[Jmol-users] lcaoCartoons
I have encountered a problem with displaying p orbital cartoons with matching colors on all atoms of SO2 molecule. select all lcaoCartoon create "pz" creates one p orbital with opposite color lobes to the other two. I can individually add p lobes to all three atoms (and adjust the "phase"): select atomno=1 lcaoCartoon create "pz" select atomno=2 lcaoCartoon create "-pz" select atomno=3 lcaoCartoon create "pz but I do not know if the "phase color" problem is a bug (Jmol 12.3.32 6/23/2012), or is there some design reason for this behavior. Any suggestions? PM -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] plot natural transition orbitals from Gaussian log-file
Gaussian can produce natural transition orbitals in the log-file by running # B3LYP 6-31g sp gfprint pop(full,nto) TD(singlets,nstates=3) Density(transition=) See the sample output http://zhugayevych.me/_sourceforge/NTO.log. In that output the natural transition orbitals are listed under the keyword "Alpha spin Natural Transition Orbitals" (the meaning of the eigenvalues is described in the paper cited in the Gaussian manual) whereas the ordinary molecular orbitals are listed under the keyword "Molecular Orbital Coefficients" (they are visualized by Jmol). It would be great if Jmol could read the natural transition orbitals, because the alternative way to visualize them, as described in the Gaussian manual, is rather cumbersome. -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] does not read Gaussian molecular orbitals
Jmol does not read molecular orbitals from a Gaussian log-file if a symmetry is present: see two examples http://zhugayevych.me/_sourceforge/doesnt_read_MO.log and http://zhugayevych.me/_sourceforge/does_read_MO.log. You probably always can add "NoSymm" keyword but usually you want to see the symmetry of molecular orbitals. -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] select all N or O atoms with their Hydrogens
select _N, _O, _H and connected(_N,_O) -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Notify user if signed applet request is declined
problem is, using your code sample from the last mail, even when using
an applet where I grant access to the machine, i get this message:
"2,scriptStatus,0,script 2 started 3,scriptStatus,0,script ERROR:
java.security.AccessControlException: access denied
(java.net.SocketPermission 130.225.101.52:80 connect,resolve) | |
load >> ''(''http://www.google.com'')'' << 4,scriptStatus,0,Script
completed 5,scriptTerminated,1,Jmol script terminated successfully
7,scriptTerminated,1,Jmol script terminated unsuccessfully: Jmol script
terminated 1,scriptStarted,2,load(''http://www.google.com'')
6,scriptError,0,Jmol script terminated "
Am 28.06.12 20:00, schrieb Robert Hanson:
just look at the return from
x = load ("http://www.google.com";)
If it reads:
java.security.AccessControlException: access denied
(java.net.SocketPermission www.google.com:80
connect,resolve)
you don't have the signed applet.
Bob
On Thu, Jun 28, 2012 at 6:19 AM, Martin Hediger > wrote:
That's a useful information. So the _signedApplet basically does not
tell if the user granted access or not, rather only if the applet is
supposed to be signed.
I can think of some rather ugly hacks in the domain of user
interaction
simulation after the pages loads to see if a "dummy"-state can be
saved
and check some kind of server response, but there must be a
smarter way
of doing this, i hope.
Best regards
Martin
On 28.06.12 12:54, Rolf Huehne wrote:
> On 06/28/2012 12:37 PM, Martin Hediger wrote:
>> ok, that might look useful
>>
>> jmolScriptWait('show _signedApplet')
>> "2,scriptStatus,0,script 2 started
>> 4,scriptStatus,0,Script completed
>> 6,scriptStatus,0,Jmol script terminated
>> 5,scriptTerminated,1,Jmol script terminated successfully
>> 1,scriptStarted,2,show _signedApplet
>> 3,scriptEcho,0,_signedapplet = true
>>
> I have actually tested this now for Jmol 12.2.2 and the result
is like I
> expected:
>
> I opened the following URL in the browser
>
(http://www.imb-jena.de/cgi-bin/3d_mapping.pl?CODE=1deh&APPLET=signed&JMOLVERSION=12.2.2
)
> and clicked onto "cancel" in the security dialog.
>
> Afterwards the command "show _signedApplet" provided the result
> "_signedapplet = true". But if I tried to save the state it
didn't work,
> because the signed applet hadn't got the rights of a signed applet.
>
> Regards,
> Rolf
--
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Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
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
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Re: [Jmol-users] Resolver Test Request
Just to close this issue: I waited a few days to make sure the problem was fixed. It seems it was a proxy server issue. I changed the FIrefox default of from "auto detect" proxy to "no proxy," and this seems to have solved the problem. Thanks again... Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Jun 28, 2012, at 1:26 PM, Otis Rothenberger wrote: > One more local suggestion came in that might be the real problem: > > http://support.mozilla.org/en-US/kb/firefox-cant-load-websites-other-browsers-can#w_dns-prefetching > > I never thought about this as a browser issue related to DNS, but there it > is. This is easy to check out. I use Firefox exclusively and only use other > browsers to check my scripting. I'll change the FF default on DNS prefetching > to see if this solves the problem. > > Thanks again... > > Otis > > > > -- > Otis Rothenberger > o...@chemagic.com > http://chemagic.com > > > > > On Jun 28, 2012, at 1:03 PM, Otis Rothenberger wrote: > >> All- >> >> Thanks for the replies both off and on list. It sure sounds like this is a >> local problem with my ISP. A local chemist suggested something that sounds >> like a likely guilty party - DNS server. He suggested that I change from the >> ISP defaults to a college, university, or open DNS. >> >> I'll get appropriate addresses and give this a try. The main importance of >> your feedback is that it shows that this is not a Resolver issue. It has to >> be a local issue. Thanks again for the feedback. >> >> Markus, thanks for looking into this. >> >> Otis >> >> >> -- >> Otis Rothenberger >> o...@chemagic.com >> http://chemagic.com >> >> >> >> >> On Jun 28, 2012, at 10:07 AM, Otis Rothenberger wrote: >> >>> Jeff, >>> >>> I'm reading the Resolver files as http, and I'm not messing with the >>> headers. It never bothered me because the load works, but maybe that's part >>> of the problem. Markus? >>> >>> Otis >>> >>> >>> >>> -- >>> Otis Rothenberger >>> o...@chemagic.com >>> http://chemagic.com >>> >>> >>> >>> >>> On Jun 28, 2012, at 8:32 AM, Jeff Hansen wrote: >>> Both links worked for me (fast, by the way) although they were formatted differently. The first had spaces and line breaks. The second didn't. *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Jun 27, 2012, at 10:18 PM, Otis Rothenberger wrote: > All, > > For quite some time, I have been having a small problem with the NIH/CADD > Chemical Identifier Resolver. Specifically, on my first attempt to > connect, I frequently timeout without making connection. Once I make my > first connection by attempting 1 or more reloads, I'm OK for that working > session. To be a bit more specific, this is a first attempt of the day > issue and a first attempt after about an hour of inactivity issue. > > To help me determine if this is a local issue, I'd really appreciate some > help. Are there list users willing to hit the links below as your FIRST > hits of your work day? Hit them wait an hour or more and hit them again. > I really appreciate any reports: > > http://cactus.nci.nih.gov/chemical/structure?string=C[C@@H]%28Cl%29CC&representation=file&get3d=True > > http://chemistry.illinoisstate.edu/osrothen/web_molecules/nih.aspx?smi2sdf=C[C@@H]%28Cl%29CC > > Jim (cc'd with this note), would you forward this note to the ISU > chemistry faculty list? > > Thanks in advance for any help. You'll either get the sdf of > (R)-2-chlorobutane or you'll timeout. > > Otis > > -- > Otis Rothenberger > o...@chemagic.com > http://chemagic.com > > > > > > > > -- > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware >
