Re: [Jmol-users] Fwd: SourceForge Project of the Week March 27th, 2017

This is great! Congratulations! :) On 23. 03. 17 17:35, Jaime Prilusky wrote: > Congratulations!! > >> On 23 Mar 2017, at 16:22, Robert Hanson > > wrote: >> >> FYI >> >> -- Forwarded message -- >> Subject: SourceForge Project of the Week March 27th, 201

Re: [Jmol-users] Hack-a-mol

Dear Bob, This is very nice!! :) Best, Max On 08. 12. 16 06:53, Robert Hanson wrote: > This is kind of fun... > > https://chemapps.stolaf.edu/jmol/jsmol/hackamol.htm > > > -- > Robert M. Hanson > Larson-Anderson Professor of Chemistry > St. Olaf College > Northfield, MN > http://www.stolaf.edu

Re: [Jmol-users] Use of variable in a call to getProperty

Dear Bob, Thanks a lot for your answer. Your solution is also the one given by Matt and it works :) I'm attaching a README file, which I wrote to keep track of what I did. It's far from being perfect. But I hope it may be helpful to someone. Thanks again, Bob, Matt and Angel! Best, Max

Re: [Jmol-users] Use of variable in a call to getProperty

something like: > > for (var i=300; i<370;i+=1){ > print getproperty('modelInfo.models['+i+'].modelProperties.FreqValue') > } I tried this latter and it works !! :D Thanks again! Best, Max > > Perhaps more skilled coders on the list could suggest improvements to thes

Re: [Jmol-users] Use of variable in a call to getProperty

On 07. 07. 16 17:04, Herráez Sánchez Ángel wrote: > Hi Max > Hi Herráez, Thanks for your mail > > I also have trouble often using variables. > > @{i} is unusual to me. The common syntax is either "i" or "@i " > :) I'm never sure when to use this; if using the bare name 'i' doesn't work, i swi

[Jmol-users] Use of variable in a call to getProperty

Dear Jmol users/developers, I would like to be able to use a variable in a call to getProperty. So far, the following command works. $ print getproperty('modelInfo.models[7].modelProperties.FreqValue') 129.529358 But I rwould like to use a variable as follows $ i=7 $ print g

Re: [Jmol-users] Orbitals not being displayed (command "mo")

On 07. 07. 15 20:59, Robert Hanson wrote: > MO 24 in Co_ just has a very tight cutoff. So the default 0.05 is too > large. You can see a bit of it with 0.03. > > I'm not seeing the problem with CuZ. Maybe the same. Also, since Jmol does > not include G orbitals, anything that is pure G will not

[Jmol-users] Orbitals not being displayed (command "mo")

Dear Bob, There is a bug which shows up when trying to view molecular orbitals with the "mo" command: some orbitals are displayed but other aren't, and even the information about the file (molden type), the model and the MO are not shown. I've made a compressed archive with two files ("Co_molden

Re: [Jmol-users] Support for molecular orbitals in molden format

Dear Bob, In order to try to understand what's going on when it comes to render the MOs, I've called jmol with the option "-logger.info=true". I've used three different files - "columbus.molden": s, p, d basis functions - "b1t_spdfg.molden": s, p, d, f, g basis functions - "b2q_spdfg

Re: [Jmol-users] Support for molecular orbitals in molden format

On 08. 04. 15 19:46, Robert Hanson wrote: > All the orbital coefficients are read, but then in creating the surfaces, > only s-f are used. > Thanks a lot for the explanations, Bob. All the best, Max > On Wed, Apr 8, 2015 at 11:03 AM, Latévi Max LAWSON DAKU > wrote: > &g

Re: [Jmol-users] Support for molecular orbitals in molden format

for download at http://www.filedropper.com/viztar It contains - viz/molden.inp_ORIG - viz/molden.inp which only differs by the presence of the [11H] line in the latter. Thanks a lot for your help. All the best, Max On 08. 04. 15 01:25, Latévi Max LAWSON DAKU wrote: > Thanks

Re: [Jmol-users] Support for molecular orbitals in molden format

.02 >> >> We can work around that. >> >> On Tue, Apr 7, 2015 at 11:25 AM, Robert Hanson wrote: >> >>> Unsupported basis type for atomno=1: 9G >>> >>> It should be able to just skip those. >>> Also, there's a normalization

[Jmol-users] Support for molecular orbitals in molden format

Dear Bob, Using Jmol 13.2.0 or 14.2.13_2015.03.23, I'm not able to view molecular orbitals output in molden format by the program package dalton2015. I'm however able to see them with gmolden version 5.2.2. The number of available orbitals is correctly detected and printed by jmol. But it is not

Re: [Jmol-users] Problem with visualizing MOs in a molden file: h-type basis function present.

On 29. 08. 13 14:48, Susi Lehtola wrote: > On Thu, 29 Aug 2013 14:43:01 +0200 > Latévi Max LAWSON DAKU wrote: >> I suspect this to be due to the fact that the h-type basis functions >> present in the >> file are not correctly handled. As you said in a previous

[Jmol-users] Problem with visualizing MOs in a molden file: h-type basis function present.

27;ve made the file ("fe3_nch.d2h.b1q_dk-rohf.molden.gz") available at the address below http://dl.free.fr/k14CG3qQn Please, don't hesitate to contact me for any further information you may need. All the best, Max -- Latévi Max LAWSON DAKU Universite de Genève / Quai E. Ans

Re: [Jmol-users] visualizing molecular orbitals in molden format

On 14. 05. 13 00:23, Robert Hanson wrote: This version does the energy sorting so that HOMO and LUMO work properly http://chemapps.stolaf.edu/jmol/Jmol-13.zip To NOT sort by energy, add FILTER "NOSORT" to the load command. You can also select by symmetry using FILTER "SYM=AU" for example. F

Re: [Jmol-users] visualizing molecular orbitals in molden format

On 13. 05. 13 20:44, Robert Hanson wrote: OK, then that's a bug in Jmol -- it is expecting the orbitals in energy-order and needs to have that for displaying homo and lumo. If it's all right with you, I would like to add a sort to those so that they are in the proper energy order and not symm

Re: [Jmol-users] visualizing molecular orbitals in molden format

th the right occupation numbers and labeling them "Alpha". The "Spin= (Alpha|Beta)" entry seems required by molden when specifying MOs. Please do not hesitate for any other question you may have. Best, Max Bob On Mon, May 13, 2013 at 2:59 AM, Latévi Max LAWSON DAKU mail

Re: [Jmol-users] visualizing molecular orbitals in molden format

) http://chemapps.stolaf.edu/jmol/jmol-13.1.16_2013.05.12a.zip Bob On Sun, May 12, 2013 at 12:41 PM, Latévi Max LAWSON DAKU mailto:max.law...@unige.ch>> wrote: Dear Bob, I have been able to generate an input file, in molden format, which can be viewed with molden/gmold

Re: [Jmol-users] visualizing molecular orbitals in molden format

the following address This file (molden.inp.gz) can be found at the a http://dl.free.fr/muBvAUeyr All the best, Max On 03. 05. 13 14:47, Robert Hanson wrote: On Thu, May 2, 2013 at 2:40 PM, Latévi Max LAWSON DAKU mailto:max.law...@unige.ch>> wrote: On 02. 05. 13 19:34, Robert Ha

Re: [Jmol-users] visualizing molecular orbitals in molden format

On 03. 05. 13 14:47, Robert Hanson wrote: Dear Bob, Thanks a lot for your reply ! [...] Q: Are you OK with ignoring the g orbitals? Yes. They should contribute little to the molecular orbitals, which I am interested in. Actually, if proceeding so, would it possible to

Re: [Jmol-users] visualizing molecular orbitals in molden format

racted Gaussian functions, consisting each in a linear combination of some of the 711 primitive Gaussian functions. I guess that the manner in which the MOs are listen takes the contractions into account. All the best, Max Bob Hanson On Thu, May 2, 2013 at 3:30 AM, Latévi Max LAWSON DAKU m

Re: [Jmol-users] visualizing molecular orbitals in molden format

On 02. 05. 13 10:30, Latévi Max LAWSON DAKU wrote: > Dear Jmol users and developers, > > > * I am trying to visualize molecular orbitals as output by Dalton2011 > in a molden format (dalton2011.molden.gz): > > http://dl.free.fr/hU653l61Y > > the orbitals are not

[Jmol-users] visualizing molecular orbitals in molden format

Dear Jmol users and developers, * I am trying to visualize molecular orbitals as output by Dalton2011 in a molden format (dalton2011.molden.gz): http://dl.free.fr/hU653l61Y the orbitals are not detected contrarily to the molecular structure, which is correctly displayed. This happens with

Re: [Jmol-users] how to display the original axes?

You can issue the command "set axes molecular" in the console Regards, Max Egon Willighagen wrote: > Moin! > > When I open the below XYZ file, and I display the axes, it show not > the original reference axes, but new ones with the origin in, it > seems, the center of mass... > > - > 9 > > O

Re: [Jmol-users] Jmol-11.5.26: two bugs

f the images exceeds the list's limit of 40kb. Bob Hanson wrote: Max, you have found some new and some not-so-new bugs. Thanks for testing this. All are fixed for 11.5.27 Bob Latévi Max LAWSON DAKU wrote: Dear Bob, Dear Jmol developers and users, I'm trying to use Jmol for re

[Jmol-users] Jmol-11.5.26: two bugs

Dear Bob, Dear Jmol developers and users, I'm trying to use Jmol for representing in a realistic manner the angles that describe the arrangement of atoms around a given centre. These angles are sketched in the attached figure "model.png". While doing this, with Jmol-11.5.26, I've found two bugs.

Re: [Jmol-users] Drawing a circle

draws a solid cylinder 1 Angstrom in diameter and 0.1 Angstrom long along that line. draw width 1.0 {0 0 0} {0 0 0.1} mesh nofill draws a ring. You will have to figure out the two points you want for the ends of the cylinder. Bob Latévi Max LAWSON DAKU wrote: Dear Bob, Your additi

Re: [Jmol-users] Drawing a circle

be considerably harder. Bob Latévi Max LAWSON DAKU wrote: Many thanks, Bob, for implementing this feature. I will download the new Jmol version and play with, as soon as possible :-) All the best, Max Bob Hanson wrote: version=11.5.25_dev # new feature draw circle: # # A circle is a

Re: [Jmol-users] Drawing a circle

atévi Max LAWSON DAKU wrote: Bob Hanson wrote: Latévi Max LAWSON DAKU wrote: Hello, Is there a (simple) way to draw a circle using Jmol ? I guess there is one but cannot find it (googling or searching the mails I received don't help). Thanks in advance for telling

Re: [Jmol-users] Drawing a circle

circle). All the best, Max Bob Hanson wrote: Are we talking about a filled-in circle or a ring? Latévi Max LAWSON DAKU wrote: Bob Hanson wrote: Latévi Max LAWSON DAKU wrote: Hello, Is there a (simple) way to draw a circle using Jmol ? I guess there is one but cannot find it

Re: [Jmol-users] Drawing a circle

Bob Hanson wrote: Latévi Max LAWSON DAKU wrote: Hello, Is there a (simple) way to draw a circle using Jmol ? I guess there is one but cannot find it (googling or searching the mails I received don't help). Thanks in advance for telling me how to proceed. All the best

[Jmol-users] Drawing a circle

Hello, Is there a (simple) way to draw a circle using Jmol ? I guess there is one but cannot find it (googling or searching the mails I received don't help). Thanks in advance for telling me how to proceed. All the best, Max -- *** Latevi Max LAWSO

Re: [Jmol-users] POV-Ray export of stereo rendering and referencing Jmol

Angel Herraez wrote: According to the FAQ, Jmol should be referenced by its website "www.jmol.org". I would like to know if there is a a paper or a book I could also cite. Not really. Cite the website as is described in http://jmol.sourceforge.net/index.en.html#How%20to%20cite%20Jmol

[Jmol-users] POV-Ray export of stereo rendering and referencing Jmol

Dear Jmol developpers and users, The "POV-Ray export" feature have improved a lot since the last time (about two months among) I tried to use: high quality pictures and also lot of fun with ! Many thanks to Pim and Bob for the very nice job ! I am interested in exporting a stereo rendering of a m

Re: [Jmol-users] Povray rendering of drawn objects (polyhedra, lines, ..)

pim schravendijk wrote: 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. Do

[Jmol-users] Povray rendering of drawn objects (polyhedra, lines, ..)

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 --

Re: [Jmol-users] Axis origin

Miguel wrote: In fact, the "ideal" solution would consist in having the possibility to draw segments using arbitrary styles and colors. Others have asked for the ability to draw arbitrary lines. Sounds like that would meet your needs too ... the ability to draw a line/cyli

Re: [Jmol-users] Axis origin

Dear Miguel, Many thanks for your kind reply. Miguel wrote: >>Actually, I would like to display the >>coordinate frame and have the possibility >>of putting its origin at positions which allow >>to easily identify the axis with some symmetry >>axis. >> >> > >Not sure what you mean. > >Q: D

Re: [Jmol-users] Axis origin

Dear Chris, Many thanks for your answer. Unfortunately, my question was not clear enough. Actually, I would like to display the coordinate frame and have the possibility of putting its origin at positions which allow to easily identify the axis with some symmetry axis. The coordinate frame which

[Jmol-users] Axis origin

Dear Jmol users, I am viewing a molecule using Jmol and I am trying to put the origin of the axis at the position of a given atom. But I cannot figure out how to this. I did not find any tip in the user guide. Is there a way to do this ? I thank you in advance for your help. (I am not on the lis