Re: [Jmol-users] SMILES

On Mon, May 31, 2010 at 9:52 PM, Otis Rothenberger wrote: > Bob, > > OK, I got it: > > 1. The url has to be encoded. > 2. Which I tried before I wrote using ASP.NET UrlEncode > 3) Hand entry of CCC%23C below works. > 4) ASP.NET must be choking on "#" with Server.UrlEncode() The # has a special me

Re: [Jmol-users] need 2-propenyl sulfenic acid molecular model

Bob, the SMILES support is really *fantastic*! In the conversion from SMILES -> 3D ... Q: ... are the atom locations more-or-less correct for a low-energy configuration? Q: ... are the bond angles more-or-less correct? Miguel ---

[Jmol-users] need 2-propenyl sulfenic acid molecular model

My son is doing a report on 2-propenyl sulfenic acid for his high school chemistry class. He would like to incorporate Jmol into his presentation ... and I think that is a good idea :) Q: Where can I get a file for 2-propenyl sulfenic acid? Thanks! Miguel --

Re: [Jmol-users] Win95 ?

>>It seems strange to me that all these things work but that your >>lysozyme.pdb does not. >> > > file corruption? can you open the pdb file in a text editor and make > sure it is readable? He said that it works with Netscape 4.5 on the same machine. Miguel --

Re: [Jmol-users] 10pre10a 2004/05/26 18:13 no abstract rendering

> I had just done > cvs up -dP > ant clean main > and recognized that there is no backbone, trace, cartoon, rocket > rendering with this version. Looks like I broke something :-) Miguel --- This SF.Net email is sponsored by: Oracle 10g Ge

Re: [Jmol-users] Jmol Version 10pre8c 2004/04/21 18:03 hangs on second loading

>>Can you shut off the clearingThread by setting the boolean variable in >>org.jmol.g3d.Platform3D.java ? >> >> > I just tried this with clearingThread false, but it is still unusable > and I had to kill JavaVM separately. Then it looks like some other problem. Miguel

Re: [Jmol-users] chain color sheme

ers mailing list > [EMAIL PROTECTED] > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- Miguel Howard [EMAIL PROTECTED] c/Peña Primera 11-13 esc dcha 6B 37002 Salamanca España Spain -- telefo

Re: [Jmol-users] Jmol Version 10pre8c 2004/04/21 18:03 hangs on second loading

Jan wrote: > using Mozilla1.7b. The first time I loaded an applet page, all works > fine, but if I loaded a second Jmol applet page, no rendering shows up > and Java hangs (I could shut off Mozilla but I had to kill JavaVM > separately). > (the same is with iExplorer) > Regards, Jan I am currentl

Re: [Jmol-users] Comments on Jmol v10 prerelease 7

Philip wrote: >>> 2. Should you be able to color chains separately? That is, should I >>> be able to "paint" the 4 chains in hemoglobin different colors? I do >>> not seem able to do so. (jmol) >> >> I did make some changes to chain colors. Perhaps I broke something. >> >> I cannot check it out

Re: [Jmol-users] paste mystery on Mac solved!

> Hey everyone, > > I solved the Paste mystery on the Mac! > > Jmol requires one to type CONTROL-V for paste, even on a Mac. On a > Mac, the usual shortcut is COMMAND-V. (The COMMAND key is also known > as the Apple key.) The CONTROL key has been so rarely used for > anything on the Mac that it

Re: [Jmol-users] Paste in Jmol on Mac

Robert wrote: >>Works fine on Linux and on Win32 ... Looks like a bug that Apple hasn't >> fixed yet :-( > > Could we discuss this some more, too? I'm not sure what Miguel > means. I've never seen a Mac app that DOESN'T have Copy/Paste > functionality. Jmol does nothing special to support cut/pa

Re: [Jmol-users] Re: Request for 'select occupancy [operator] [value]' in Jmol

Karsten wrote: > Occupancy refers to the percentage of unit cells in a crystal that > contain a certain atom. ... [snip] > > Sorry, failed to adhere to the 25 word limit ;-) It was perfect ... you are forgiven :-) Miguel --- This SF.Net

Re: [Jmol-users] -script option to Jmol application

Judith wrote: > I've tried using the -script option to the Jmol application (Jmol.jar) > in version 8, 9 and the 10pre6 beta. I cannot get it to work. This is a bug. > Any suggestions as to something I am doing wrong? I have submitted > this as a bug since it does not work as advertised. Than

[Jmol-users] How to make the Jmol.jar application launchable on MacOSX

Bob wrote: > Henry, can you give detailed directions for someone who doesn't know > anything about Java, beginning with where I get the developer kit and > how I install it? Here are Henry's instructions ... along with a Step 0 and Step 5 from Tim Driscoll. Miguel step 0. a. if you installed

[Jmol-users] Re: select [5MC]2498B -> FIXED

> with 1c2w I got the following error: > 3 letter residue specification expected : select [5MC]2498B; > and there are others, e.g. [5MU]1939B, [7MG]2069B, [1MA]2030B Fixed and checked in. The problem was that caused by the fact that the group/residue names start with digits. Do you happen to kno

[Jmol-users] Re: 3 letter residue specification expected : select [5MC]2498B;

Jan & Miguel wrote: >> with 1c2w I got the following error: >> 3 letter residue specification expected : select [5MC]2498B; >> and there are others, e.g. [5MU]1939B, [7MG]2069B, [1MA]2030B > > Which PDB file? Sorry ... I see ... 1c2w Miguel --

Re: [Jmol-users] Measurements in JmolApplet

>>>like in RasMol, if I said: >>> set picking distance >>>Atom #1: [ARG]97:E.NH2 (1062) >>>Atom #2: [ARG]173:E.NH2 (1722) >>>Distance [ARG]97:E.NH2 - [ARG]173:E.NH2 = 19.211 >> >>Are you saying that you get all this text sent to you as a single >> string? >> > yes, in RasMol But does it happen in

[Jmol-users] Re: 3 letter residue specification expected : select [5MC]2498B;

> Hi Miguel, > with 1c2w I got the following error: > 3 letter residue specification expected : select [5MC]2498B; > and there are others, e.g. [5MU]1939B, [7MG]2069B, [1MA]2030B Which PDB file? Did this work before and get broken as a result of my recent changes to support x/y/z ? Miguel

Re: [Jmol-users] Jmol as an application on OS X

Henry wrote: > Found a mechanism to wrap the Jmol.jar into an application on OS X > (thus converting it to jmol.app ) which CAN be treated as a proper > application. Use /Developer/Applications/Java Tools/Jar Bundler > and indicate the main class as org.openscience.jmol.app.Jmol Good. > Wh

Re: [Jmol-users] Re: Jmol-users digest, Vol 1 #252 - 11 msgs

Robert wrote: > But we have lots of talented > computer science graduate students here, all looking for challenging > master's projects. Lots of free labor! I'll ask around. If you can find a graduate student that is self-motiviated and if you can provide a small amount of management from your

Re: Pluglets (was: [Jmol-users] Browser enhancement technologies tutorial)

Egon wrote: > I would like to add a possible option: > > http://www.mozilla.org/projects/blackwood/java-plugins/ > > It's been around for years now, but it is not mainstream (yet)... > > Pluglets: mozilla plugins written in Java. > > I have absolutely no idea what the current status is of this proj

Re: [Jmol-users] Browser enhancement technologies tutorial

>> The web browser will launch MS Word every time it sees a >> document with the mime-type 'application/msword'. < > Can I add only to this section that MIME types were never originally > intended for use within browsers; they were supposed to be used only for > email Very true. > In the early da

Re: [Jmol-users] Re: shift-left zoom

Tim wrote: >>Unfortunately, Java has no 'Human Interface Guidelines'. It is >>*supposed* to run on all platforms and be agnostic to the platform that >> it is running on. >> > > what about this? > > :-) Very good! Miguel

[Jmol-users] Browser enhancement technologies tutorial

Robert & Tim wrote: >>The user will need a way to tell Safari which file extensions should >> make it call Jmol. And yes, there needs to be some simple mechanism >> that installs the plug-in or whatever that trains Safari to call >>Jmol. (A *very* simple mechanism, please. I know almost no UNIX,

Re: [Jmol-users] Web browser plug-in?

>>Henry's message seemed to say that making these associations on Safari >> may be difficult. > > There is no GUI in Safari for setting these things > (unlike eg Mozilla) :-O and every other web browser on the planet! > It gets worse! [snip] > Yes, it is incredible that Apple could produce su

Re: [Jmol-users] Re: shift-left zoom

Tim & Jan wrote: >>>versions. in addition, Jmol implements features that other mol vis >>> apps may not. I certainly hope that Jmol will implement some features that others do not. And I want to put functionality into the applet so that people can use it without writing scripts. Hence the measure

Re: [Jmol-users] Measurements in JmolApplet

Jan wrote: >>>please keep this compatible with single click and PickCallBack >>Single click should now call the PickCallBack > OK, > set picking ident > is the default. It is the default ... and there currently is nothing else. >>>and give >>>a MessageCallBack which could be checked by a script

Re: [Jmol-users] Web browser plug-in?

>>Q: Would it be valuable to have a simpler mechanism to associate the >> Jmol application with web browsers as a helper application? > > If the Jmol application can be launched automatically whenever a file > with MOL or PDB extension was loaded by Safari, that would be a big > help. Henry's mess

Re: [Jmol-users] Web browser plug-in?

>>Q: Would it be valuable to have a simpler mechanism to associate the >> Jmol application with web browsers as a helper application? > > This of course was the MIME handling mechanism, and the reason for > chemical/x-pdb etc MIME types. As far as I can tell, OS X does > not have a clear mechani

Re: [Jmol-users] Web browser plug-in?

Robert wrote: > Back to the issue of loading Jmol in a browser when Jmol is not > delivered by the server that also delivers the content. I found this > page on plug-in development for Safari. > > http://developer.apple.com/technotes/tn/tn2020.html This is a useful document for me. Thanks for se

[Jmol-users] RE: Request for 'select occupancy [operator] [value]' in Jmol

Christopher wrote: >>Q: Do you want to use lowercase 'o' or uppercase 'O' ? (we would use >> the lowercase version unless we want to reserve it for some other atom >> property that is more popular) > > The abbreviations I've seen (and used) for occupancy are "Q" (or "q"), > or less commonly "Occ"

[Jmol-users] Re: shift-left zoom

> Hi Miguel, > the shift-left zoom didn't work with 10pre6e 2004/03/15 23:00 > Regards, Jan Correct. I have broken all the mouse gestures. We cannot use shift-left for zoom because it will conflict with shift clicking in order to make selections. As of right now there is no way to zoom using

Re: [Jmol-users] Measurements in JmolApplet

Jan wrote: >> * RasMol was not developed as a GUI application. Rather, >> it was developed as a command-line tool. >> > please keep this compatible with single click and PickCallBack Single click should now call the PickCallBack > and give > a MessageCallBack which could be checked by a script

[Jmol-users] Measurements in JmolApplet

Geoff wrote: > Recent postings have considered 'monitor' and possible alternatives to > display measurements, bond and torsion angles etc > > e.g. Miguel said >>It seems that many people want to use 'monitor' to create artificial >> bonds. The combination of 'monitor 1 2' and 'set monitor off'. >

[Jmol-users] Re: Jmol too nice behaviour

Miguel & Jaim wrote: > Please send me the entire file so that I can look at it. You indicated that the entire file was what was in your original message. I have included it below for reference purposes >> We find out that we're sending some incorrect data to Jmol, >> like a CONNECT with a non-ex

[Jmol-users] Re: Jmol too nice behaviour

Jaim, Please send me the entire file so that I can look at it. > Dear Miguel, > > We find out that we're sending some incorrect data to Jmol, > like a CONNECT with a non-existing atom name (see the example > at the end). > > It turns out that Jmol is too nice with us and draws something. > Since

Re: [Jmol-users] chain Y or chain Z ?and water?

Jan wrote: >> Q: Please remind me ... under what circumstances should PickCallBack be >> called? Single click on an atom? > > yes Q: All the time? Q: Only when 'set picking' is turned on? Q: Only the left mouse button? Q: What happens on double-click? Miguel -

Re: [Jmol-users] chain Y or chain Z ?and water?

Jan wrote: > but atom picking (PickCallBack) seems to be completely disabled I am sure that I broke it this weekend. I made a number of changes to the implementation of the mouse code. In part to support wheel mice, in part to support Mac OSX, and in part to support gestures for measuring distanc

Re: [Jmol-users] chain Y or chain Z ?and water?

> At the moment I'm not able to test Jmol, because after cvs update Jmol > failed to build, Sorry. Keep trying 'cvs up' from time-to-time until the file 'Font3D.java' comes down. > but with the last version 10pre6c I tried to > select [HOH]206Y > in 1ocm I got the unexpected error "end of express

Re: [Jmol-users] Eval.java:30: cannot resolve symbol

> I just updated my Jmol > cvs update -dP > and tried to compile > ant clean main > and got these errors > > Jmol/src/org/openscience/jmol/viewer/script/Eval.java:30: cannot resolve > symbol > [javac] symbol : class Font3D > [javac] location: package g3d > [javac] import org.opensci

[Jmol-users] Re: How remove the lines and distances in Jmol?

Gerzon wrote: > 1. In Chime - If I select a pair of atoms and run 'monitor', I get the > line between these two atoms and distance. - The same in Jmol Correct. monitor 1 2 Will draw a dotted line and measure the distance between atom numbers 1 and 2. In addition, Jmol supports the following

[Jmol-users] Re: How remove the lines and distances in Jmol? ( all previous lines and distances or one previous line and distance)

ous lines and distances. > with command 'monitor off'. > > How remove the lines and distances in Jmol?. > ( all previous lines and distances or one previous line and distance) > > > Best regards > > > >>= Original Message From "Miguel Howard

[Jmol-users] Re: HETATM with large atom sequence number

Jaim wrote: > You might be right in that the problem was related to a particular > version of Jmol. > > Now I'm using 10pre6 and it's able to display with no problems > the hetgroup 2BM that has the described problem: Very good. Miguel ---

[Jmol-users] HETATM with large atom sequence number

Jaim wrote: > I think that Jmol fails interpreting PDB files when there's no space > between the label (HETATM) and the value (17519), as in these lines from > 1FZ9: > > HETATM17519 C1 ETI 9001 61.663 49.780 58.929 0.60 40.01 > HETATM17520 C2 ETI 9001 60.395 49.983 58.173 0.60

[Jmol-users] Re: Wildcard behavior

But even select [C]3:A.O5* is not working at the moment http://www.imb-jena.de/cgi-bin/SCOPlnk.exe?JMOL=264d in current RasMol select [C]3:A.O5* select C3:A.O5* select C3A.O5* all select the same expected atom. I just checked in code to correct this. All of

[Jmol-users] Sphere rendering

I recently made some improvements to the graphics rendering of the spheres in Jmol. The small spheres looked pretty good, but the big spheres suffered from 'banding'. They are really only visible when you zoom in close, but it always bothered me a little bit :-) I posted a request to a 'game deve

Re: [Jmol-users] Chain Colors

Jan & Eric wrote: >>> I would suggest to avoid both, white and black in color schemes, >>> because I like to use >>> background white >>> for presentation and printing. >>> Regards, Jan >> >> >> "White" as a backbone trace is actually quite visible on a white >> background due to shading, at least

Re: [Jmol-users] Wildcard behavior

Jan wrote: >>> select c3a.c?* >>>selects the sugar carbons >>> >> >>This one is different. You are using the trialing * to indicate a >> wildcard match within a 'field'. >> >> > no, I used a wildcard for the second position and a prime at the third. OK >>It was not clear to me from reading the Ra

[Jmol-users] remote URL loading

Jan wrote: > jmol.sh -e 'load pdb > http://www.rcsb.org/pdb/cgi/export.cgi/1PLC.pdb?format=PDB&pdbId=1PLC&compression=None"; > jmol.sh -script http://www.imb-jena.de/cgi-bin/rascript.exe?CODE=1plc > this would be nice. Jan, If all you want to do is load a file from a web server then it works tod

Re: [Jmol-users] Web browser plug-in?

Jan wrote: > configure Jmol like RasMol make a script file, starting Jmol with the > temporary file from the browser > http://www.imb-jena.de/ImgLibPDB/docs/RasMolInfo.html If I understand you correctly, this will launch the Jmol application as a "helper application" outside the browser. Unfortu

Re: [Jmol-users] open Gaussian output file with Jmol

Egon is not around to help ... perhaps someone else can ... > I am a new user of Jmol. I just want to know what output file of > Gaussian Jmol can open? I tried *.log, *.chk and *.com. But I can't open > them > Anyone of you can help me with this? My *guess* is that you pipe the output of gaussia

Re: [Jmol-users] Web browser plug-in?

Robert wrote: >> > Specifically, the American Chemical Society now provides MOL files >> and >>> other online content in the Web versions of their publications, but >>> it does not deliver applets to render the content. (Maybe it >>> should, but it doesn't.) >> >>(Perhaps we should suggest tha

Re: [Jmol-users] Web browser plug-in?

Robert wrote: >>> I've recently upgraded to MacOS 10.3, and I use Safari nearly >>> exclusively. I was wondering whether there are plans or has been >>> progress in creating a Jmol plug-in for the Safari Web browser? >> >>Panther 10.3/Safari works well with the existing JmolApplet. > > Hi Miguel

Re: [Jmol-users] Web browser plug-in?

Robert, > I've recently upgraded to MacOS 10.3, and I use Safari nearly > exclusively. I was wondering whether there are plans or has been > progress in creating a Jmol plug-in for the Safari Web browser? Panther 10.3/Safari works well with the existing JmolApplet. You should be able to see som

[Jmol-users] Re: nucleic rendering

>>>Because nucleic acids have a polarity like protein, too >>> (biosynthesis), which run from *.O5* to *.O3* a small arrowhead on the >>> 3* end would be nice and I like the rendering of the bases as plates >>> like MIDAS or MolMol do, e.g. on: >>>http://www.imb-jena.de/cgi-bin/ImgLib.pl?CODE=264d

[Jmol-users] Wildcard behavior

Jan wrote: >>>But even >>> select [C]3:A.O5* >>>is not working at the moment >>>http://www.imb-jena.de/cgi-bin/SCOPlnk.exe?JMOL=264d >>>in current RasMol >>> select [C]3:A.O5* >>> select C3:A.O5* >>> select C3A.O5* >>>all select the same expected atom. >>> >>> >> >>It is not clear to me what role

Re: [Jmol-users] Chain Colors

Jan wrote: > I would suggest to avoid both, white and black in color schemes, because > I like to use > background white > for presentation and printing. Agreed. Miguel --- This SF.Net email is sponsored by: IBM Linux Tutorials Free Linux

[Jmol-users] Re: nucleic rendering

> neither of the abstract rendering is supported for nucleic acids in > current Jmol. That is correct. I am unable to work on this item because of a pending grant application. > RasMol used *.P for backbone and trace and the RasMol cartoon isn't very > nice, this could be made better. OK > Bec

[Jmol-users] Chain Colors

Eric wrote: > Please do not apply white to all molecules with a single chain. > These are quite common. > White is not good for these cases. Understood. > Please apply the colors in the order in which I listed them. > > No, there is no document about these colors, not even in PE. That is why >

Re: [Jmol-users] FOLLOWUP: Re: example animation in Jmol

> According to Miguel Howard: >> [param name="progressbar" value="true"] >> [param name="progressmessage" value="Downloading JmolApplet ..."] >> [param name="boxbgcolor" value="#rrggbb"] >&g

[Jmol-users] Re: [Jmol-developers] 'Toggle' button

Michael wrote: > Has anyone implemented the equivalent of a 'toggle' button as an > AppletControl parameter? Michael, Within a JmolAppletControl you can say [param name="type" value="chimetoggle"] [param name="script" value="... ..."] [param name="altscript" value="... ..."] The other type

Re: [Jmol-users] FOLLOWUP: Re: example animation in Jmol

Jaim, >> BTW, you may also retrieve structural and bioinfo related data to a >> PDB entry by pointing to >>http://bip.weizmann.ac.il/oca-bin/ocashort?id=1c8r >> Your page looks good. You may want to add the following to give feedback to people who are first downloading the applet: [p

[Jmol-users] v10pre6 unitcell bug - fixed

Geoff, > However there are still problems with unitcells where at least one of > alpha beta or gamma <> 90 degrees e.g. Be and S8 monoclinic. Have > perhaps alpha, beta or gamma got transposed in the Jmol10pre6 code? or > perhaps sin got switched for cos somewhere? - There's something not > right

Re: [Jmol-users] spin syntax

Phil wrote: > What is the script syntax to turn spin on and off -- I know -- spin on; > spin off. But that spins around one axis and I cannot seem to get it > to spin any other using scripting in either the applet or the > application. I have tried spin x on and spin y on, and even spin y 50 > o

[Jmol-users] Re: applet for Win2000 with JIT

Jaim, > I think that the problem is that IExplorer does not refresh > crashed code. > > To test your 'modified' applet, I gave it a new name > (JmolAppleDebug.jar), so the browser had no other option than to load it > from new, and worked. [snip] > I need to find a way of really refreshing the app

[Jmol-users] New colors

I have posted a new set of proposed JmolColors on http://jmol.sf.net/colors Changes were made to a few atom colors. In particular: Nitrogen is a slightly different shade of blue fluorine is now a yellow-green Nickel is now a shade of green * I have never seen aqueous nickel ions, pleas

Re: [Jmol-users] Cyclohexane Tutoral Correction

Phil wrote: > A couple of comments. I apparently had a typo in the original address > I sent. It should be: > > http://www.saintmarys.edu/~pbays/DCC/DCC.htm Works fine for me on Linux. Looks very good. Miguel --- This SF.Net email

Re: [Jmol-users] pre-6 color shapely

Paul wrote: > The command "color shapely" colors pink both thymines and cytosines. IMO > they should be distinguishable as they are in the drums color scheme > proposed here http://www.umass.edu/molvis/drums/ > (with the chime color scheme for shapely, some of my slightly color > blind students fou

Re: [Jmol-users] spacefill radius limits

Geoff wrote: > My experience with the Jmol 10 beta Applet is that > "spacefill" does not correctly render atom spheres > with a radius equal or greater than 2.00 Ångstrom (500 > RasMol units). [snip] > It would be good (for me at least) if Jmol also > supported spacefill up to 3.00/750, Implement

[Jmol-users] Re: Jmol on Win2000 with JIT

Jaime wrote: > I found problems when running Jmol 10pre6 on Windows 2000, IE 6.06, with > JIT enabled, With no JIT enabled, Jmol works fine. Good bug report. The console output is exactly what I need. There seem to be a lot of differences in the behavior of the various JVMs on various platforms

Re: [Jmol-users] pre-6

>> > you are correct; pre6 is slower to load compared to pre5. Miguel >> changed the popupMenu so that it loads when the applet is first >> instantiated, instead of when the menu is first clicked. this was > to >> > remove an awkward 2-3 second delay between right-click and menu >> appearance. >>

Re: [Jmol-users] pre-6

Phillip wrote: > Just to clarify. It is not the applet loading that I am concerned > about. If I load a molecule, the applet loads initially. If I then > call for another molecule, the applet is already loaded and should not > reload via my javascript. The only thing that should happen is a

Re: [Jmol-users] pre-6

> you are correct; pre6 is slower to load compared to pre5. Miguel > changed the popupMenu so that it loads when the applet is first > instantiated, instead of when the menu is first clicked. this was to > remove an awkward 2-3 second delay between right-click and menu > appearance. It is true t

[Jmol-users] Jmol v10 prerelease 6

Jmol v10 prerelease 6 is now available. http://jmol.sf.net/betatest There have been a large number of changes over the past few weeks. Hopefully we fixed more things than we broke :-) Miguel --- This SF.Net email is sponsored by: IBM Linu

Re: [Jmol-users] popup menu disable

> can someone please remind me how to turn off access to the popup menu in > the Jmol applet? I distinctly recall discussing this recently, but I > can't find any reference to it. The bad news is ... it was discussed, but not implemented. The good news is ... I just put it in for you. The synta

[Jmol-users] unitcell packing & default behavior

Geoff wrote: > As I understand it, the 'old' applet draws the unit cell 'starting' from > the origin of the .pdb file (i.e. from 0 0 0) and for a cubic system > draws the a, b and c 'edges' of the unit cell in the positive direction > i.e coincident with X Y & Z for a cubic system. This is what I

[Jmol-users] EXPDTA nmr

> Eric wrote: >> I think Jmol should ignore crystal cell data when EXPDTA is NMR. > > Very good. > I was not familiar with the EXPDTA record. > That is the correct criteria to use. > This bug has been fixed. When the EXPDTA record starts with a description that says "nmr" (case insensitive) then

[Jmol-users] trace temperature interpretation

This message is about graphical renderings of the 'temperature/B-factor' value. I previously exchanged a few emails offlist with Jan regarding the interpretation of 'temperature' values for the graphic rendering of 'trace temperature'. 'trace temperature' shows a snake/worm rendering where the d

Re: [Jmol-users] unitcell 'bug'?

Eric wrote: > I think Jmol should ignore crystal cell data when EXPDTA is NMR. Very good. I was not familiar with the EXPDTA record. That is the correct criteria to use. Miguel --- This SF.Net email is sponsored by: IBM Linux Tutorials Free

Re: [Jmol-users] unitcell 'bug'?

> I don't think this is a PDB data quality bug, it is a PDB format > feature. Every NMR PDB file contains this: > > REMARK 4 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT *CRYST1* AND > REMARK 4 *SCALE* RECORDS BE INCLUDED, BUT THE VALUES ON THESE > REMARK 4 RECORDS ARE MEANINGLESS. If that is

Re: [Jmol-users] proposed default Jmol colors

Rich wrote: >> Look at the 'proposed changes' periodic table and give me feedback >> ... especially you inorganic folks. > > Well, I'm not inorganic but I was organo-metallic and I am organic and > I could live with this colour set. > I don't like the F colour (I grew up with a different one) Wha

[Jmol-users] Miguel still has no email + checked-in code

1. I still have no inbound email. 2. I 'roto-tilled' a lot of code. That is to say, I made some rather broad changes and checked them in. In general, most things work. But the user preferences are not saved, and other things may be broken. Miguel

Re: [Jmol-users] proposed default Jmol colors

Jan wrote: > what is the reason to make the nitrogen pale? C,O,N,P,S should give a > good contrast (green, red, blue, magenta, yellow:-). I think, I'm > against letting the N fade away. I am not sure I understand. Are you saying that you are in favor of a blue which is #FF ... as in ghemical?

[Jmol-users] proposed default Jmol colors

Folks, I am pursuing the 'colors' subject again. First, let me say that Jmol will continue to support the RasMol/Chime colors for those who know and love them. We will also support user-defined colors a little further down the road. For now, I want to talk about the default Jmol colors. The cu

[Jmol-users] special applet attributes

The Sun Java Plug-in supports a few 'Special Applet Attributes' which are of interest. The most important for the Jmol users is that !!! you can display a progress bar !!! which will show the % progress as the JmolApplet downloads. Additionally, you can control colors and things. You can also re

Re: [Jmol-users] using percent dimensions in applet

> a few weeks ago there was some discussion around using percent values > for width and height in the applet tag. I've searched the list archives > but I can't find anything useful. IIRC the consensus was that percent > values are not stable on OSX, but ok everywhere else. > > can anyone confirm

Re: [Jmol-users] models and frames

Hens wrote: > What I meant is that there should be an option to display the frames > sequentially or (all or some selected) on top of each other. That's > clear now. OK >> Please let me know if you see any fundamental problems with this. > > I don't, I agree completely. Good! Miguel --

Re: [Jmol-users] Re:xyz vs pdb

> The PDB file-format is an *extremely* poor one for use in a more > expressive crystallographic environment. It works for proteins, but as > far as the more complicated crystallography questions? I'd not recommend > trying to force other information into that format. Understood. > A far more fl

Re: [Jmol-users] xyz vs pdb

Hens & Tim wrote: >> > How to create such PDB models (from computational packages) is >> another question; I'm willing to edit the files by hand if need >> arises. >> >> That may be our only option :-) >> > a simple perl uitility could drop different sets of atom records into > whatever format - in

Re: [Jmol-users] multi-frame .xyz files & pdb MODELs

Oliver wrote: > But don't worry about Chime's Bugs. That is good advice! Miguel --- SF.Net is sponsored by: Speed Start Your Linux Apps Now. Build and deploy apps & Web services for Linux with a free DVD software kit from IBM. Click Now! ht

Re: [Jmol-users] pdb and xyz

Hens wrote: > Most of the time I use MOPAC and its options to scan a coordinate > (distance, dihedral angle). > Then I read the output into MOLDEN (not only because I share the office > with its author) that will write out an m-XYZ file. With Gaussian the > same path is followed. > > (B.t.w. we als

Re: [Jmol-users] animation models

Eric wrote: > Correction: RasMol 2.6 *DID* have multiple-model support (MODEL/ENDMDL). > The trick was that you had to use "load nmrpdb filename". If you loaded > the PDB file from the File menu, it only loaded the first model. > > This caused most RasMol users to be unaware when multiple models

Re: [Jmol-users] unitcell 'bug'?

Tim wrote: > can someone duplicate/explain this? (using the latest CVS build of Jmol > on OSX.) > > launch Jmol. > load samples/1LCD. > open the script window. > enter the following commands: > >set boundbox 0.2 >color boundbox gold >set axes 0.1 >color axes dodgerblue >set un

Re: [Jmol-users] Re: MODEL term appropriate?

>> I would like to disucss the use of the term MODEL in the context of >> animations. > > First of all let's agree on "animation" in this context. Very good. The terminology will be very important in these discussions. > The visualization of a sequence of structures, normally slightly > different

Re: [Jmol-users] pickCallback returns Object

Tim wrote: > greetings, > > after some fiddling, I realized that Jmol's pickCallback returns the > atom data as an Object, not a String. I can't seem to cast it into a > String using javascript, which means I can't do grep, split, slice, etc. > any help? > > (I've tried toString() but it does not

Re: [Jmol-users] load inline?

t; > On Wed, 25 Feb 2004, Miguel Howard wrote: > >> Dan, >> >> Tim Driscoll are in the process of discussing this offlist. I will >> send you the email. >> >> >> Miguel >> >> > >> > Does this work with jmol?

Re: [Jmol-users] xyz vs pdb

Hens wrote: > Well, it is not so much the size that matters, as does the extra > information a pdb file carries for proteins: > e.g. secondary structure, amino acid labels, chains, models, and connect > records. > For non-proteins only the latter apply: bonding information in HETATM > lines. Agreed

Re: [Jmol-users] animation models

Jan wrote: > but then it would be easier to do something like this > # animation list of selections loopmode frametime > anim qw(*/1 */2 */3 */4 */5 */6 */7 */8 */9&(nucleic|hetero) > */10&(nucleic|hetero) */11&(nucleic|hetero) ) rock 0.3 > > (but this is not compatible :-) We are going to do some

Re: [Jmol-users] animation models

Tim said: >> Huh? You said "Chime can only 'show' all models" ... >> >> But can't I also say >> >>show model 1 >> >> As an alternate mechanism of restricting the rendering to a single >> model? >> > sorry - this does not work in Chime. Thanks for settling this issue. Miguel

Re: [Jmol-users] animation models

>> >> > Q: In Chime, can you only show one model, or can you show several >> > >> >select (model=1,model=2,model=3) >> >wireframe 0.3 >> >> :-) To my way of thinking, this is showing all of the models ... but >> some of them just happen to be turned off. >> > different perspectives, eh? :-

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