[Jmol-users] jmol load trajectory and lammps xyz output
Hi there! I will send this to the lammps and the jmol list, because any
solution will probably involve either of the programs :)
I have problems when reading a lammps xyz trajectory with jmol :(
It's a system consisting of LJ particles and a metal, in different parts of
the box, obviously
pair_style hybrid eam lj/cut 10.0
pair_coeff 1 1 eam Pt_u3.eam
pair_coeff * 2 lj/cut 0.00673850588 3.165648
...
dump1 gbigbox xyz 1 rawdump.1.xyz
I run this as a parallel job on 8 processors.
Afterwards I substitute the atom types 1, 2 with awk into something that
jmol can read (Se is chosen for its nice color ;):
awk '{if ($1 == '1'){print "Pt ",$2," ",$3," ",$4}else if($1 == '2'){print
"Se ",$2," ",$3," ",$4} else{print $0}}' $1 > tempdump.$1.xyz
I make a file with the 10 last snapshots. From that file I make another
file, containing the first of those 10 snapshots.
This opens correctly in jmol, so far so good.
Then, I try to open the file with all 10 last snapshots, and open it with
'load trajectory'
The last snapshot is correct:
http://www.molmod.com/~schraven/jmol/last_frame_out_of_ten__ten_frame_file.jpg
But it created a misrepresentation of the first 9 of these 10 snapshots:
some of the atoms within the metal and the LJ layer seem all mixed up :(
http://www.molmod.com/~schraven/jmol/first_frame_out_of_ten__ten_frame_file.jpg
That happening is not very possible due to the quite solid nature of the
metal ;)
I also checked by just reading the first snapshot of the 10 from a file with
only this snapshot in it:
http://www.molmod.com/~schraven/jmol/first_frame_out_of_ten__single_frame_file.jpg
That is the same structure as the previous picture, but with the correct
distribution of atom types.
My conclusion is that jmol assumes that the atom order in the last frame of
a trajectory is the order in all frames, and that lammps does not keep the
atom order constant in the printing of xyz files. For all practical
purposes, is there a way to make lammps always use the same order of atoms?
I hope anyone can shed some light on this issue!
Greetings, Pim
--
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Re: [Jmol-users] jmol load trajectory and lammps xyz output
Solution given on the lammps list already! As long as you write away the
group 'all' (the whole system) in xyz, it makes sure it puts it in the right
order. Or by using a different file format from xyz... I have to admit that
this is perfectly documented behavior of lammps, sorry for disturbing ;)
Greetings, Pim
On Mon, Jan 18, 2010 at 5:36 PM, Robert Hanson wrote:
> That would be crucial for sure. Not necessary, though to load as a
> trajectory if you only want a few models. Just load the file normally.
>
>
> On Mon, Jan 18, 2010 at 9:35 AM, pim schravendijk > wrote:
>
>> Hi there! I will send this to the lammps and the jmol list, because any
>> solution will probably involve either of the programs :)
>>
>> I have problems when reading a lammps xyz trajectory with jmol :(
>>
>> It's a system consisting of LJ particles and a metal, in different parts
>> of the box, obviously
>>
>> pair_style hybrid eam lj/cut 10.0
>> pair_coeff 1 1 eam Pt_u3.eam
>> pair_coeff * 2 lj/cut 0.00673850588 3.165648
>>
>> ...
>>
>> dump1 gbigbox xyz 1 rawdump.1.xyz
>>
>> I run this as a parallel job on 8 processors.
>>
>> Afterwards I substitute the atom types 1, 2 with awk into something that
>> jmol can read (Se is chosen for its nice color ;):
>>
>> awk '{if ($1 == '1'){print "Pt ",$2," ",$3," ",$4}else if($1 ==
>> '2'){print "Se ",$2," ",$3," ",$4} else{print $0}}' $1 > tempdump.$1.xyz
>>
>> I make a file with the 10 last snapshots. From that file I make another
>> file, containing the first of those 10 snapshots.
>> This opens correctly in jmol, so far so good.
>>
>> Then, I try to open the file with all 10 last snapshots, and open it with
>> 'load trajectory'
>>
>> The last snapshot is correct:
>>
>> http://www.molmod.com/~schraven/jmol/last_frame_out_of_ten__ten_frame_file.jpg<http://www.molmod.com/%7Eschraven/jmol/last_frame_out_of_ten__ten_frame_file.jpg>
>>
>> But it created a misrepresentation of the first 9 of these 10 snapshots:
>> some of the atoms within the metal and the LJ layer seem all mixed up :(
>>
>> http://www.molmod.com/~schraven/jmol/first_frame_out_of_ten__ten_frame_file.jpg<http://www.molmod.com/%7Eschraven/jmol/first_frame_out_of_ten__ten_frame_file.jpg>
>>
>> That happening is not very possible due to the quite solid nature of the
>> metal ;)
>>
>> I also checked by just reading the first snapshot of the 10 from a file
>> with only this snapshot in it:
>>
>> http://www.molmod.com/~schraven/jmol/first_frame_out_of_ten__single_frame_file.jpg<http://www.molmod.com/%7Eschraven/jmol/first_frame_out_of_ten__single_frame_file.jpg>
>>
>> That is the same structure as the previous picture, but with the correct
>> distribution of atom types.
>>
>> My conclusion is that jmol assumes that the atom order in the last frame
>> of a trajectory is the order in all frames, and that lammps does not keep
>> the atom order constant in the printing of xyz files. For all practical
>> purposes, is there a way to make lammps always use the same order of atoms?
>>
>> I hope anyone can shed some light on this issue!
>>
>> Greetings, Pim
>>
>>
>>
>>
>>
>>
>> --
>> Throughout its 18-year history, RSA Conference consistently attracts the
>> world's best and brightest in the field, creating opportunities for
>> Conference
>> attendees to learn about information security's most important issues
>> through
>> interactions with peers, luminaries and emerging and established
>> companies.
>> http://p.sf.net/sfu/rsaconf-dev2dev
>> ___
>> 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
> 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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attendees to learn about information security's most important issues through
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[Jmol-users] Exporting planes and (iso)surfaces to povray
Hello there jmol fans! I have a question. I can create planes, polyhedra, and isosurfaces in jmol, but since I want a presentable picture of it as well, I want to export this complete system to povray. Just doing the menu-function 'export to povray' doesn't seem to do the trick. Is there a command line function that I missed, or is it not implemented yet? I searched all over google but couldn't find any hint in this direction. -- 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] Keeping track of all jmol features?
Dear Jmol people, As a jmol user, I am highly impressed of all the new features that jmol has gotten in the last year, it's becoming an amazingly versatile program. BUT, I just noticed that I really lost track of all the features that have been implemented and are still being implemented. There are a lot of things that I know can be done with the program, but I just don't know anymore where it is written. I know there are the pages of Bob at stolaf, ( http://www.stolaf.edu/academics/chemapps/jmol/docs/ ) and then the interactive scripting examples at http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/new0.htm or "new.htm" or new1 or new2. And then, for isosurfaces there is http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/isosurface.htm and for surfaces there is http://jmol.sourceforge.net/docs/surface/ And then there is the wiki Jmol doesn't have the in-script help like rasmol has I guess, but at the moment having that would probably just mean another heap of work to keep it updated. I really think that it would be a good thing for jmol to have a single clear structure in the documentation. For a versatile program like this, with the amount of features it currently has, it is very important to give the users clear access to these features. The list of functions in http://www.stolaf.edu/academics/chemapps/jmol/docs/ is already very good as a reference, but the lists with interactive examples have the disadvantage that they mostly show the functions in the new version, of which there are a lot :) I guess it would be useful to have therefore interactive pages with examples corresponding each of the entries in the reference. Then, next to the reference, it will be useful to have a page of interactive examples from the point of view of the user, that wants to know how-to do this and this? Of course there the reference is not enough, no new user can know which function-name to look at. The surface page is an example of such a solution. Sorry for the long blurb, but I think it would be an important point to make sure that all the effort done by the developers doesn't get lost. Are there already plans to make a more structured documentation and tutorial? Is there a way to integrate this into the wiki-idea, so it can be done with the help of user contributions? -- 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
Re: [Jmol-users] Keeping track of all jmol features?
Hi again! All the main info is there, especially the very good /doc/ page at stolaf. The biggest problem is that the rest of the website is very dispersed. The sourceforge page is hard to change, being old-style html :) so the wiki must be the way to go then. I will see if I can do something there, at least trying to collect how-to's from other pages or making a clear structure, which is not as easy as I think it is :) What would be ideal is if it were possible to include jmol scripts on the wiki. Can this be done? Wikis are not so very flexible when it comes to embedding things so it might be problematic. And another question: does a link like: http://www.stolaf.edu/academics/chemapps/jmol/docs/index.htm#setbondstyles always point to the latest version? Because a link like: http://www.stolaf.edu/academics/chemapps/jmol/docs/index.htm?ver=11.2#setbondstyles will be outdated very quickly at the current pace of things :) (which is good, of course) -- 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
Re: [Jmol-users] Jmol-users Digest, Vol 13, Issue 2
> At 17:12 05/06/2007, [EMAIL PROTECTED] wrote: > >I was wondering if any of you could recommend a program that would allow me > >to create the molecules so that I could load them into Jmol. The dundee Prodrg server lets you draw a molecule in an applet, then do some configuration optimization on it. It will actually return you forcefield information, BUT be careful with that part, because it is not parameterized to anything, just makes a guess based on existing forcefield data or some quantum calculations (I don't really know how they do it, correct me if I'm wrong). http://davapc1.bioch.dundee.ac.uk/programs/prodrg/ These people could apply a jmol applet there as well, although I figure they might already have enough bandwith issues :) -- 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
Re: [Jmol-users] Citing Jmol
Wouldn't a program like this deserve a publication? rasmol had some, back in the days ( http://www.umass.edu/microbio/rasmol/rasbib.htm ). The flexibility of in-webpage jmol, the new density map algorithm by Bob Hanson, etc. this is all pretty advanced and new stuff. On 6/4/07, David Leader <[EMAIL PROTECTED]> wrote: > Is there any prefered way of citing Jmol in publications? > -- 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
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
Re: [Jmol-users] The future of Java?
On 6/13/07, Angel Herraez <[EMAIL PROTECTED]> wrote: > I understood that iPhone uses plain MacOSX, so how is Java prevented > from working? Do they block installation? What happens with other plugins, > like Flash? Can't the browser be supplemented? If it is true that he puts MacOSX in mobile phone, than how is he calling java "big and heavyweight"? This is pure nonsense. My cheap prepaid mobile phone from 4 years ago has a java interpreter in it, but it sure can't run OSX. Even if the iPhone wouldn't run OSX, it still has enough processing power to run all the java one wants. Also, as far as I understood it, java is also way faster than it used to be (also relative to computing power of course) and Steve Jobs is just digging up old cows, as we say in Holland. This smells of dusty old politics and fud-spreading. Another reason why Jobs is talking out of his rear end: on my old pc I can run Jmol in a browser slowly but it works, whereas some of the more heavy stupid flash banners (trying to put whole movie trailers in a flash banner) will fire up the CPU to 100% usage and bring my browser to a halt. That is also a matter of the quality of the programmer, the youtube flash plugin is excellent in that aspect, runs without problems on older machines as well. (to Egon: it couldn't have been anyone from Sun, since otherwise they would have suggested iPhone to work as a light client connecting to some mainframe, as that is the future for many years already now ;) Gotta love Sun, though, they've been doing some pretty good stuff lately, I really hope they manage to survive and get on top this way.) -- 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
Re: [Jmol-users] The future of Java?
... And if the iPhone would be a measure for the state of things, it doesn't look too good for flash either ;) http://www.wirelessinfo.com/content/No-Flash-Support-For-The-iPhone.htm -- 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
Re: [Jmol-users] Inserting the applet into a webpage
Also check the information on: http://wiki.jmol.org/index.php/Jmol_Applet and http://wiki.jmol.org/index.php/Files_Description On 6/26/07, Angel Herraez <[EMAIL PROTECTED]> wrote: > Hello, David > > > Are there any tutorials currently available for inserting the applet into a > > webpage? > > Not very comprehensive, but you can get some example code from Jmol pages: > http://jmol.sourceforge.net/demo/jssample1/ > http://jmol.sourceforge.net/demo/ > > (oops, I see now that that example 1 is not working, the model does not get > loaded; this is an > error in the source code or in the file location; I will take care of it > later. But the code shown in > the page is correct.) > > > Ah, and you also have my templates, referenced in the Wiki, > http://wiki.jmol.org:81/index.php/Recycling_Corner#Dynamically_resized_panels_layout > but those are not written for novices, they require some experience on your > part. They are > interesting because they provide automatic resizing of the applet according > to browser's > window size. > > > > I am trying to make something similar to this: > > http://www.rpc.msoe.edu/cbm/jmol/acetyl.php > > In fact, you could copy the code from any web page using Jmol (in html rather > than php, > unless you know your php well). > > > > - > 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 > -- http://www.molmod.com - 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] Bad experience editing wiki
On 7/4/07, Eric Martz <[EMAIL PROTECTED]> wrote: > "save early and often" comes to mind. Especially, save before you go > elsewhere to do some research even though you haven't finished your edit! > > -Eric I also noticed the logging out, is this a new feature or was it always like this? I was saving intermediate files anyway, because I trust my browser as much as I trust windows word (also, firefox seems to forget input when accidentally pressing a link and then using the back button, opera does that a bit better, or is there some option in firefox?). The only disadvantage of saving a lot is that the changelog list gets huge, but better that than being demoralized from losing your editing work :) -- Greetings, Pim http://www.molmod.com - 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] how do I reset Jmol applet menus on reload etc?
I just tried, when I select a new molecule on the left it opens with the original settings. Then I change it, select the other molecule, and go back again, and all changes are lost, back to default as well. So, the applet seems to have the behavior you want, at least here. Using firefox on linux, version 2.002 and sun java 1.42_12 if that matters. -- Greetings, Pim http://www.molmod.com - 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] Questions and wishes
I would be pretty happy with these features as well, and would like to add: - the possibility to switch between the unit cell and "filled" supercell representation (only adding copies of those atoms that are filling the unit cell). - the possibility to create periodic copies of the unit cells / supercells, not only the copies along the cell vectors. Now, to get a view of a rectangular part of my cell, I end up making a huge amount of copies in the hkl directions, until there is a solid cubic part large enough in the middle of all this, which I cut out by defining planes around it. A bit of a fuss :) If someone knows an already existing better way, please tell. BTW I already tried drawing surface vectors, you'd have to give the starting and end points yourself, but this can be done in unit cell vectors. Doable, but it could be fancier of course :) -- Greetings, Pim http://www.molmod.com - 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] Isosurface and Color
Couldn't you just add the string ";color isosurface red" to the end of the command that is send to jmol? That way it still send one _line of text_, but due to the semicolon that can be multiple commands. I can't imagine something like that is not possible in javascript. Otherwise show the part of your code that is doing this. On 8/3/07, Einar Coutin <[EMAIL PROTECTED]> wrote: > Yep, that works but I want to do it in a simple sentence, when I create the > Isosurface. IT HAS TO BE THAT WAY BECAUSE THE WAY I CREATED THE User > Interface for JMOL. I create my isosurfaces using an expandible Menu and > JavaScript functions. -- Greetings, Pim http://www.molmod.com - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now >> http://get.splunk.com/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol 11.3.23 and scripting
Excellent looping (I didn't like the looping before much), and pretty straightforward to understand, but why the goto? For all fortran addicts? :) I didn't install the new release yet, will jmol still interpret javascript in load files? Can the languages be mixed? On 9/16/07, Bob Hanson <[EMAIL PROTECTED]> wrote: > Jmol just took a quantum leap in the area of scripting. > -- Greetings, Pim http://www.molmod.com - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. 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] SMILES in Jmol?
In Jmol, you can use the SMILE notation to select (sub)groups of
connected atoms, e.g.:
select substructure("C(O)C")
That's the reason there is a SMILES package in Jmol.
> On 8/21/07, Li Yang <[EMAIL PROTECTED]> wrote:
> > Has anyone try view SMILES molecules in Jmol? Are there any examples
> and
> > how-to? I noticed there is SMILES package in Jmol.
--
Greetings, Pim
http://www.molmod.com
-
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Re: [Jmol-users] jmol
That is an impressive program! But as far as I can see, the builder in that suite is also using the Jmol interface. Porting the building capacity to Jmol shouldn't be too much of a problem then, should it? On 9/4/07, Bob Hanson <[EMAIL PROTECTED]> wrote: > no plans for this as part of Jmol itself. See, however, Molecular > Workbench: http://xeon.concord.org:8080/modeler/faq.html#jmol -- Greetings, Pim http://www.molmod.com - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. 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] any known issues with Jmol/Java with large files
Just today I saw that the molecular workbench software has to deal with the same problem. apparently, default memory is 64 MB. When loading via command line it is possible to get more memory available (e.g. java -Xmx512M -jar program.jar) but I have no idea if a similar thing can be done for web applets. see: http://mw.concord.org/modeler/xmx.html -- Greetings, Pim http://www.molmod.com - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. 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 11.3.15 -- custom menus
I've just been playing around with the molecular workbench 3D modeler, which has a completely different menu structure, but it's no effort at all to work with this new menu set. Actually I am glad they didn't leave the jmol interface and put everything under 'macros' for example, it would have made the program unworkable. This is exactly a case where you remove standard menu items to remove confusement for the user (especially useful in education purposes: less is more), and I do not think many people will have problems with jmol applets interacting differently. You automatically use the menu items you get presented. So I would think that the current jmol menu can be the default 'full' set, for which translations are already there anyway. There can be a default 'small' set and I would prefer it if all menu options can be removed easily, leaving room for a set of only custom options. Excellent! Many thanks (especially) to Bob for his dedication on the Jmol program in the last year. In this year, the possibilities of the program grew faster than one could learn and remember how to use them all! For me, Jmol grew from just a substitute for rasmol and xmol to an innovative, versatile visualization program, I think this. counts for most of us! -- Greetings, Pim http://www.molmod.com - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. 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] Visualize MOs from Mopac
I'm sorry, I have no experience with MOPAC, but just a few hints: Jmol should be able to read mopout and graphf files: http://wiki.jmol.org/index.php/File_formats#MOPAC http://openmopac.net/manual/graph.html You will probably need the mo or isosurface command http://chemapps.stolaf.edu/jmol/docs/#mo http://chemapps.stolaf.edu/jmol/docs/#isosurface Can you describe what you have done so far? On 9/17/07, Fabrice Gardebien <[EMAIL PROTECTED]> wrote: > > Dear Users, > I just want to visualize molecular orbitals obtained from Mopac, either > from the 'gpt' file or the 'wob' (and 'wmp') file. > Can someone explain how I could do this with Jmol. > Thank you very much in advance. > Best wishes, > Fabrice. -- Greetings, Pim http://www.molmod.com - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. 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] FW: Internal error - embedding Jmol in MediaWiki
Oh, and could you (or someone else) update this fixes to the wiki.jmol.org page as well? Since you are apparently the last person who followed the instructions of that page you probably know best how to put it :) On 9/26/07, Shiller, Paul J. <[EMAIL PROTECTED]> wrote: > The following fix was sent to me and I am posting it to the list server for > others to see. > > Along with the fix below I also tried: > > Replace:$this->mJmolTagPresent = false; in function onParserBeforeStrip > With:return $this->mJmolTagPresent = false; > > And > > Replace: $this->mJmolTagPresent = false; in function onParserAfterStrip > With: return $this->mJmolTagPresent = false; > > These replacements work on my system. > > Paul Shiller > Tribological Specialist > Ph:+1-330-471-3344 > EMail: [EMAIL PROTECTED] > -Original Message- > From: Nicolas Vervelle [mailto:[EMAIL PROTECTED] > Sent: Wednesday, September 26, 2007 3:18 PM > To: jmol-users@lists.sourceforge.net > Cc: Shiller, Paul J. > Subject: Re: [Jmol-users] Internal error - embedding Jmol in MediaWiki > > Hi, > > My mail probably won't reach the mailing list (problems with my ISP), > can you forward it to the jmol-users mailing list so that other users > can participate ? > > I haven't worked for a long time on the extension mostly due to a lack > of time. I know people are interested in getting it on Wikipedia (sorry > for having not worked on it recently), so if someone is interested in > continuing development (especially the security part), he would be very > welcome :) > > Concerning your problem, it seems that recent versions of Mediawiki are > more strict on the hooks. > I think the fix is quite simple. Can you try it ? > Simply add "return true;" at the end of both onParserBeforeStrip and > onParserAfterStrip ? > Mediawiki should be happy with this fix. > > Keep us posted with the results. > > Nico -- Greetings, Pim http://www.molmod.com - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. 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] Povray rendering of drawn objects (polyhedra, lines, ..)
On 9/29/07, Latévi Max LAWSON DAKU <[EMAIL PROTECTED]> wrote: > Dear all, > > I cannot figure out wether it is possible to > have a povray renderering of a whole Jmol > "scene" that contains polyhedra and other > drawn objects. I have had no success so far. > Does support exist for doing such a thing ? > > Thanks in advance for your answer, > > Max Hi! There was no such thing, we are working on it at the moment! Bob Hanson has set up a general exporting method for any kind of 3D file format, I'm now filling in the povray parts. I hope I can do a patch for the polyhedrals by next week. If you want, you can join the developer list and contribute. Ciao, Pim -- Greetings, Pim http://www.molmod.com - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. 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] Aromatic bond rendering
> After I have read Bob's recent explanation on bond orders in Jmol > > OK, here is a total generalization of partial bonds. With this (11.3.28) > > you can draw any type of partial whatever up to 5 bonds. Works in > > bondOrder and connect, both: Did you get the latest CVS already? Your version (11.3.25) seems older than the version Bob mentions (11.3.28). > Test System > Jmol: 11.3.25, application > Java: 1.5.0_12 > OS : Linux, OpenSuSE 10.2 > - -- Greetings, Pim http://www.molmod.com - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now >> http://get.splunk.com/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] any known issues with Jmol/Java with large files
I couldn't use Jmol to open a 185 MB multiframe xyz file. I increased the memory available for java (via -Xms and -Xmx) to 1 GB, but this didn't help. The file opens in vmd without problems, using 5 % memory on a 1 GB system. That is about 50 MB, java allocates 64 MB on default (one can see that because jmol normally stops after using up 62 MB), so in theory, one should be able to do systems that are big enough without having to cross the default java memory barrier. What is the issue here? I guess Jmol creates an object for every single coordinate in the xyz system. Otherwise one wouldn't be able to manipulate objects over all the frames instantaneously. The size of an object is probably larger than just the coordinates given in the input file, so memory size is blown up when going from xyz file to working memory. Cutting the file up seems the way to go. But would it be possible to have Jmol do that by itself? some sort of 'read multiframe' option where it detects multiframe files and reads them one frame at a time? Or are there too many disadvantages to that (not being able to edit objects in frames that aren't read yet, long loading times per frame). I guess also a problem is that one cannot always assume that the atom types and order stay constant over the multiframe file. Just some thoughts here, would be nice if Jmol could handle files like this without human interference or external shell scripts :) -- Greetings, Pim http://www.molmod.com - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now >> http://get.splunk.com/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] any known issues with Jmol/Java with large files
On 10/5/07, Bob Hanson <[EMAIL PROTECTED]> wrote: > load "myfile" 3 > > loads just the third frame. Haven't considered > > load "myfile 3-4 > > But it's certainly worth looking at. Only problem here is that it would > require some retooling of all the multifile readers. Not so bad, really, > but a task. Ah yes, that is what I was looking for, something like: for (var i=1;i<100;i=i+1) save ORIENTATION movie load /tmp/file.xyz @i restore ORIENTATION movie delay 0.5 delay on end for But then less flickery :) By keeping the orientation the same during the loop, you can turn around the animation while it is playing, which is cool & practical. > >Or are there too many disadvantages to that (not being able to edit > >objects in frames that aren't read yet, long loading times per frame). > >I guess also a problem is that one cannot always assume that the atom > >types and order stay constant over the multiframe file. > > > > > > > Be more specific about your plans for that large file? Could it stream? Actually I mean as above, but streaming is also nice :) I remember that vmd can handle streaming data. Watching simulations in real-time seems to be one of those dreams of the 90s that never really caught on, though. > I've certainly thought about this. There is the concept, undocumented, > of a "trajectory" that doesn't have quite the overhead of a full file > load. In a trajectory, the atoms are all the same in each frame, so > there is just one reasonably sized set of atoms, and only the > coordinates are changed when you go from frame to frame. That's in Jmol > now, but I haven't experimented with it much. If Jmol could do the per-frame reading in a fluent way, 'trajectory-mode' might not even be needed. Otherwise it's probably a good way to save memory while watching simulations in Jmol. -- Greetings, Pim http://www.molmod.com - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now >> http://get.splunk.com/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] using a for loop with select command?
So many options, I'm getting confused :) Just for completeness: in which cases should one call variables via "@variable"? On 10/14/07, Frieda Reichsman <[EMAIL PROTECTED]> wrote: > Thanks, Bob - does the trick, and makes more tricks possible. > Frieda -- Greetings, Pim http://www.molmod.com - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now >> http://get.splunk.com/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] possible change in script behavior for "SET"
I'm in favor with option 2. It allows more flexibility for people that use their own variables. And it will still be an advantage towards the current situation. -- Greetings, Pim http://www.molmod.com - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now >> http://get.splunk.com/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] new resizable Window
Test of the resize script:
Most models there automatically resize fine.
BUT: watermo, bdno, and t2 seem to crash (black screen, mouse still
works) when I increase the size above a certain point (or too fast).
Memory usage at the point of crash is still under 64 MB. Reloading the
page doesn't help. Also not when the page is first resized to a
smaller point. Closing and opening helps.
It might be the complex isosurfaces, but then again the cartoon views
render fine no matter what I do.
Using: java 1.5.0 in firefox, under linux
On 10/19/07, Bob Hanson <[EMAIL PROTECTED]> wrote:
> Check my new POV-Ray example,
>
> http://chemapps.stolaf.edu/jmol/docs/examples-11/povray.htm
>
> It provides a simple example of a page with a popup based on a script.
> In this case, the xxx.pov file.
>
>
> Angel Herraez wrote:
>
> >Nick,
> >
> >As Rolf says, the function is not in Jmol.js, but in one of Bob's
> >files, new.js It says:
> >
> >function newAppletWindow() {
> > var sm=""+Math.random()
> > sm=sm.substring(2,10)
> > var newwin=open("JmolPopup.htm","jmol_"+sm,woptions)
> >}
> >
> >So, it just opens a resizable* window loading JmolPopup.htm page
> >
> >(*) since it uses
> >woptions="menubar=yes,resizable=1,scrollbars,alwaysRaised,width=600,
> >height=600,left=50"
> >
> >BTW, as far as I know you can shorten to
> >woptions="menubar,resizable,scrollbars,alwaysRaised,width=600,
> >height=600,left=50"
> >
> >JmolPopup.htm has a standard call to jmolApplet
> >but with the size arguments made to fit the window:
> > jmolApplet(["100%","90%"]
> >and then to collect a script from the opening page
> >
> >El 19 Oct 2007 a las 16:27, Nick Greeves escribió:
> >
> >
> >
> >>I'm still struggling with creating a button to pop out a large Jmol
> >>window like you have below your windows as standard.
> >>
> >>
> >
> >So, you can just do something like
> >
> > >onClick='newAppletWindow()'>
> >
> >if you
> >1) create a JmolPage.htm or copy Bob's JmolPopup.htm
> >2) define (or copy) newAppletWindow() in your page
> >3) a mechanism for passing the script from parent to child window, or
> >to read it from opener window as Bob's does.
> >
> >
> >
> >-
> >This SF.net email is sponsored by: Splunk Inc.
> >Still grepping through log files to find problems? Stop.
> >Now Search log events and configuration files using AJAX and a browser.
> >Download your FREE copy of Splunk now >> http://get.splunk.com/
> >___
> >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: Splunk Inc.
> Still grepping through log files to find problems? Stop.
> Now Search log events and configuration files using AJAX and a browser.
> Download your FREE copy of Splunk now >> http://get.splunk.com/
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
--
Greetings, Pim
http://www.molmod.com
-
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Re: [Jmol-users] new resizable Window
Strangely enough I didn't manage to start the Java console. I followed the instructions here: http://www.java.com/en/download/help/521200.xml but no console started. Has anyone experience with this? Maybe I need to make sure java quits and then restarts. At my second try watermo didn't crash anymore, but t2 did. It could be a local problem. It would be nice if anyone else can get results with java under firefox under linux. Just use the open jmol link and start increasing the size of the screen like a madman :) In the mean time let's assume it's not a general problem. On 10/31/07, Bob Hanson <[EMAIL PROTECTED]> wrote: > Pim, I can't reproduce this problem with Windows/Mozilla/Jmol 11.9.39_dev > > What do you see in the Java console? > > Bob > -- Greetings, Pim http://www.molmod.com - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now >> http://get.splunk.com/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] pov-ray images
You should set: hermitelevel =5; in your jmol script. That will make your trace look much better in jmol! And povray just copies that. So actually it was already looking irregular in jmol, just less clearly noticeable. As far as shadows are concerned: The jpgs on bobs website are from a version that had shadows, I don't get any shadows by default with his system using the current application. Often shadows of heaps of atoms obscure a clear view, but I have to admit that they can help with the feeling of depth and dramatic effects as well, so it should be easy to choose between having shadows on or off. I don't get the "no file was written" warning, and I can't remember if this is some specific povray case. On Nov 7, 2007 7:15 PM, Frieda Reichsman <[EMAIL PROTECTED]> wrote: > Sure, will email the files to you off list. Thanks. > When I compared Bob's pov-ray file to mine I saw lots of "no_shadow" > elements in both. So I did not try removing them from mine. > > On Nov 7, 2007, at 1:08 PM, pim schravendijk wrote: > > I have no idea about the lack of smoothness, but the fact that no shadows > are present might be understandable. There are by default no shadows in the > povray output for jmol. They can be turned on by removing the no_shadow > elements in the povray script. I will make this more easy to do, and maybe > it should be an option for the export menu and/or write command. > > Could you e-mail your trna.pov file and pdb? > > On Nov 7, 2007 6:13 PM, Frieda Reichsman <[EMAIL PROTECTED]> wrote: > > > I am working on creating a pov-ray image as nice as those Bob posted at > > http://chemapps.stolaf.edu/jmol/docs/examples-11/povray.htm > > > > When I run Bob's povray scripts in povray, I get the same beautiful > > images he posted. > > > > My tRNA povray script exported from Jmol comes out disappointingly > > crude-looking when I run it in povray. When I compare it to the DNA image on > > the above page (3rd image on the page) the differences are that the > > structure rendering is not nearly as smooth, and there are no shadows. > > > > I am using Jmol 11.3.40, and the command > > write povray 800 800 trna.pov > > > > Frieda > > > > /// > > > > Frieda Reichsman > > Molecules in Motion > > Interactive Molecular Structures > > http://www.moleculesinmotion.com > > > > /// > > > > > > > > > > - > > This SF.net email is sponsored by: Splunk Inc. > > Still grepping through log files to find problems? Stop. > > Now Search log events and configuration files using AJAX and a browser. > > Download your FREE copy of Splunk now >> http://get.splunk.com/ > > ___ > > Jmol-users mailing list > > Jmol-users@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > > > > -- > Greetings, Pim > http://www.molmod.com > - > This SF.net email is sponsored by: Splunk Inc. > Still grepping through log files to find problems? Stop. > Now Search log events and configuration files using AJAX and a browser. > Download your FREE copy of Splunk now >> > http://get.splunk.com/___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > /// > > > Frieda Reichsman > > Molecules in Motion > > Interactive Molecular Structures > > http://www.moleculesinmotion.com > > > /// > > > -- Greetings, Pim http://www.molmod.com - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now >> http://get.splunk.com/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] pov-ray images
I have no idea about the lack of smoothness, but the fact that no shadows are present might be understandable. There are by default no shadows in the povray output for jmol. They can be turned on by removing the no_shadow elements in the povray script. I will make this more easy to do, and maybe it should be an option for the export menu and/or write command. Could you e-mail your trna.pov file and pdb? On Nov 7, 2007 6:13 PM, Frieda Reichsman <[EMAIL PROTECTED]> wrote: > I am working on creating a pov-ray image as nice as those Bob posted at > http://chemapps.stolaf.edu/jmol/docs/examples-11/povray.htm > When I run Bob's povray scripts in povray, I get the same beautiful images > he posted. > > My tRNA povray script exported from Jmol comes out disappointingly > crude-looking when I run it in povray. When I compare it to the DNA image on > the above page (3rd image on the page) the differences are that the > structure rendering is not nearly as smooth, and there are no shadows. > > I am using Jmol 11.3.40, and the command > write povray 800 800 trna.pov > > Frieda > > /// > > > Frieda Reichsman > > Molecules in Motion > > Interactive Molecular Structures > > http://www.moleculesinmotion.com > > > /// > > > > - > This SF.net email is sponsored by: Splunk Inc. > Still grepping through log files to find problems? Stop. > Now Search log events and configuration files using AJAX and a browser. > Download your FREE copy of Splunk now >> http://get.splunk.com/ > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Greetings, Pim http://www.molmod.com - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now >> http://get.splunk.com/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] pov-ray images
I commited a simple change to revision 8585. After creating the povray file, you should set the value: noShadows = 'false'; in the .pov file. Run povray again on the .ini file and you will get the same picture, but with shadows. Eventually this could/should be configurable via jmol, either as an option to the 'write' command, or as a jmol variable that can be set. On Nov 8, 2007 7:58 PM, Frieda Reichsman <[EMAIL PROTECTED]> wrote: > Thanks, Pim, I didn't think of hermiteLevel for nucleic acid cartoon > display! Makes a huge difference. > However, the absence of shadows is still unsolved. Maybe Bob can > elaborate? > > Frieda > > > On Nov 7, 2007, at 1:46 PM, pim schravendijk wrote: > > You should set: > > hermitelevel =5; > > in your jmol script. That will make your trace look much better in jmol! > And povray just copies that. So actually it was already looking irregular in > jmol, just less clearly noticeable. > > As far as shadows are concerned: The jpgs on bobs website are from a > version that had shadows, I don't get any shadows by default with his system > using the current application. Often shadows of heaps of atoms obscure a > clear view, but I have to admit that they can help with the feeling of depth > and dramatic effects as well, so it should be easy to choose between having > shadows on or off. > > I don't get the "no file was written" warning, and I can't remember if > this is some specific povray case. > > On Nov 7, 2007 7:15 PM, Frieda Reichsman < [EMAIL PROTECTED]> wrote: > > > Sure, will email the files to you off list. Thanks. > > When I compared Bob's pov-ray file to mine I saw lots of "no_shadow" > > elements in both. So I did not try removing them from mine. > > > > On Nov 7, 2007, at 1:08 PM, pim schravendijk wrote: > > > > I have no idea about the lack of smoothness, but the fact that no > > shadows are present might be understandable. There are by default no shadows > > in the povray output for jmol. They can be turned on by removing the > > no_shadow elements in the povray script. I will make this more easy to do, > > and maybe it should be an option for the export menu and/or write command. > > > > Could you e-mail your trna.pov file and pdb? > > > > On Nov 7, 2007 6:13 PM, Frieda Reichsman <[EMAIL PROTECTED]> wrote: > > > > > I am working on creating a pov-ray image as nice as those Bob posted > > > at http://chemapps.stolaf.edu/jmol/docs/examples-11/povray.htm > > > When I run Bob's povray scripts in povray, I get the same beautiful > > > images he posted. > > > > > > My tRNA povray script exported from Jmol comes out disappointingly > > > crude-looking when I run it in povray. When I compare it to the DNA image > > > on > > > the above page (3rd image on the page) the differences are that the > > > structure rendering is not nearly as smooth, and there are no shadows. > > > > > > I am using Jmol 11.3.40, and the command > > > write povray 800 800 trna.pov > > > > > > Frieda > > > > > >/// > > > > > > Frieda Reichsman > > > Molecules in Motion > > > Interactive Molecular Structures > > > http://www.moleculesinmotion.com > > > > > > /// > > > > > > > > > > > > > > > - > > > This SF.net email is sponsored by: Splunk Inc. > > > Still grepping through log files to find problems? Stop. > > > Now Search log events and configuration files using AJAX and a > > > browser. > > > Download your FREE copy of Splunk now >> http://get.splunk.com/ > > > ___ > > > Jmol-users mailing list > > > Jmol-users@lists.sourceforge.net > > > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > > > > > > > > > -- > > Greetings, Pim > > http://www.molmod.com- > > This SF.net email is sponsored by: Splunk Inc. > > Still grepping through log files to find problems? Stop. > > Now Search log events and configuration files using AJAX and a browser. > > Download your FREE copy of Splunk now >> > > http://get.splunk.com/___ > > Jmol-users mailing list >
[Jmol-users] Jmol Version 11.4.1 : two small script oddities
Hi there again! 2 minor oddities I found when opening a simple script with jmol commands in 11.4.1: ..1.. when writing to povray in a script, it is bothered by relative paths in the output filename: In other contexts, relative paths work, for example, this works: $ write JPG "./out.jpg" type=JPG; file=jpg./out.jpg; width=774; height=751; quality=75 Script completed Whereas this doesn't: $ write povray "./out.pov" type=POV; file=povray./out.pov; length=0 Script completed With the java console outputting to me the following: Cannot export POV IO Exception: povray./out.pov (No such file or directory) Seems like some string handling being messed up? ..2.. It is not possible to comment out multiple commands on a single line in one go, for example the line: #if (1==1); frame next; end if; will give a script compiler error: script compiler ERROR: invalid context for end line 20 command 15 ofjmol.script: end if; line 1 command 1 of file null: script "jmol.script" << It seems commenting out is only valid until the next semicolon, not until "end of line". This might be either a bug or a feature, in any case I didn't expect it. -- Greetings, Pim http://www.molmod.com - This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] bug? Setting calculation of bonds on molecule load
Hi all, I would like to disable the automatic calculation of bonds on startup. This is needed for viewing large metal structures. There is an option in "edit"->"properties"->"Bonds" and then "Don't Compute Bonds". However: It doesn't seem to do anything. I tried setting autoBonds in ~HOME/.jmol/properties to false, true, 0, 1, off, on, that at least removes the "checked" sign in the properties menu, but calculation of bonds still occurs. I tried to look in the code a bit but couldn't find an easy solution. Using jmol 11.6.20. Any hints? -- Greetings, Pim http://www.molmod.com -- Greetings, Pim http://www.molmod.com -- This SF.net email is sponsored by: High Quality Requirements in a Collaborative Environment. Download a free trial of Rational Requirements Composer Now! http://p.sf.net/sfu/www-ibm-com___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] variable in bitset not recognized for "load trajectory" (was: Jmol-developers)
Thank you! This should probably have been in the jmol-user mailing
list, sorry for that, moved it now.
One related question: I would like to apply a saved state to the next
frame in the loop, but obviously not load the same frame again. Is
there a way to access/change individual properties of a saved state?
On 6/17/09, Robert Hanson wrote:
> The construct:
>
> $ load trajectory ({...@i})
>
> is not valid, because ({...}) are evaluated at compile time, and @i has to
> be evaluated at run time.
>
> You should be able to do this:
>
> i = 0
> load trajectory @{ "({" + i + "})" }
>
> because that will evaluate the string "({0})" at run time, and that will be
> turned into a bitset.
>
>
>
>
> On Wed, Jun 17, 2009 at 5:24 AM, pim schravendijk
> wrote:
>
>> Hi!
>>
>> it seems that the scriptevaluator does not recognize my bitset as a
>> bitset when I try to put a variable in it.
>>
>> It goes wrong in svn release 11.7.42_dev and all versions before that I
>> tried:
>>
>> $ load trajectory ({0})
>> "/home/schraven/WORK/LAMMPS/goldwire_20090610/split.0001"
>>
>> ... Works!
>>
>> $ var i = 0
>> $ echo @i
>> 0
>>
>> ... fine so far
>>
>> $ load trajectory ({...@i})
>> "/home/schraven/WORK/LAMMPS/goldwire_20090610/split.0001"
>> script ERROR: filename expected
>>
>> load trajectory >> { << ( 0 ) }
>> "/home/schraven/WORK/LAMMPS/goldwire_20090610/split.0001"
>>
>> kaputt! :(
>>
>> I am taking a look at the code now, but since Bob made a pretty
>> complex scripting machine out of Jmol, this might be troublesome :)
>>
>> --
>> Greetings, Pim
>> http://www.molmod.com
>>
>>
>> --
>> Crystal Reports - New Free Runtime and 30 Day Trial
>> Check out the new simplified licensing option that enables unlimited
>> royalty-free distribution of the report engine for externally facing
>> server and web deployment.
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>> ___
>> Jmol-developers mailing list
>> jmol-develop...@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>>
>
>
>
> --
> 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
>
--
Greetings, Pim
http://www.molmod.com
--
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server and web deployment.
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Re: [Jmol-users] maximum number of models in xyz file?
if you really really really would need to perform operations on all the frames, you could also split the xyz before reading them in jmol: Say, if you have 1 atoms in your system, and you want to split your trajectory in batches of 100 frames, you could use the bash command split: p...@mypc:~> split -a 4 -d -l 1000200 trajectory.xyz trajectory.xyz.split. (in xyz there are probably 2 comment lines in each frame) this gives you trajectory.xyz.split.0001 trajectory.xyz.split.0002 etc. You could then load them separately or use a jmol script greetings, Pim On 6/19/09, Nicolas Bock wrote: > Hi Bob, > > thanks for clarifying this. > > nick > > > On Thu, Jun 18, 2009 at 22:12, Robert Hanson wrote: > >> The maximum number of models in a file is limited by the format for >> describing models: >> >> x.y >> >> where x is the file number and y is the model number in the file. The >> limitation on y is . >> >> If you have more than that number of models in a single file, you should >> consider using a trajectory and probably load only, say, every 5th model. >> >> Bob >> >> >> On Thu, Jun 18, 2009 at 8:53 AM, Nicolas Bock >> wrote: >> >>> Hello list, >>> >>> I am trying to read an xyz file into Jmol that has a lot of frames. Jmol >>> doesn't load the file and on the java console I get this error message: >>> >>> 34106 models in this collection. Use getProperty "modelInfo" or >>> getProperty "auxiliaryInfo" to inspect them. >>> Exception in thread "QueueThread0" >>> java.lang.ArrayIndexOutOfBoundsException: -32768 >>> at org.jmol.modelset.ModelLoader.iterateOverAllNewAtoms(Unknown >>> Source) >>> at org.jmol.modelset.ModelLoader.initializeModelSet(Unknown Source) >>> at org.jmol.modelset.ModelLoader.(Unknown Source) >>> at org.jmol.viewer.ModelManager.setClientFile(Unknown Source) >>> at org.jmol.viewer.Viewer.openClientFile(Unknown Source) >>> at org.jmol.viewer.Viewer.getOpenFileError(Unknown Source) >>> at org.jmol.viewer.Eval.load(Unknown Source) >>> at org.jmol.viewer.Eval.instructionDispatchLoop(Unknown Source) >>> at org.jmol.viewer.Eval.runEval(Unknown Source) >>> at org.jmol.viewer.Viewer.evalStringWaitStatus(Unknown Source) >>> at >>> org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runScript(Unknown >>> Source) >>> at >>> org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runNextScript(Unknown >>> Source) >>> at org.jmol.viewer.ScriptManager$ScriptQueueRunnable.run(Unknown >>> Source) >>> at java.lang.Thread.run(Thread.java:619) >>> >>> My completely uneducated guess is that Jmol uses a short signed int for >>> the number of models and that's why it's failing, but of course I might >>> be >>> completely off here. What is the maximum number of models an xyz file can >>> have? Can one raise this limit? >>> >>> Thanks already, nick >>> >>> >>> >>> -- >>> Crystal Reports - New Free Runtime and 30 Day Trial >>> Check out the new simplified licensing option that enables unlimited >>> royalty-free distribution of the report engine for externally facing >>> server and web deployment. >>> http://p.sf.net/sfu/businessobjects >>> ___ >>> 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 >> 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 >> >> >> -- >> Crystal Reports - New Free Runtime and 30 Day Trial >> Check out the new simplified licensing option that enables unlimited >> royalty-free distribution of the report engine for externally facing >> server and web deployment. >> http://p.sf.net/sfu/businessobjects >> ___ >> Jmol-users mailing list >> Jmol-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> > -- Greetings, Pim http://www.molmod.com -- Are you an open source citizen? Join us for the Open Source Bridge conference! Portland, OR, June 17-19. Two days of sessions, one day of unconference: $250. Need another reason to go? 24-hour hacker lounge. Register today! http://ad.doubleclick.net/clk;215844324;13503038;v?http://opensourcebridge.org ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] maximum number of models in xyz file?
hi!
split is just a command in bash, cutting any ascii file after a " -l
"amount of lines, and appending 000x after the name, where " -d "
creates a number suffix and " -a " says how many digits there should
be. It might not be necessary to use this for jmol anymore, because
the load trajectory per frame or stride appears very memory-efficient,
but it's anyway a handy trick for other analysis.
As in my previous mails, I am currently experimenting with the "load
trajectory" option and the conversion to a movie file within the same
viewing state.
For testing, I just created a trajectory of about 100 atoms, and
actually managed to read in 4 (>!) frames, and after reading
in I could move around between frames, although jmol crashed when I
tried to click on atoms etc. :)
In any case, it is indeed perfectly possible to read in even the
biggest file in little bits:
load trajectory {199000 20 1} "/WORK/LAMMPS/meam/dump.xyz"
and create a loop around it that increments the first and last frame
of the strides with e.g. 1000 frames.
Now the printing part:
For frames that are counted as x.y, "load trajectory" seems to load
all the timesteps in 1.y, because it is just one file, did I get that
correctly?
Unfortunately for my case, it appears that the easiest image printing
solution via "write frames" only prints images of incrementing files
x and ignores the incrementing frames .y , is that correct?
I did get a bit further with extracting state information to
variables, the only thing I need to do is replace a string, I guess by
calling a fitting javascript command from jmol...
greetings, pim
On 6/23/09, Robert Hanson wrote:
> Also, Jmol's load TRAJECTORY command allows you to use the same idea to
> load
> only specific trajectories from a set using the first, last, and "stride"
> familiar to AMBER users.
>
> load TRAJECTORY {first last stride} or ({i j k:l m..}) "filename"*
>
> Loads the specified subset of models from the file as a trajectory.
> **In the first syntax, first and last models along with a "stride" (step)
> are specified. Models are then read using an equivalent of for (i = first;
> i
> <= last; i = i + stride). Numbers start with 0 for the first model; -1 for
> last indicates "to the end of the file." For example, load MODELS {0 10 2}
> "..." would load six models, models 0, 2, 4, 6, 8, and 10.*
> *
>
> *So, Pim, can you explain those split command parameters? How do they
> indicate to do this?
>
> Bob
>
>
> On Tue, Jun 23, 2009 at 4:12 AM, pim schravendijk
> wrote:
>
>> if you really really really would need to perform operations on all
>> the frames, you could also split the xyz before reading them in jmol:
>>
>> Say, if you have 1 atoms in your system, and you want to split
>> your trajectory in batches of 100 frames, you could use the bash
>> command split:
>>
>> p...@mypc:~> split -a 4 -d -l 1000200 trajectory.xyz
>> trajectory.xyz.split.
>>
>> (in xyz there are probably 2 comment lines in each frame)
>>
>> this gives you trajectory.xyz.split.0001 trajectory.xyz.split.0002
>> etc. You could then load them separately or use a jmol script
>>
>> greetings, Pim
>>
>> On 6/19/09, Nicolas Bock wrote:
>> > Hi Bob,
>> >
>> > thanks for clarifying this.
>> >
>> > nick
>> >
>> >
>> > On Thu, Jun 18, 2009 at 22:12, Robert Hanson
>> > wrote:
>> >
>> >> The maximum number of models in a file is limited by the format for
>> >> describing models:
>> >>
>> >> x.y
>> >>
>> >> where x is the file number and y is the model number in the file. The
>> >> limitation on y is .
>> >>
>> >> If you have more than that number of models in a single file, you
>> >> should
>> >> consider using a trajectory and probably load only, say, every 5th
>> model.
>> >>
>> >> Bob
>> >>
>> >>
>> >> On Thu, Jun 18, 2009 at 8:53 AM, Nicolas Bock
>> >> wrote:
>> >>
>> >>> Hello list,
>> >>>
>> >>> I am trying to read an xyz file into Jmol that has a lot of frames.
>> Jmol
>> >>> doesn't load the file and on the java console I get this error
>> >>> message:
>> >>>
>> >>> 34106 models in this collection. Use getProperty "modelInfo" or
>> >>> getProperty "auxiliaryInfo" to inspect them.
>> >>> Exception in thr
Re: [Jmol-users] maximum number of models in xyz file?
Thanks! That works perfectly! greetings, Pim On Tue, Jun 23, 2009 at 7:18 PM, Robert Hanson wrote: > Hi, Pim, > > > > On Tue, Jun 23, 2009 at 8:38 AM, pim schravendijk > wrote: > >> hi! >> >> Now the printing part: >> For frames that are counted as x.y, "load trajectory" seems to load >> all the timesteps in 1.y, because it is just one file, did I get that >> correctly? >> > > Yes, I think so. > > >> Unfortunately for my case, it appears that the easiest image printing >> solution via "write frames" only prints images of incrementing files >> x and ignores the incrementing frames .y , is that correct? >> > > It's probably not aware of trajectories. Should be model-by-model. > > OK, I've uploaded the changes for 11.7.44 that take care of this. All you > should need is > > write frames "xxx.jpg" > > Bob > > > -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
