Re: [Jmol-users] script variables treated differently in headless version than in application?

Thanks, Bob My recollection of my path to using -s headless.spt arg is that I found that construction somewhere on the web. I cannot relocate that now. In any case, my self-deception is found in JmolData's loading $CC as a model: java -jar %JMOL_HOME%\JmolData.jar -ion -s headless.spt

[Jmol-users] script variables treated differently in headless version than in application?

Hello, I'm using JmolData.jar to load a SMILES string and output the molecule in xyz format: java -jar %JMOL_HOME%\JmolData.jar -ion -s headless.spt $CC where headless.spt consists of: molunit = _arguments[1] load @molunit ml = molunit.length xyzwrite = molunit[2][ml] + .xyz write

Re: [Jmol-users] Jmol 14.2.14/14.3.14 write(xyz) misbehavior?

Hi, It seems the write() function now returns the result value rather than the output from the write command. The commands: asymunit=write(xyz) print asymunit should load the variable with a structure file format and give: 14 Model[1]: Jmol 14.3.14_2015.05.25 2015-05-25 23:36 C

[Jmol-users] boundbox, unitcell and Tinker arc files

Greetings, The first two items developed while working with Tinker 6 output. boundbox I am loading Tinker 6 molecular dynamics arc files (which are catenated Tinker xyz files) that were the result of an NPT dynamics run with periodic boundary conditions. Subsequently, I read the log file

Re: [Jmol-users] script() function path question

that, not ones with directories. Bob On Wed, Jan 29, 2014 at 4:25 PM, Whitwell, George gwhitw...@ncwc.edumailto:gwhitw...@ncwc.edu wrote: Hi, I'm using the output of a script() function to gather data to be output as a file. I can run the script from another folder as script

Re: [Jmol-users] Tinker xyz files as Jmol input

on using them next year for an Instrumental Analysis class. George From: Robert Hanson [mailto:hans...@stolaf.edu] Sent: Monday, February 03, 2014 12:28 AM To: jmol-users@lists.sourceforge.net Cc: Whitwell, George Subject: Re: [Jmol-users] Tinker xyz files as Jmol input George, did I mention that http

[Jmol-users] auxiliaryInfo.MO_ENERGY syntax?

Hello, I'm using isosurface to display MOs and want to reproduce something like the top left echoed info from the MO command. The Jmol docs note that auxiliaryInfo.MO_ENERGY has the needed MO energy and I can see that it does by running this: print

[Jmol-users] script() function path question

Hi, I'm using the output of a script() function to gather data to be output as a file. I can run the script from another folder as script ../Jmolspts/writeout.spt without difficulty. When I direct the output to a variable, I'm finding that the target must be in the current

Re: [Jmol-users] Tinker xyz files as Jmol input

Angel, Thanks. For the record, Jmol rejects the file as output by Tinker (no cut ad paste involved). Quite oddly, based on your recount of the pdb spec, simply removing the SOURCE line does make it partially digestible; although this is without proper identification of atom types. As Bob

Re: [Jmol-users] Tinker xyz files as Jmol input

, and apparently it has no header with which to identify itself. So if we do write a reader, it will never load these files directly. More likely it would read them with a prefix such as: load tinker::out.xyz On Mon, Jan 20, 2014 at 2:31 PM, Whitwell, George gwhitw...@ncwc.edumailto:gwhitw...@ncwc.edu

[Jmol-users] Tinker xyz files as Jmol input

Hi, I've been loading Tinker's version of .xyz files into Jmol with unexpected connections displayed. Jmol writes a file with number of atoms followed by a blank line and a 4 column atom format (symbol, x, y, z - 5 dec places). 17 C -0.55370 1.43900 -0.14471 C -0.46130 -0.00500

Re: [Jmol-users] NaN, @, var and minimizer energy confusions

enough to come up with _minimizationEnergy as the answer to my last question. Not being lazy there, just couldn't see 'round the blinders. Thanks for your help and I hope that you enjoy the holidays, George From: Whitwell, George Sent: Saturday, December 21

[Jmol-users] NaN, @, var and minimizer energy confusions

Greetings, I've no doubt that there is a simple explanation for each of these items; however, I haven't been able to search any out. From the following script: zap; load SYNC file:///C:/Compchem/s-pentane/spentane.xyz rotdeg = 120 var steps=360/rotdeg measure {C5}{C3}{C1}{H6} targang

[Jmol-users] constructing atom expression with variables

Hello again, The following script: modcnt = getproperty(modelinfo.modelcount) // modcnt=6 gmsmodel = {1..add(@modcnt).add(}) //gmsmodel = {1.6} print gmsmodel print (@gmsmodel).label(%-3[element]%4.0[elemno]%13.6[xyz]) produces the following output $ writeout.spt

Re: [Jmol-users] why do I get averaged values?

%5.3y\t%5.3z) or even print {1.53}[1][17].label(%-3[element]%4.0[elemno]%10.3[xyz]) Bob On Wed, Dec 18, 2013 at 10:32 AM, Whitwell, George gwhitw...@ncwc.edumailto:gwhitw...@ncwc.edu wrote: when I use a command like: print ({1.53}[1][17]).element.add(\t).add(({1.53}[1][17]).elemno).add

Re: [Jmol-users] minimize constraints in a script

runs in its own thread. If it is desired to wait until the process has completed prior to continuing, use set useMinimizationThread false. So I'm guessing that without that the rotation command halts the ongoing minimization before you notice anything. On Wed, Dec 18, 2013 at 7:19 PM, Whitwell

[Jmol-users] why do I get avereaged values?

when I use a command like: print ({1.53}[1][17]).element.add(\t).add(({1.53}[1][17]).elemno).add(\t).add(({1.53}[1][17]).x).add(\t).add(({1.53}[1][17]).y).add(\t).add(({1.53}[1][17]).z) result: C 2.4705882 -0.08696627 -0.8534151 1.8308194 C 2.4705882 -0.08696627 -0.8534151 1.8308194 C

[Jmol-users] minimize constraints in a script

Greetings, I'm trying to explore rotational steric hindrance with partial success. From the console, this series of commands: minimize constraint {C5} {C3} {C1} {H6} 60 // or whatever angle is indicated minimize minimize energy work as advertised. I can: rotate branch {C3}

Re: [Jmol-users] how to glean a recurring bond length from a series of models?

From: Angel Herráez [angel.herr...@uah.es] Sent: Sunday, December 08, 2013 6:24 AM To: Whitwell, George; jmol-users@lists.sourceforge.net Subject: Re: [Jmol-users] how to glean a recurring bond length from a series of models? Hi George http://chemapps.stolaf.edu/jmol/docs/?ver=13.2#measure says

Re: [Jmol-users] scripts in 14.0?

that problem On Sat, Dec 7, 2013 at 8:31 PM, Whitwell, George gwhitw...@ncwc.edumailto:gwhitw...@ncwc.edu wrote: I'm finding that a simple Jmol script that works in 13.3.4_dev_2013.08.20c is not working in 14.0.1_2013.12.04. An example is pasted here: zap; load file:///C:/Compchem/tbutyl/C4H9-Br

[Jmol-users] scripts in 14.0?

I'm finding that a simple Jmol script that works in 13.3.4_dev_2013.08.20c is not working in 14.0.1_2013.12.04. An example is pasted here: zap; load file:///C:/Compchem/tbutyl/C4H9-Br-Clircf.out filter REVERSEMODELS load append file:///C:/Compchem/tbutyl/C4H9-Br-Clircr.out rotate y 90

[Jmol-users] how to glean a recurring bond length from a series of models?

I'm trying to get bond lengths from a collection of models from a Gaussian saddle point exploration (Cl Br exchange by SN2). I can get a single distance with the measure command (although not with the distance function, so far), but I've been unsuccessful in finding the key to getting the same

Re: [Jmol-users] reordering IRC frames and pasting two halves together

: On Mon, Aug 19, 2013 at 9:37 PM, Whitwell, George gwhitw...@ncwc.edumailto:gwhitw...@ncwc.edu wrote: Thanks, Bob. REVERSEMODELS works as advertised. I have to load the first file reversed - they both start at the saddle point. I tried getproperty modelinfo.models.energy to retrieve

[Jmol-users] reordering IRC frames and pasting two halves together

Hi, I have GAMESS output from both sides of the reaction coordinates from a Cl-CH3-Br anion intermediate as an example of an SN2 reaction. I can load both output files in Jmol as different models and animate them consecutively; however, since they both run downhill, it isn't really the

Re: [Jmol-users] reordering IRC frames and pasting two halves together

for Spartan files. After that, you might have to delete one or more models. You also may need to do some alignment. For that see http://chemapps.stolaf.edu/jmol/docs/index.htm?search=frame%20alignver=13.3.4_dev_2013.08.19 On Mon, Aug 19, 2013 at 3:22 PM, Whitwell, George gwhitw

Re: [Jmol-users] Jmol and crystallography: the paper

Congratulations! I enjoyed reading the preprint before BCCE. George From: Robert Hanson [mailto:hans...@stolaf.edu] Sent: Thursday, September 02, 2010 3:22 PM To: jmol-users@lists.sourceforge.net Subject: [Jmol-users] Jmol and crystallography: the paper This just in! J. Appl. Cryst. (2010).