Re: [Jmol-users] Application button problems

Bob, The problems do not appear in today's build so I guess it's fixed - thanks. -- Find and fix application performance issues faster with Applications Manager Applications Manager provides deep performance insights into

Re: [Jmol-users] Application button problems

Sorry, I misedited the results. They should have been as follows where the most recent versions fails: >14.4.3_s016.03.02 - works > 14.4.4_s016.03.25 - no error messages but center button does nothing > 14.4.4_s016.03.29 - works > 14.4.4_s016.04.11 - works > 14.4.4_s016.04.13 - error messages

Re: [Jmol-users] Application button problems

Bob, On a Windows 10 machine, I download from SourceForge and execute Jmol.jar. I then open a console, load =2fha and test: 14.4.3_s016.03.02 - works 14.4.4_s016.03.25 - no error messages but center button does nothing 14.4.4_s016.03.29 - works 14.4.4_s016.04.11 - works 14.4.4_s016.03.13 - error

[Jmol-users] Application button problems

Bob, In recent releases of the Jmol application, the "center" button no longer works. Also the "measure" and "select set" buttons though working pop error messages in the console. -- Find and fix application performance

[Jmol-users] Calculate hydrogens anomaly

After protein double bonds are made explicit, CALCULATE HYDROGENS adds no hydrogens to any double-bonded atom in the aromatics. $ print _version 1404000 $ load =2fha ... $ calculate hydrogens true 160 hydrogens added < double-bonds now explicit> $ delete hydrogens 160 atoms deleted $

[Jmol-users] SHOW PROPERTIES only works for numeric properties

SHOW PROPERTIES only works for numeric properties and crashes with some: $ print _version 1404000 $ load =2fha ... $ show properties resno 1 N 5.0 2 CA 5.0 ... $ show properties group [nothing displays] $ show properties identify

[Jmol-users] frame create

The FRAME CREATE command (which has done nothing for a while) now freezes LOAD APPEND in the latest Jmol application candidate: $ print _version 1403016[Jmol 14.3.16_2015.10.04 (2015-10-03 23:16)] $ load =2fha ... $ load append =1d66 2 models $ load append =1d66 3 models $ frame 2 $

[Jmol-users] draw ramachandran broken

Draw ramachandran is broken after Jmol 14.2.13_2015.03.23 $ print _version 1402013 $ draw RAMACHANDRAN $ ... $ print _version 1402014 $ draw RAMACHANDRAN script ERROR: invalid argument draw >> ramachandran << $

[Jmol-users] Issue with calculate hydrogens and sidechain

All hydrogens added with CALCULATE HYDROGENS are selectable by the SIDECHAIN criterion including non-sidechain hydrogens. This is not the case with hydrogens loaded from a file. -- Monitor Your Dynamic Infrastructure at

[Jmol-users] Hbonds delete

HBONDS DELETE appears to do nothing in the application: ... $ print _version 1403016 $ select all 1414 atoms selected $ calculate hbonds 343 hydrogen bonds $ hbonds delete $ --

[Jmol-users] Freeze-up scenario with WITHIN() selector

In the Jmol application (Windows 10), the following totally freezes it: $ print _version 1403016 $ print {within( 0.1, {0 0 0})} -- Monitor Your Dynamic Infrastructure at Any Scale With Datadog! Get real-time

[Jmol-users] Jmol -- testing requested

"plot properties" without parameters (I know - user error) now freezes the Jmol application. then: $ print _version 1402015 $ plot properties script ERROR: invalid argument plot property << $ now: $ print _version 1403016 $ plot properties $ !exit script execution halted with !exit

[Jmol-users] Calculate hydrogen and the peptide bond

I notice that when I apply the calculate hydrogen command to a polypeptide, the N hydrogens are not in the peptide plane. Is this correct chemically speaking? -- ___ Jmol-users

Re: [Jmol-users] Calculate hydrogen and the peptide bond

Nevermind; I see that set pdbAddHydrogens true before a load puts the hydrogens in the right place as documented. It also doubles the bonds where appropriate and that seems to be what is required to place the hydrogens correctly. With the double bonds in place I can delete hydrogens and then

[Jmol-users] hover highlighting

trematodeo wrote As I understand basically I'm doing the same as you but you are scripting inside jmol and I'm using javascript, right? Yes, no javascript for me. Incidentally if I reduce the timeout to 0.4 the highlight flashes!

[Jmol-users] (no subject)

Am 02.08.15 um 20:34 schrieb tremato...@gmail.com: Hi, I'm trying to create a highlight effect when the user keeps the mouse over a residue, so besides the label I'm also changing the residue color. I'm using hoverCallback to set the color but I also need a hover out to set the color back

[Jmol-users] Hover highlighting

Slightly larger I meant... -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users

[Jmol-users] New feature request: vr support

How about a new stereo rendering to barrel distort the dual images? This in conjunction with the existing navigation functions would allow jmol/jsmol to be used with virtual reality headsets like Google cardboard, etc. and would be totally rad.

Re: [Jmol-users] Amino Acid Mutation Is Finally in Jmol

What about nucleotide mutation? I have a much less elegant script in the wiki http://wiki.jmol.org/index.php/User:Remig/plico/convert to convert both AAs and NTs but your approach is much better. Do you have any plans to mutate nucleotides as well?

[Jmol-users] Hover text problem in 1402009 application

The hover text problem I reported earlier still exists where all labels blank out when hovering after hover text format has been changed. I see it in a number of instances in my work, not just on plots. Again the following test script will demonstrate the problem in the application: print

[Jmol-users] Hover text my problem, not Jmols

Sorry about my last post. I should have used hover %D %U not set hoverlabel %D %U . Then there is no problem. Nevermind... -- Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly

[Jmol-users] Error scenario

The following script results for me in all labels blanking when an atom is hovered over on the graph and the console dead to all input except !zap. print _version load =6tna set hoverlabel %D %U plot properties x y resno $1403007 $ [Hover blanks all labels]

[Jmol-users] Another freeze-up scenario

The following script causes the Jmol application to freeze when throw context follows any try/catch block within a function. function x { zap print _version set appendNew false x1 =data \append a\\nATOM 1 N GLY A 1 0.000 0.000 0.000\nend \append a\ x2 =data

[Jmol-users] A freeze-up scenario

The following script causes the Jmol application to freeze after the translate command. This does not happen if the dots on command is commented out. zap print _version set appendNew false x1 =data \append a\\nATOM 1 N GLY A 1 0.000 0.000 0.000\nend \append a\ x2 =data \append

[Jmol-users] frame create

What is the utility of the 'frame create' command in the application? If I do: zap load x.pdb set appendNew true load append y.pdb print _version I get what I expect: appendNew = true 2 models 1402002 If instead I do in one shot: zap set appendNew false load x.pdb frame

[Jmol-users] Problem with .find?

*Why does the following:* print _version a=abcd x=b print ((a.find(x) 0) and (x.size = 1)) print ((x.size = 1) and (a.find(x) 0)) x=x print ((a.find(x) 0) and (x.size = 1)) print ((x.size = 1) and (a.find(x) 0)) x=bc print ((a.find(x) 0) and (x.size = 1)) print ((x.size = 1) and (a.find(x)

[Jmol-users] Case sensitive?

Jmol 14.013 fails the following where 14.0.8 does not: script x.spt: function X { return X } script test.spt: (testing case sensitivity) function z { return 1 } load $SCRIPT_PATH$x.spt print z print Z X print x print X When test.spt is loaded in 12.0.13 it prints: 1 1 X script ERROR:

[Jmol-users] More on case sensitive:

Sorry, x.spt in my previous email should be: script x.spt: function x { == lower case return X } When upper case, it fails 12.0.8 as well in the Jmol application. -- Put Bad Developers to Shame Dominate

[Jmol-users] Var on globals

Not that there's anything wrong with it but release 14.0.13 of the application fails a script if globals are defined with var whereas earlier versions do not. test script: var x = X function test { print _version print x } In version 14.0.13 test prints: 1400013 whereas in 14.0.12 it prints

[Jmol-users] Direct assignment in arrays

The 14.0.12 release still fails the following: x = array() x[1] = A print x == blank whereas: x = array(A) print x A == ok x[1] = B print x B but: x[2] = C print x B == blank Is this now the new behavior of arrays, that memory allocation must be

[Jmol-users] array assignment

In Jmol 14.0.8: x=array() x[1]=A x[2]=B print x A B In Jmol 14.0.11 x=array() x[1]=A x[2]=B print x [ ] Is this broken or was I doing something wrong? -- Learn Graph Databases - Download FREE O'Reilly Book Graph

[Jmol-users] Bugs in 14.0.11

I'm seeing some anomaly with THROW in the application: $ function test_throw(doit) { for (var i = 0; i 4; i++) { if (doit) throw CONTEXT test print i } } $ test_throw(false) 0 1 2 3 $ test_throw(true) $ print test { _path : [script] function test_throw _retval : 0 doit

[Jmol-users] ModelKit fix

The problem I saw in the Java stand-alone seems to be fixed in 14.0.11_2014.02.21 where the system would lock up when any ModelKit action was tried. !exit would then report script execution halted with !exit but not resolve the lock up. There is, however, still a problem. Although the ??

[Jmol-users] ModelKit broken in 14.0.10

My issue with newly immutable strings in 14.0.9 seems resolved but 14.0.10 ModelKit crashes. -- Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.

[Jmol-users] String difference in 14.0.9

In version 14.0.8 this works: print _version x = abcd x[1] = X print x 148 Xbcd In 14.0.9 it gives an error: 149 script ERROR: invalid argument x [ 1 ] = X Am I abusing strings and the law has finally caught up with me or is this a bug?

Re: [Jmol-users] Protein specific display features e.g. Cartoons, Ribbons, etc.

I have a script remaphttp://wiki.jmol.org/index.php/User:Remig/plico/remap that can put in the missing info. On Thu, Feb 13, 2014 at 8:02 AM, Robert Hanson hans...@stolaf.edu wrote: Thanks for the files. Do complain to WaveFunction. These PDB files are total trash: HETATM1 N UNK

[Jmol-users] (no subject)

. On Wed, Jan 22, 2014 at 1:27 PM, Ron Mignery remign...@gmail.com wrote: Could a play audio.file command similar to the Java play function be added to scripting? This would allow clicks and beeps or even entire narrations to be added to Jmol animations. Hopefully it would run in a separate

Re: [Jmol-users] Model Kit add atom kills ALL sidechain atomNames

, 24 Jan 2014 at 5:09 PM, Robert Hanson hans...@stolaf.edu wrote: Makes sense. There's no way to know the atom name. On Wed, Jan 22, 2014 at 1:06 PM, Ron Mignery remign...@gmail.com wrote: The atomName of all polypeptide side-chain atoms is reduced to just the element name when an atom is added

[Jmol-users] Bug in break command in the Jmol application 14.0.4?

Is break n broken in Jmol 14.0.4? function xxx { for (i=0;i4;i++) { for (j=0;j4;j++) { print i break 0 } } } xxx 0 \ 1 \ ok 2 / 3 / function xxx { for (var i=0;i4;i++) { for (var j=0;j4;j++) { print i break 1 } } } xxx 0 \ not

[Jmol-users] Some commands inside user function fail only when the function is called for its return value

Is calling a user function for a return value broken in Jmol application 14.0.4? Delay, rotateSelected etc. seem to fail in the function only when called for the return value function xyz { print now(xxx) delay 1 print now(xxx) return true } function test { xxx=now() xyz

[Jmol-users] ModelKit add atom kills side-chain atomNames in polypeptides?

The atomName of all polypeptide side-chain atoms is reduced to just the element name when an atom is added anywhere with the model kit in Jmol 14.0.4. *example:*CB=C -- CenturyLink Cloud: The Leader in Enterprise Cloud

[Jmol-users] Audio?

Could a play audio.file command similar to the Java play function be added to scripting? This would allow clicks and beeps or even entire narrations to be added to Jmol animations. Hopefully it would run in a separate thread.