain contains gaps the different pieces are split by the dragging process (for example : 1qln, 2bg9) - to make chains go back to where they came from, I had to store the c

Re: [Jmol-users] Question to "Load Append" in Jmol

You need to store them in a variable at some point before you start moving things. Really, Paul, you are among the first to experiment with this, so understand that it could be trickier than I make it out to be! On Sun, May 8, 2011 at 3:29 PM, Paul Pillot wrote: > It works great now ! Thanks Bob

Re: [Jmol-users] Question to "Load Append" in Jmol - spiders's invasion

Ah, right! That's a problem. It's going to take some work to fix this, because it requires some major rethinking on my part as to how to define a molecule. You would think that would be trivial, but it's not. Biopolymers are special -- their base molecule is completely defined even though the atoms

Re: [Jmol-users] Question to "Load Append" in Jmol - spiders's invasion

In a previous mail, I reported that the set picking dragmolecule command could lead to strange visions when moving a protein bonded to an heteroatom compound such as an heme. For example this image was made with an hemoglobin model (1gzx) : http://librairiedemolecules.education.fr/divers/spider.

Re: [Jmol-users] Question to "Load Append" in Jmol

It works great now ! Thanks Bob ! You mentioned in one of your previous messages that one can use the ROTATE COMPARE command to move the chains smoothly back to where they came from. I've seen in the docs that the ROTATE COMPARE command requires the coordinates from the previous position to be st

Re: [Jmol-users] Question to "Load Append" in Jmol

Problem was exactly as described -- once ROTATE COMPARE is used, then any future rotation is accompanied by an unwanted translation. See http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip for this update. (Jmol 12.1.46) It will be fixed also in the next release of 12.0 (12.0.43), probab

Re: [Jmol-users] Question to "Load Append" in Jmol

got it -- that's checked in for 12.1.46 and 12.0.43 On Fri, May 6, 2011 at 1:49 PM, Paul Pillot wrote: > Well, I just tried to run the "set picking dragmolecule" command for the > structures displayed at the link you gave and there is a strange bug when I > try to rotate the molecules independen

Re: [Jmol-users] Question to "Load Append" in Jmol

Otis Rothenberger Department of Chemistry Illinois State University Normal, IL 61790-4160 http://chemagic.org From: "Paul Pillot" Sent: Friday, May 06, 2011 5:08 PM To: osrot...@chemagic.com, jmol-users@lists.sourceforge.net Subject: Re: [Jmol-

Re: [Jmol-users] Question to "Load Append" in Jmol

I've just made another try, with the same structure. Everything worked fine (I could translate or rotate all molecules in every direction, and rotating with the cursor outside an atom just moved the entire scene). But once I clicked on the left column link with the "rotate compare" command, the

Re: [Jmol-users] Question to "Load Append" in Jmol

://chemagic.org From: "Robert Hanson" Sent: Friday, May 06, 2011 3:10 PM To: jmol-users@lists.sourceforge.net Subject: Re: [Jmol-users] Question to "Load Append" in Jmol OK! I'll look into that. We don't want any molecules to esc

Re: [Jmol-users] Question to "Load Append" in Jmol

There is also a funny bug (in the biological meaning) with files such as 1gzx, 1hba (hemoglobin) where the proteins acts as spiders retained by their silky strings to the hemes. But if the hemes are dragged, the whole corresponding chain is actually dragged ! Le 6 mai 2011 à 21:09, Robert Hanso

Re: [Jmol-users] Question to "Load Append" in Jmol

OK! I'll look into that. We don't want any molecules to escape. On Fri, May 6, 2011 at 1:49 PM, Paul Pillot wrote: > Well, I just tried to run the "set picking dragmolecule" command for the > structures displayed at the link you gave and there is a strange bug when I > try to rotate the molecule

Re: [Jmol-users] Question to "Load Append" in Jmol

Well, I just tried to run the "set picking dragmolecule" command for the structures displayed at the link you gave and there is a strange bug when I try to rotate the molecules independently (it happens at the second try) : the molecules flies away in an unexpected direction (translation I suppo

Re: [Jmol-users] Question to "Load Append" in Jmol

when combined with set pickingstyle DRAG, just > LEFT-dragging moves the atoms, and the ALT and SHIFT keys are not required. > > > > > > > > Best > > Alex > > > > - Ursprüngliche Mail - > >> Von: "Reinhold Störmann" > >> An: jmo

Re: [Jmol-users] Question to "Load Append" in Jmol

ckingstyle DRAG, just LEFT-dragging > moves the atoms, and the ALT and SHIFT keys are not required. > > > > Best > Alex > > - Ursprüngliche Mail - >> Von: "Reinhold Störmann" >> An: jmol-users@lists.sourceforge.net >> Gesendet: Fre

Re: [Jmol-users] Question to "Load Append" in Jmol

SHIFT keys are not required. Best Alex - Ursprüngliche Mail - > Von: "Reinhold Störmann" > An: jmol-users@lists.sourceforge.net > Gesendet: Freitag, 6. Mai 2011 10:31:46 > Betreff: [Jmol-users] Question to "Load Append" in Jmol > At the moment I'

Re: [Jmol-users] Question to "Load Append" in Jmol

Hello Reinhold You are right, rotation, zoom etc. affects all frames/models. The only way is to use the "rotateSelected" command. But that doesn't work by mouse, only does defined angles. I think there is no way to do interactive rotation of a single model. --

[Jmol-users] Question to "Load Append" in Jmol

At the moment I'm trying to load more than one molecule from multiple pdb data files into one Jmol instance. It works fine using the load append command, and I can display any of the loaded molecules separately or all together. But I can't seem to find any function that allows me to manipulate

Re: [Jmol-users] Question regarding printing stereo images from Jmol

Peter, This was a bug. It is fixed for Jmol 12.1.39 and Jmol 12.0.36. See http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip If the STEREO command is given to produce two side-by-side images, when you would go to print those (using write t.png, for example), you would get only one eye's

Re: [Jmol-users] question about Jmol's surface

For Jmol, we have two kinds of surface -- solvent accessible and solvent excluded. In addition, we can set the solvent "probe" radius to just about anything, including 0. isosurface sasurface 1.2 is very fast. It traces the center of the solvent along as the probe is "rolled" along. This is the "

Re: [Jmol-users] question about Jmol's surface

Welcome to Jmol ! best documentation on Jmol's surfaces is to be found here : http://biomodel.uah.es/Jmol/surfaces/ -Paul Le 13 déc. 2010 à 01:54, Anbang Li a écrit : > > Could anyone explain to me what "solvent surface" is? ---

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