Re: [Jmol-users] PubChem SDF

. Otis -- Otis Rothenberger Department of Chemistry Illinois State University Normal, IL 61790-4160 http://chemagic.org From: Angel Herráez angel.herr...@uah.es Sent: Tuesday, January 18, 2011 5:18 AM To: osrot...@chemagic.com, jmol-users

Re: [Jmol-users] PubChem SDF

= chgs[x].split( ); scpt1 += {atomno= + chgis[0] + }.partialCharge= + chgis[1] + ; } scpt2 = {*}.partialCharge = 0; + scpt1 + isosurface vdw 80% map mep translucent;; jmolScript(scpt2); } -- Otis Rothenberger Department of Chemistry Illinois State University Normal, IL 61790

[Jmol-users] PubChem SDF

PUBCHEM_COORDINATE_TYPE 2 5 255 -- Otis Rothenberger Department of Chemistry Illinois State University Normal, IL 61790-4160 http://chemagic.org -- Protect Your Site and Customers from Malware Attacks Learn

[Jmol-users] Edited Model Question

text, I'll set the remote global with that. The new state transfers between multi users seem faster. My imagination or has something changed to make state reading and loading faster? Otis -- Otis Rothenberger Department of Chemistry Illinois State University Normal, IL 61790-4160 http

Re: [Jmol-users] Edited Model Question

Bob, Got it. Thanks. Now that you point me, I also see a atomName set. These strings will let me set the JavaScript globals. Otis -- Otis Rothenberger Department of Chemistry Illinois State University Normal, IL 61790-4160 http://chemagic.org

[Jmol-users] Extract Molfile

-- Otis Rothenberger Department of Chemistry Illinois State University Normal, IL 61790-4160 http://chemagic.org -- Gaining the trust of online customers is vital for the success of any company that requires sensitive

Re: [Jmol-users] Extract Molfile

://www.symyx.com/downloads/public/ctfile/ctfile.jsp Otis -- Otis Rothenberger Department of Chemistry Illinois State University Normal, IL 61790-4160 http://chemagic.org From: Otis Rothenberger osrot...@chemagic.com Sent: Monday, January 10, 2011 2:17 PM

[Jmol-users] MEP Surface Problem

Bob, Molecular Electrostatic Potential appears to be broken on 12.1.30_dev. I can't map the surface via the Jmol menu or Jmol script on my page. The Jmol menu sees that partial charges are there, but no mapping occurs. Otis -- Otis Rothenberger Department of Chemistry Illinois State

Re: [Jmol-users] MEP Surface Problem

as a decimal for a non-split surface. It now comes back as an array with one item. Otis -- Otis Rothenberger Department of Chemistry Illinois State University Normal, IL 61790-4160 http://chemagic.org From: Otis Rothenberger osrot...@chemagic.com Sent: Sunday

[Jmol-users] Extract Molfile

is read into JME editor (depicted). Either approach (JME file or stereo bond encoded molfile) will work. I have agendas associated with this too numerous to mention here! Otie -- Otis Rothenberger Department of Chemistry Illinois State University Normal, IL 61790-4160 http://chemagic.org

[Jmol-users] Another Useful External Connection for Jmol

is: Jmol model --- Jmol SMILES --- Resolver SMILES --- http://www.nmrdb.org/predictor?smiles=XXX Once again, a working example is at http://chemagic.com/web_molecules/script_page_large.aspx The Model Tools link, followed by Predict HNMR Otis -- Otis Rothenberger Department of Chemistry

Re: [Jmol-users] Another Resolver Thought

that seems to be important to their data release approach. Perhaps they would be agreeable to Jmol users arriving at the disclaimer with a CAS# good to go. As usual, an operational example is at http://chemagic.com/web_molecules/script_page_large.aspx Use Tools menu. Otis Otis Rothenberger

[Jmol-users] Another Resolver Thought

using the information returned from Resolver. An example can be found at: http://chemagic.com/web_molecules/script_page_large.aspx Follow The Model Tools link. Otis -- Otis Rothenberger chemagic.com -- Lotusphere

Re: [Jmol-users] Another Resolver Thought

in the window. Otis Otis Rothenberger chemagic.com On 12/13/2010 4:03 PM, Robert Hanson wrote: If you have the signed applet, there should be no need for server-side scripting. Just use the file() function to load the contents of the resolver file -- which would be the InChI string, right

Re: [Jmol-users] Another Resolver Thought

pop-up headaches. Consequently, I write a dynamic link to make the user take the pop-up legal action. Otis Otis Rothenberger chemagic.com -- Lotusphere 2011 Register now for Lotusphere 2011 and learn how to connect

[Jmol-users] Jmol SMILES

diphenylcarbinols, including ring alkyl substituents, showed the same type of result. Bug or inherent kekule aromatic SMILES limitation? Otis -- Otis Rothenberger chemagic.com -- This SF Dev2Dev email is sponsored

Re: [Jmol-users] Random Bond Picking Event

carbon that he was disposing with a single bond click to the carbonyl, but in trying to recreate the problem, I realized I could create it with a 4 bond carbon. Otis Otis Rothenberger chemagic.com On 12/6/2010 9:54 AM, Robert Hanson wrote: Hmm. Probably a coding error. You mean when the bond

[Jmol-users] Random Bond Picking Event

slightly to destroy the parallel alignment solves the problem. A carbonyl group seems more susceptible to this than other bonds. This is obviously not a huge problem, but if anything comes to mind, let me know. Otis -- Otis Rothenberger chemagic.com

[Jmol-users] Backslash Confusion

, of course, shows a single backslash, but what is it really in the string? I thought I had this all under control, but I'm getting some confusing find results. Help??? Otis -- Otis Rothenberger chemagic.com

Re: [Jmol-users] Backslash Confusion

is a non-stereo version of a stereo containing {*} But not conversely - i.e. SOMESMILES .find(smiles,STRINGEQUIVALENTof{*}SMILES) will evaluate false. Am I correct on this point? Otis Otis Rothenberger chemagic.com On 12/1/2010 12:44 PM, Robert Hanson wrote: Yes, quite a pain. You'll

Re: [Jmol-users] Backslash Confusion

Bob, Thanks again. Your comments that I'm leaving in this response are a good FIND primer for me to keep handy. Otis Otis Rothenberger chemagic.com On 12/2/2010 12:51 AM, Robert Hanson wrote: On Wed, Dec 1, 2010 at 12:09 PM, Otis Rothenberger osrot...@chemagic.com mailto:osrot

Re: [Jmol-users] Jmol Variables

;echo;')); alert(msg); works beautifully. The second echo is just to make the first echo disappear. Otis Otis Rothenberger chemagic.com On 11/25/2010 4:57 AM, Alexander Rose wrote: Hi, Bob recently showed me you can use script with evaluate, i.e. jmolScriptWait('var foo = bar;'); var

Re: [Jmol-users] Jmol Variables

Rolf, Print works. Thanks for the suggestion. Otis Otis Rothenberger chemagic.com Couldn't you use 'print @foo' instead of the two 'echo' commands, avoiding to show something in the Jmol window the user isn't supposed to see there anyway? Or is there a problem with 'print

[Jmol-users] Jmol Variables

to lose them. In your opinion, what's the best way to take a Jmol script variable and pass it to JavaScript for subsequent Web page display, preferably without use of a timeout. Otis -- Otis Rothenberger chemagic.com

Re: [Jmol-users] SMILES Problem

/C=C\C#C.C4CC1.C5CC3.C\2=C/C#C but that first /2 can be just 2 without any ambiguity. Bob On Mon, Nov 22, 2010 at 5:14 PM, Otis Rothenberger osrot...@chemagic.com mailto:osrot...@chemagic.com wrote: Bob, I copied Markus with this problem because I don't know if it's a Resolver

[Jmol-users] SMILES Problem

be an issue that's already on the table. Otis -- Otis Rothenberger chemagic.com -- Increase Visibility of Your 3D Game App Earn a Chance To Win $500! Tap into the largest installed PC base get more eyes on your game

Re: [Jmol-users] Jmol SMILES Questions

Bob, Thanks. That fixes it. As a point of information, I think Resolver gets deuterium stereochemistry exactly backwards. I'll write Markus about this, but I want to check myself first. Otis Otis Rothenberger chemagic.com On 11/18/2010 8:45 AM, Robert Hanson wrote: OK, that's fixed. see

Re: [Jmol-users] Jmol SMILES Questions

return, etc. Resolver gets it exactly backwards I think. Otis Otis Rothenberger chemagic.com On 11/18/2010 10:51 AM, Robert Hanson wrote: Shouldn't matter what the group is. On Thu, Nov 18, 2010 at 9:21 AM, Otis Rothenberger osrot...@chemagic.com mailto:osrot...@chemagic.com wrote: Bob

[Jmol-users] Jmol SMILES Questions

]) = Resolver Otis -- Otis Rothenberger chemagic.com -- Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 L3. Spend less time writing and rewriting code

Re: [Jmol-users] Coordination Compound Questions

for coordination compounds. This will allow me to do some quick checking. I've played a bit, and this approach seems to work. Square planar is fine. Octahedral will take more testing. I'll get back to you on this. Otis Otis Rothenberger chemagic.com On 11/15/2010 6:53 AM, Robert Hanson wrote: Otis

Re: [Jmol-users] Coordination Compound Questions

. As a said above, this seems to work perfectly. Since this is my main concern (atom substitution), I'm a happy camper. The drag/SMILES change sounds like great fun, however. Otis Otis Rothenberger chemagic.com On 11/14/2010 3:17 PM, Robert Hanson wrote: Otis, I have something for you. Woke up

Re: [Jmol-users] Coordination Compound Questions

are setting up was simply a .js JSON structure. The size got way out of hand, so I moved it to the server side and write JSON from it as needed. I can see that I have some SMILES to change in the database in light of some of the things you've been doing. Otis Otis Rothenberger chemagic.com On 11/14

Re: [Jmol-users] Coordination Compound Questions

that in our mini-internal system I can use them to pick up isomer types in coordination complexes. This would not be a general algorithm, but it would allow detecting isomer types in our database for problem exercises. Otis Otis Rothenberger chemagic.com On 11/12/2010 7:50 AM, Robert Hanson

Re: [Jmol-users] Coordination Compound Questions

in model 1}.find(SMILES,string for selected atoms in model 2) ??? Do you mean that you think you can actually detect cis/trans and enatiomers in octahedral systems? Otis Otis Rothenberger chemagic.com On 11/12/2010 10:39 AM, Robert Hanson wrote: On Fri, Nov 12, 2010 at 9:22 AM, Otis

Re: [Jmol-users] Coordination Compound Questions

of Jmol. Otis Otis Rothenberger chemagic.com On 11/11/2010 8:37 PM, Otis Rothenberger wrote: All- I'm looking for some advice from inorganic chemists (or others) on the subject of appropriate molfiles for coordination compounds. To put the question in perspective, we are assembling

[Jmol-users] Coordination Compound Questions

]%10[C@@H]6[C@@H]7[C@@H]8[C@@H]9%10; var y = {*}.find(SMILES,x);echo @y Help! Otis -- Otis Rothenberger chemagic.com -- Centralized Desktop Delivery: Dell and VMware Reference Architecture Simplifying enterprise

Re: [Jmol-users] rotate selected atoms using the mouse

has a plan! Bob, what's that sulfur bond going to do during the movement? Otis Otis Rothenberger chemagic.com On 11/9/2010 7:23 AM, Robert Hanson wrote: Alex, That's what I needed. We will need a new parameter: set rotateSelectedAtoms It will be in Jmol 12.1.21, to be released later today

[Jmol-users] Jmol SMILES problem

was surprised by the result: {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15} I take it that the elements and the = are being matched (found) - not the dot?? Otis -- Otis Rothenberger chemagic.com -- The Next 800 Companies to Lead

Re: [Jmol-users] Jmol SMILES problem

obvious. Otis Otis Rothenberger chemagic.com On 11/9/2010 12:35 PM, Robert Hanson wrote: what's with the lower case (c=O)? On Tue, Nov 9, 2010 at 11:03 AM, Otis Rothenberger osrot...@chemagic.com mailto:osrot...@chemagic.com wrote: Bob, I think the following are two correct SMILES

Re: [Jmol-users] Jmol SMILES problem

automatically creating the correct database entries, but I have 300 of these that predate this approach. I'm trying to clean this up by hand. SmiR is unique, but I want a Jmol SMILES reference in the database. That's the reason for the two entries. Otis Otis Rothenberger chemagic.com On 11/9/2010

Re: [Jmol-users] Java security: mix of unsigned and signed content

out. My feeling is that many potential new users will simply take a pass on exploring Jmol when they run up against issues like this. There is not much that applet developers can do about this. I'm just whining. Otis Otis Rothenberger chemagic.com On 11/8/2010 6:53 AM, Angel Herráez wrote

Re: [Jmol-users] Java security: mix of unsigned and signed content

with an attempt to load a molfile via a local path. My local server should have served those files without the security violation. Jmol under 1.6.0_22 was not allowed to load them - under 1.6.0_21, all was well. Otis Otis Rothenberger chemagic.com On 11/8/2010 10:39 AM, Angel Herráez wrote: Might

Re: [Jmol-users] rotate selected atoms using the mouse

will do a conformation rotation. Alternatively, you can enter Jmol's mode lkit mode and do all of this via menus - right-click/computaion/model kit. Otis Otis Rothenberger chemagic.com On 11/8/2010 1:39 PM, Alexander Rose wrote: Hi, From the manual set allowRotateSelected FALSE When

Re: [Jmol-users] rotate selected atoms using the mouse

will do the same thing. After you click the drag link, you can click-drag individual atoms within a model - i.e. sculpt the model one atom at a time. Is that what you would like to do, albeit several atoms rather than just one? Otis Otis Rothenberger chemagic.com On 11/8/2010 3:19 PM, Alexander

Re: [Jmol-users] rotate selected atoms using the mouse

is bound in there, then things get icky. Your going to end up with the connected bond stretching like a taffy pull. In this case, however, the substrate is a separate entity. I hope I'm on the right track here and not wasting your time! Otis Otis Rothenberger chemagic.com On 11/8/2010 4:12 PM

Re: [Jmol-users] rotate selected atoms using the mouse

will simulate docking back into place. I just love this thing! Otis Otis Rothenberger chemagic.com On 11/9/2010 12:06 AM, Otis Rothenberger wrote: Hi Alexander and Bob- I'm going to go out on a limb here and say that I think Alexander wants to do something that's not as complex as it seems

[Jmol-users] Fwd: Re: Jmol 12.1.17 released

Bob, The only difference between these 2 pages is the function below: http://chemagic.com/web_molecules/script_page_large.aspx http://chemagic.com/web_molecules/script_page_large2.aspx On the Model Tools screen, changing a color (or simply clicking an atom) locks up the applet for

Re: [Jmol-users] Fwd: Re: Jmol 12.1.17 released

Bob, Every select; or select on the page was broken. I just changed them to select * That fixed them all. It might be a problem for other users, however. Otis Otis Rothenberger chemagic.com -- The Next 800

Re: [Jmol-users] Jmol 12.1.17 released

() { jmkLnksOff(x); jmkLnksOff(y); jmolScript(set picking assignAtom_C;set picking assignBond_p;); } What do you think? Problem on my end, Jmol bug, corrupt applet? Otis PS I cleared cache, update Java, and rebooted. Otis Rothenberger chemagic.com On 11/6/2010 11:24 AM, Robert Hanson wrote

Re: [Jmol-users] Jmol 12.1.17 released

Bob, I can bring up the Jmol menu now, but an atom click after the picking changes still locks the applet. Same behavior there. Otis Otis Rothenberger chemagic.com On 11/6/2010 3:16 PM, Robert Hanson wrote: Otis, please try 12.1.18. On Sat, Nov 6, 2010 at 1:44 PM, Robert Hanson hans

Re: [Jmol-users] Jmol 12.1.17 released

been around a long time. That's what broke it. Changing it to select * solved the problem. I think I have other cases of using select to mean select all. I'd better check. Otis Otis Rothenberger chemagic.com On 11/6/2010 7:38 PM, Otis Rothenberger wrote: Bob, I can bring up the Jmol menu

[Jmol-users] Inversion Question

Bob, I need to determine the new SMILES after a click inversion. I don't see a message callback on the click inversion. Do you have any suggestions for triggering the new SMILES determination after this click/invert? Otis -- Otis Rothenberger chemagic.com

[Jmol-users] Nitrogen Calculate Hydrogens

for this current problem. So I have a temporary solution to the problem if this is a Jmol issue that you would rather put on a back burner for now. Otis -- Otis Rothenberger chemagic.com -- The Next 800 Companies

Re: [Jmol-users] strange behaviour

the chair properly. Otis Otis Rothenberger chemagic.com On 10/22/2010 6:03 AM, Mio_libero wrote: Hi people, i tried to use my page http://pinostriccoli.altervista.org/?page_id=873 with JME sending the code to JMOL. When drawing a simple cyclohexane, i have a planar ring with the C6H12 formula

Re: [Jmol-users] strange behaviour

, but the direct JME load is easier. Otis Otis Rothenberger chemagic.com On 10/22/2010 10:47 AM, Angel Herráez wrote: This is interesting and intriguing... What is the reason why Jmol minimizes correctly the model coming from JME string but not the MOL string? As I said, I'm quite confident

Re: [Jmol-users] Random Errors

variables from Jmol to JavaScript. I also use print. There was a reason that I did not use it here, but I don't recall the reason! I'll try print. Otis Otis Rothenberger chemagic.com On 10/19/2010 8:36 AM, Robert Hanson wrote: Otis, Here's a possible culprit. I see: function processMessage

Re: [Jmol-users] Random Errors

. Without the timeout Jmol beat the page on load to the punch. The above code is a page testing remnant that I never removed. Another timeout bites the dust! I'm hoping I can complete the removal of these darn things before I go to bed tonight. Otis Otis Rothenberger chemagic.com On 10/19/2010 1

Re: [Jmol-users] Random Errors

it to the applet load javascript init. I'm hoping that fixes the original problem. Otis Otis Rothenberger chemagic.com On 10/19/2010 7:50 PM, Otis Rothenberger wrote: Bob, I found the problem with the getFormula() on load. The javascript call from the load script works when the timeout is used, but I

Re: [Jmol-users] Random Errors

new SMILES for JavaScript global variable is fired. I know that 2 and 3 must wait for 1 to complete. I think the order of 2 and 3 is irrelevant - not sure?? I'd sure like to lose setTimeOut as the referee that keep these guys in order. Will jmolScriptWait() do this? Otis Otis Rothenberger

Re: [Jmol-users] Random Errors

loads, and I can supply this as string without the jmolScript calls in getFormula. Otis Otis Rothenberger chemagic.com On 10/18/2010 10:30 AM, Otis Rothenberger wrote: Bob, I know that I need to try to get rid of those JavaScript timeouts. The construct jmolScriptWait(scpt) sounds

Re: [Jmol-users] Random Errors

() is pretty involved: 1) An immediate jmolScript() call. 2) A JavaScript setTimeout() that makes a jmolGetPropertyAsArray() call and another jmolScript call. Maybe that jmolInit() function is getting me into trouble. Otis Otis Rothenberger chemagic.com On 10/17/2010 2:52 PM, Robert Hanson wrote: Otis

Re: [Jmol-users] Random Errors

is pretty important to us, but there may be a better way to do it. Any suggestions welcome! Otis Otis Rothenberger chemagic.com On 10/17/2010 10:09 PM, Robert Hanson wrote: oh, I see. I think I missed the semicolon there. Sure. On Sun, Oct 17, 2010 at 4:37 PM, Otis Rothenberger osrot

Re: [Jmol-users] Random Errors

of an on applet load event - i.e. the terminal JavaScript does not get executed until the applet is loaded. Wrong assumption?? Better way to do this?? Otis Otis Rothenberger chemagic.com On 10/15/2010 1:00 PM, Robert Hanson wrote: On Fri, Oct 15, 2010 at 9:08 AM, Otis Rothenberger osrot

[Jmol-users] Random Errors

in 12.1.14_dev) - applet.script(script) is not a function. 2) An applet freeze (lock) after sequential model kit actions. There are no obvious cause and affect actions. When these problems occur, they are not reproducible by simply repeating the previous actions. Otis -- Otis Rothenberger

Re: [Jmol-users] Pleasant Save State Surprise

Otis Rothenberger chemagic.com On 10/5/2010 6:05 PM, Robert Hanson wrote: Hmm. Not finding that reference. On Wed, Sep 29, 2010 at 3:57 PM, Otis Rothenberger osrot...@chemagic.com mailto:osrot...@chemagic.com wrote: I may have missed a recent isosurface discussion, but documentation

[Jmol-users] Pleasant Save State Surprise

is the surface displayed on restore 12.1.14_dev. I guess this is a belated thanks. Otis -- Otis Rothenberger chemagic.com -- Start uncovering the many advantages of virtual appliances and start using them to simplify

[Jmol-users] State and Inline Load

); doUFF(1); setTimeout(lnkSwitch(), 1000); } Any suggestions? Otis -- Otis Rothenberger chemagic.com -- Start uncovering the many advantages of virtual appliances and start using them to simplify application

Re: [Jmol-users] State and Inline Load

; _setVariableState; _setModelState; _setPerspectiveState; _setSelectionState; set refreshing true; set antialiasDisplay false; set antialiasTranslucent true; set antialiasImages true; } _setState; Otis Rothenberger chemagic.com

Re: [Jmol-users] State and Inline Load

Bob, You are correct. All is good. I have a code mess that I need to clean up and then I'm going to upload the toy and do some playing with my partner in this project. Thanks. Otis Otis Rothenberger chemagic.com On 9/27/2010 1:35 PM, Robert Hanson wrote: Right. I fixed that, too, I

Re: [Jmol-users] Renew State Issue

moveto -1.0 {0 0 1 0} 100.0 0.0 0.0 {0.0 -5.0008297E-5 0.0} 2.7502866 {0.0 0.0 0.0} 0.0 -9.05576E-4 0.0; save orientation "default" moveto 0.0 { 499 859 -114 7.8} 100.0 0.0 0.0 {0.0028723478 0.0047832727 0.0016583204} 3.9663374 {0.0 0.0 0.0} -0.040259466 0.05

Re: [Jmol-users] Renew State Issue

data, I assume this problem is related to the fact that the NIH model url has only a temporary existence. I'm thinking extracted molfiles are my best bet at this point. Otis Otis Rothenberger chemagic.com On 9/25/2010 12:33 AM, Otis Rothenberger wrote: Bob, I'm working on a multi-user

Re: [Jmol-users] Renew State Issue

file below (end of email) should be 2-butyne that started from an ethene molfile load. The model kit edit shows 2-butyne, but here is what the above script produces from the state file: Otis Rothenberger chemagic.com On 9/25/2010 8:46 AM, Otis Rothenberger wrote: Bob, I stand corrected

[Jmol-users] Renew State Issue

transfer, one user can send another user a conformer rotation. This is all using 12.1.11_dev. Otis -- Otis Rothenberger chemagic.com -- Start uncovering the many advantages of virtual appliances and start using them

Re: [Jmol-users] MEP Color Range

molfiles Jmol loads Spatan files with the Z axis in the plane of the screen. Is this a bug in the reader? Otis Otis Rothenberger chemagic.com so you have two ranges -- the actual data (shown first) and the range you have designated (or Jmol has chosen by default) for the color range from

Re: [Jmol-users] MEP Color Range

Bob, I may not understand what should be happening here, so I'll be a bit more specific. It's suppose to load with the same orientation to the viewer that the user left it in when saved with Spartan. Is it not doing that? Rotate the model in Spartan, save it, and load it into Jmol.

Re: [Jmol-users] Spartan file reading oddity

with a user confusing Z displacement of the models. If Tom can't make Spartan behave, I guess I can write a separate routine for Spartan files with an initial YZ displacement. Fortunately, we keep these things in a separate load menu. Thanks for checking. Otis Otis Rothenberger chemagic.com

[Jmol-users] JME Question

they are not my global variables. Do you have a global jmeString at work here? Otis -- Otis Rothenberger chemagic.com -- Start uncovering the many advantages of virtual appliances and start using them to simplify application

Re: [Jmol-users] Spartan file reading oddity

Bob, Tom at the University of Southern Maine is the Spartan guy. I'll copy him with this note and send him a separate email with the other information. Otis Otis Rothenberger chemagic.com On 9/16/2010 9:25 PM, Robert Hanson wrote: Otis, can you send me some Spartan files? I don't have

Re: [Jmol-users] MEP Color Range

On Mon, Sep 13, 2010 at 9:10 PM, Otis Rothenberger osrot...@chemagic.com mailto:osrot...@chemagic.com wrote: The data range 0.41223556 to 0.6573585 seems to vary with the partial charges, but seems unrelated to the actual partial charges. The result below is for range all on the allyl

[Jmol-users] An Old Problem Comes Back

Otis -- Otis Rothenberger chemagic.com -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http:

[Jmol-users] MEP Color Range

numbers. Can you give me any information on the origin of these numbers - calculated from my charges??? Otis PS Thanks for the feedback on the array question. -- Otis Rothenberger chemagic.com -- Start uncovering

[Jmol-users] Spartan Load Question

Bob, The Spartan load ESP charge filter does not appear to be part of 12.0.12. Was this feature too late for the version release or has the syntax possibly changed? Otis -- Otis Rothenberger chemagic.com

[Jmol-users] Jmol arrays

I would like to multiply each element of a Jmol array by a constant value. Is this possible with Jmol math? If so, what is the script syntax? For example [1,2,3,4,5] multiplied by 5 to produce the new array [5,10,15,20,25] Otis -- Otis Rothenberger chemagic.com

Re: [Jmol-users] Jmol arrays

Oops, I gave up too quickly. A for loop through the elements of the array gets the job done. Still, if there is a direct math operation, it would be good to know. Otis Otis Rothenberger chemagic.com On 9/11/2010 9:53 PM, Otis Rothenberger wrote: I would like to multiply each element

[Jmol-users] Report on Partial Charge Load Filter and Related Question

. not just like Spartan. Is there any way to still get the full color range affect in 12.1.10_dev? Otis -- Otis Rothenberger chemagic.com -- This SF.net Dev2Dev email is sponsored by: Show off your parallel programming

Re: [Jmol-users] Report on Partial Charge Load Filter and Related Question

neat, and it tells the full story. Currently, this partial charge coloring is set at rwb. Can this color range be tweaked in Jmol Script? I think the rwb is great, but the intesity variation is hard to see through the translucent mep. Otis Otis Rothenberger chemagic.com On 9/6/2010 12:41 PM

Re: [Jmol-users] True Jmol Depict Jmol to JME

the correct syntax for swapping in a new set of partial charges?? var x = Array(partialChargesAsCommaDelimetdStrings) {*).partialCharge = {*}.partialCharge.x Otis Otis Rothenberger chemagic.com On 9/4/2010 8:37 PM, Robert Hanson wrote: On Fri, Sep 3, 2010 at 3:02 PM, Otis Rothenberger osrot

[Jmol-users] Spartan Partial Charges

. But if there's an easy way to tell Jmol to get the ESP numbers directly, let me know. Thanks Otis -- Otis Rothenberger chemagic.com -- This SF.net Dev2Dev email is sponsored by: Show off your parallel programming

Re: [Jmol-users] More on NIH Resolver

if the stereo drawing renders. JME does not read files from server. You have to feed it a string. Further the molfile string needs to be line break tweaked. I'm just now looking into this. Otis Otis Rothenberger chemagic.com On 9/3/2010 10:50 AM, Robert Hanson wrote: Ho, ho, HO! No kidding! Wow

Re: [Jmol-users] More on NIH Resolver

Oh my, it's this simple! http://cactus.nci.nih.gov/chemical/structure/CCC%28C%29CC/file?format=jme OR http://cactus.nci.nih.gov/chemical/structure/CCC(C)CC/file?format=jme Otis Otis Rothenberger chemagic.com On 9/3/2010 11:26 AM, Otis Rothenberger wrote: Bob, Yeah, it's amazing how fast

[Jmol-users] True Jmol Depict Jmol to JME

for the signed Jmol applet to pass the data to JME via JavaScript??? Otis -- Otis Rothenberger chemagic.com -- This SF.net Dev2Dev email is sponsored by: Show off your parallel programming skills. Enter the Intel(R) Threading

Re: [Jmol-users] Find SMILES problem

Jmol lower case cyclohexane, which is, of course synonymous with aromatic SMILES for benzene. Evidently, the Resolver is just ignoring = in this lower case context. Otis Otis Rothenberger chemagic.com On 9/2/2010 1:52 AM, Robert Hanson wrote: On Wed, Sep 1, 2010 at 10:21 PM, Otis

[Jmol-users] More on NIH Resolver

. Play with editing, and you'll see that Resolver gets it right. You need to click the image capture link each time. There are some problems with complex aromatics (e.g. taxol), but I'm working on this problem. Otis -- Otis Rothenberger chemagic.com

Re: [Jmol-users] More on NIH Resolver

deal with the 2 digit ring (or fragment) closure notation - i.e % notation. Otis Otis Rothenberger chemagic.com On 9/2/2010 10:24 PM, Otis Rothenberger wrote: The NIH Resolver will generate a gif image of the Lewis line structure of a submitted SMILES. I ignored this feature because I

[Jmol-users] Find SMILES problem

affects. Otis -- Otis Rothenberger chemagic.com -- This SF.net Dev2Dev email is sponsored by: Show off your parallel programming skills. Enter the Intel(R) Threading Challenge 2010. http://p.sf.net/sfu/intel-thread-sfd

Re: [Jmol-users] jmol script terminated

will be a problem. They produce direct 404 errors as well. Hope this helps. Otis Otis Rothenberger chemagic.com On 8/30/2010 11:16 PM, Ernst, Craig S. wrote: I am trying to help our chemistry department in solving an issue with jmol. The pages they created use to work during last spring, but now

[Jmol-users] Useful Compare Operation with JME

return on a SMILES is computed. Otis -- Otis Rothenberger chemagic.com -- Sell apps to millions through the Intel(R) Atom(Tm) Developer Program Be part of this innovative community and reach millions of netbook users

Re: [Jmol-users] Useful Compare Operation with JME

Bob, Sorry about the lack of specificity. Verbose not concise is my major writing flaw! The Fisher projections were definitely bond wedge, albeit two solid wedges per carbon as per the FP convention. I'm using 12.1.7. calculate H seems OK there. Otis Otis Rothenberger chemagic.com On 8

[Jmol-users] Note re NIH Resolver and Jmol

be possible with the signed applet. Am I correct on this Bob? Otis -- Otis Rothenberger chemagic.com -- Sell apps to millions through the Intel(R) Atom(Tm) Developer Program Be part of this innovative community and reach

Re: [Jmol-users] Mac User Request and NIH site

) They welcome the correction of errors. Consequently, I'll just keep passing them on. I will definitely mention the hexose issues. I picked Markus' name at random, but it looks like he is the go to guy on the Chemical Identifier Resolver. Otis Otis Rothenberger chemagic.com

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