Re: [Jmol-users] Jmol-users Digest, Vol 59, Issue 1

Hi Bob, > I think you have to be careful not to call JmolScriptWait from a script that > is already running from a callback message. Not sure if that's the case I think you just pointed out the problem here. I was calling JmolScriptWait from a "pickCallBack". But what goes wrong with that? > he

[Jmol-users] jmolResizeApplet() behaves strangely in Firefox

Hi Jmolers, I use jmolResizeApplet() on my HTML page, and it works perfectly in Safari. However, it behaves strangely in Firefox. You can try it here: http://scbx.mssm.edu/sitecomp/mypage2.HTML (300*300) (600*600) (600*300) Any ideas? Yingjie

Re: [Jmol-users] bond picking and draw picking problems

Hi, OK Bob. thanks for all. Could you tell me where I can find a documentation about modelkit. Yves Le 01/04/2011 20:00, Robert Hanson a écrit : Yves, there were two problems. First, somehow you must have engaged the model kit or otherwise set the picking to DELETEBOND. And because of that an

Re: [Jmol-users] color temperature relative to each protein loaded

sure color property temperature absolute 0.0 8.0 On Fri, Apr 1, 2011 at 1:33 PM, Daniel Carbajo wrote: > Thanks I know Jmol can calculate DSSP secondary structures, but I mainly > use it to calculate solvent accessibilities (secondary structures are a side > effect). I also use other programs li

Re: [Jmol-users] show measurements as echo

OK I will try it again on Monday and let you know! Thanks! 2011/4/1 Robert Hanson > May seem to work, but it isn't a general solution. Trust me, you need to > specify models the way I showed you and use script inline. > > > On Fri, Apr 1, 2011 at 10:19 AM, Daniel Carbajo > wrote: > >> Well it m

Re: [Jmol-users] color temperature relative to each protein loaded

Thanks I know Jmol can calculate DSSP secondary structures, but I mainly use it to calculate solvent accessibilities (secondary structures are a side effect). I also use other programs like PSAIA or SPEEDFILL to calculate other things... (my main concern it's not just show secondary structures, sol

Re: [Jmol-users] baby-steps in crystal structures

On 4/1/2011 1:24 PM, Paul Pillot wrote: > The Cristallography Open Database is a good open resource for cif files : > http://www.crystallography.net/ > -Paul > Thank you: a very good source of cif files, indeed. PM -- C

Re: [Jmol-users] baby-steps in crystal structures

On 4/1/2011 1:13 PM, Robert Hanson wrote: It does, and it doesn't always work properly for all metals. So you may have to do some connect commands for a given specific case to get it exactly the way you want it. I like the brevity of that file format. Is there a good source of cif

Re: [Jmol-users] bond picking and draw picking problems

Yves, there were two problems. First, somehow you must have engaged the model kit or otherwise set the picking to DELETEBOND. And because of that and the fact that there was no way to undo that, it remained. This is fixed for the next version of Jmol. Unfortunately there is no workaround, since as

Re: [Jmol-users] baby-steps in crystal structures

The Cristallography Open Database is a good open resource for cif files : http://www.crystallography.net/ -Paul Le 1 avr. 2011 à 16:58, Pshemak Maslak a écrit : > Is there a good source of cif files for (crystalline) elements somewhere? > This would help to avoid "manual" mistakes and cases whe

Re: [Jmol-users] baby-steps in crystal structures

On Fri, Apr 1, 2011 at 9:58 AM, Pshemak Maslak wrote: > On 4/1/2011 10:18 AM, Robert Hanson wrote: > > > > On Fri, Apr 1, 2011 at 9:10 AM, Pshemak Maslak wrote: > > My questions: >> >> Where is the connectivity information in that file? The Jmol shows the >> nice tetrahedron "subunits" {1,1,1}

Re: [Jmol-users] show measurements as echo

May seem to work, but it isn't a general solution. Trust me, you need to specify models the way I showed you and use script inline. On Fri, Apr 1, 2011 at 10:19 AM, Daniel Carbajo wrote: > Well it might sound strange, but what really works for me is what I send > you, i.e.: without script inline

Re: [Jmol-users] color temperature relative to each protein loaded

Daniel, First note that Jmol has DSSP included now -- an authorized and verified implementation of "real" DSSP -- you should have no need to do this separately. I have no idea what you mean by "DSSP might crash" -- that's very odd. Why would DSSP crash? Anyway, if you just use calculate structure

Re: [Jmol-users] I cant copy mol file from applet console

Otis, i tried and it seemed to work. when i checked the file (that originally had the MO) cannot display the MO and MEP. Maybe the size of file is an issue in alert box? As for the signed applet, my problem is how i can get the file that other people build or display. Sometime i consider myself

Re: [Jmol-users] color temperature relative to each protein loaded

Sorry for the title, it should read "color temperature with a user fixed range", or something like that 2011/4/1 Daniel Carbajo > Hi everybody, > I have a little problem that probably is so simple to solve but I do not > get it... > I have a native structure plus some homology models, and I chan

[Jmol-users] color temperature relative to each protein loaded

Hi everybody, I have a little problem that probably is so simple to solve but I do not get it... I have a native structure plus some homology models, and I change the temperature factor column of each pdb with DSSP predicted secondary structures encoded from 1 to 8. I first load the native structur

Re: [Jmol-users] I cant copy mol file from applet console

Ok Otis, I followed your advice about alert box. It works. Maybe as Bob suggests, i should move to signed applet ... Any copy and paste from console is not working :( Pino -- Create and publish websites with WebMatrix Use

Re: [Jmol-users] show measurements as echo

Well it might sound strange, but what really works for me is what I send you, i.e.: without script inline in the function, and calling the function adding the curly brackets and the .ca to the php variables. What I cannot make work anyhow is the other way, i.e.: with script inline in the function,

Re: [Jmol-users] baby-steps in crystal structures

On 4/1/2011 10:18 AM, Robert Hanson wrote: On Fri, Apr 1, 2011 at 9:10 AM, Pshemak Maslak > wrote: My questions: Where is the connectivity information in that file? The Jmol shows the nice tetrahedron "subunits" {1,1,1} with "bonds" between atoms. Is

Re: [Jmol-users] show measurements as echo

well, that won't work. See my previous posts. On Fri, Apr 1, 2011 at 3:41 AM, Daniel Carbajo wrote: > At the end I left it like this (without script inline): > > function crossMeasure(atomListN, atomListM){ > set measurementUnits angstroms > set measurements 3 > font measure 16 serif

Re: [Jmol-users] I cant copy mol file from applet console

this shouldn't have anything to do with Jmol. Note that if you use the signed applet, you can just save files; no need to cut and paste. On Thu, Mar 31, 2011 at 4:31 PM, Mio_libero wrote: > Hi everybody, can anybody explain me why on my PC i cannot copy and past > the code of file pdb, or txt or

Re: [Jmol-users] I cant copy mol file from applet console

Pino, One More Idea: You mention that you can copy from the Jmol console output field (upper) to the Jmol console input field (lower). Have you tried copying or cutting then pasting that new lower field information. You may run into the same problem, but it's worth a try if the alert box appro

Re: [Jmol-users] baby-steps in crystal structures

On Fri, Apr 1, 2011 at 9:10 AM, Pshemak Maslak wrote: My questions: > > Where is the connectivity information in that file? The Jmol shows the > nice tetrahedron "subunits" {1,1,1} with "bonds" between atoms. Is that > based on proximity of these atoms? > > exactly Could I manually generate a ci

[Jmol-users] baby-steps in crystal structures

I am just beginning to learn and explore display of crystal structures in Jmol. For now, I am just looking at elements and their basic crystal lattices. I have started with excellent Jmol Crystal Symmetry Explorer (http://chemapps.stolaf.edu/jmol/docs/examples-11/jcse/explore.htm) [Thank

Re: [Jmol-users] jmolScriptWait() and jmolEvaluate()

Hi Robert, The call was all in one line. I just broke it up so it's easier for you to read. On Apr 1, 2011, at 4:42 AM, jmol-users-requ...@lists.sourceforge.net wrote: > I don't see that JavaScript call working for any browser, unless you for the > purposes of Email broke up those lines. In JavaS

Re: [Jmol-users] I cant copy mol file from applet console

Ok Pino, bummer. It sounds like an XP issue. Try the following approach. It will get you out of trying to copy/paste directly from an applet feature. Into the location (URL) box, type: javascript: alert(jmolGetPropertyAsString("fileContents")) After hitting Enter, this will put the file in the

Re: [Jmol-users] I cant copy mol file from applet console

Otis, I tried again. I selected with Ctrl A, copied with Ctrl C and i pasted also in same console in lower part to check the copied. I copied. When i attempt to copy in notepad, nothing is copied. I remember that in past i succeded to do it sometime. I dont know if it is an iessue with java ver

Re: [Jmol-users] I cant copy mol file from applet console

Ciao Otis, the trouble is that i can make ctrl A to select, copy and past in the same console. If i make ctrl V in notepad, I cannot do it. Nothing seems copied. I suppose a trouble with java windows xp. I will retry again anyway in case of my mistake Pino Il 01/04/2011 2.55, Otis Rothenberge

Re: [Jmol-users] show measurements as echo

At the end I left it like this (without script inline): function crossMeasure(atomListN, atomListM){ set measurementUnits angstroms set measurements 3 font measure 16 serif bold var n = atomListM.length for (var i = 2; i <= n; i++) { measure @{atomListN[1]} @{atomListM[i