[Jmol-users] Minimize Seems to be Broken Jmol 12.0.RC13_dev

Bob, Earlier today you fixed a problem with Jmol 12.0.RC13_dev. Specifically, minimize seemed to be broken on the initial load. That fix worked. There seems to be another problem, however. It's taken me a while to track it down, but after an atom delete, minimize breaks. Interestingly, minimiz

Re: [Jmol-users] getting script error on new example topic 135 (sculpt)

I think you have to be careful about using UFF for energies. As stated in the original paper, "It is possible to construct a force field from simple rules and atomic parameters that is capable of reproducing most structural features across the periodic table with errors less than 0.1 A in bond dis

Re: [Jmol-users] getting script error on new example topic 135 (sculpt)

Something like that. Oddly it required a complete reboot. Maybe my javaVM got mangled in RAM. And Yep, this is cool. This makes me think again about using the UFF and an easier to specify rotation of a group to do simple energy plots for rotation about a single bond...Still thinking about

Re: [Jmol-users] Uses for MDL Sculpt

Fun. It makes a nice point that molecules are flexible. Probably still a notch above what we are talking about here -- so far, the minimization is restricted to the molecule containing the atom pulled, and all other atoms are ignored. Bob On Fri, May 21, 2010 at 12:20 PM, Eric Martz wrote: > A

[Jmol-users] Uses for MDL Sculpt

At 5/21/10, Philip Bays wrote: >Yes, both the Sculpt and the smiles conversion applet are fixed. Thanks. > >I tend to agree with Angel and Rich on the Sculpt >capability. While it is really cute, I am not sure how to use >it. I played with Sculpt when it first came out years ago. Could >nev

Re: [Jmol-users] ah, this is very, ah, WEIRD

Just FANTASTIC, Bob!! You keep amazing me! (I didn't look at it until after you had fixed the Mac bug, and it worked perfectly the first time I looked.) -Eric At 5/20/10, Robert Hanson wrote: >Well, sorry, I had to do it. I don't know exactly what to say about >it. Just try it. > >

Re: [Jmol-users] getting script error on new example topic 135 (sculpt)

Some kind of caching problem on your end, I think. Close your browser and reopen it. On Fri, May 21, 2010 at 10:29 AM, Jonathan Gutow wrote: > I'm now getting this script error when I try to run the example. > > script ERROR: unrecognized SET PICKING SELECT parameter: dragminimize > set pic

[Jmol-users] getting script error on new example topic 135 (sculpt)

I'm now getting this script error when I try to run the example. script ERROR: unrecognized SET PICKING SELECT parameter: dragminimize set picking >> dragminimize << 10:30 CDT Dr. Jonathan H. Gutow Chemistry Department gu...@uwosh.ed

Re: [Jmol-users] select within(BASEPAIR woes

Oh, I see what you mean. Yes, I agree that needs to be clearly mentioned. 2010/5/21 Angel Herráez > > I don't think so. There may have been CG in RasMol, but there was > > never any capability that I know of in Jmol to detect hydrogen-bonded > > base pairs like that. > > Well, certainly no detec

Re: [Jmol-users] select within(BASEPAIR woes

> I don't think so. There may have been CG in RasMol, but there was > never any capability that I know of in Jmol to detect hydrogen-bonded > base pairs like that. Well, certainly no detection of base pairs. That's why I think the distinction must be made clear. The sets are indeed defined in

Re: [Jmol-users] select within(BASEPAIR woes

fixed -- will upload shortly. Simple logic error. On Fri, May 21, 2010 at 8:37 AM, Robert Hanson wrote: > > > 2010/5/21 Angel Herráez > > I am seeing this as a nice, recent addition in the "new.htm" >> document: >> >> 122. select within(BASEPAIR) >> # Jmol 12.0.RC5 adds the capability to select

Re: [Jmol-users] Fixed

oops -- ok. That fix will be uploaded within the hour. On Fri, May 21, 2010 at 8:27 AM, Otis Rothenberger wrote: > Bob, > > Needless to say, I'm heavy into playing with this already. One problem on > my end: The minimize command by itself seems to be broken. This is on a > fresh page load prior

Re: [Jmol-users] select within(BASEPAIR woes

2010/5/21 Angel Herráez > I am seeing this as a nice, recent addition in the "new.htm" > document: > > 122. select within(BASEPAIR) > # Jmol 12.0.RC5 adds the capability to select atoms based on RNA or > DNA base pairing. Thank you, Neena Grover! load 2qnh.pdb.gz;zoom > 300;wireframe -0.4;display

Re: [Jmol-users] Fixed

Bob, Needless to say, I'm heavy into playing with this already. One problem on my end: The minimize command by itself seems to be broken. This is on a fresh page load prior to "set picking dragMinimize." Harping on a Point: As chemists, the model kit was our first educational touch of intima

[Jmol-users] select within(BASEPAIR woes

I am seeing this as a nice, recent addition in the "new.htm" document: 122. select within(BASEPAIR) # Jmol 12.0.RC5 adds the capability to select atoms based on RNA or DNA base pairing. Thank you, Neena Grover! load 2qnh.pdb.gz;zoom 300;wireframe -0.4;display rna;select *.P;label %n%r;select rn

Re: [Jmol-users] Fixed

First - I should point out that this required almost no coding -- we already had minimization and bindings; this just added a couple of new options and a bit of stitching. I'm not sure "set picking dragMinimize" is quite the right way to do this, but it's OK for this week. Ah, yes, what to do with

[Jmol-users] Fixed

Yes, both the Sculpt and the smiles conversion applet are fixed. Thanks. I tend to agree with Angel and Rich on the Sculpt capability. While it is really cute, I am not sure how to use it. I played with Sculpt when it first came out years ago. Could never figure out what to use it for then

Re: [Jmol-users] Jmol "3D-SCULPT" mode

I agree with Angel. I think Jmol should be a professional-level display tool and there should be an educational-level tool for the molecule manipulation functions. The focus/needs of the two groups are different enough that one program is never going to satisfy the two groups and the compromis

Re: [Jmol-users] ah, this is very, ah, WEIRD

Yep, fixed. Rich Robert Hanson wrote: > Mac-side bug fixed. Please do check this out: > > http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm?topic=135 > > Bob > -- ___

Re: [Jmol-users] Jmol "3D-SCULPT" mode

I have mixed feelings about this idea. On the one hand, it is exciting to think that Jmol could do this. On the other, I'm not sure if it should expand into this land, or leave it to other software. Although I have not used it regularly, the most similar idea I know is Avogadro --open source to

Re: [Jmol-users] ah, this is very, ah, WEIRD

Wonderful value, Bob! "Plastic mode", maybe? I also had trouble last night (WinXP) to see it, the applet didn't finish loading, but today it is working fine. -- ___ Jmol-u