Re: [Jmol-users] Definitions

d be the definitive authority on this topic, though it's likely that Bob would know, too. I only point this out because OP confessed to writing a manuscript, and it's probably good to be clear on this point in any publication. happy new y

Re: [Jmol-users] Jmol/ChemDoodle

On Apr 6, 2012, at 4:49 pm, Kevin Theisen wrote: > Of course, as development continues, WebGL and Javascript will continue to > get faster, graphics cards will be handled and removed from blacklists, WebGL > will appear in more browsers on more machines, and ChemDoodle will have more > and more

Re: [Jmol-users] Jmol/ChemDoodle

On Apr 6, 2012, at 4:32 pm, Robert Hanson wrote: > > Chrome is the same, except Chrome has software rendering, allowing for WebGL > pretty much everywhere. > > > OK, I get it. So Chrome's WebGL is a fake, essentially, and that explains why > it is absolutely destroying my battery life right n

Re: [Jmol-users] Jmol/ChemDoodle

On Apr 6, 2012, at 4:01 pm, Philip Bays wrote: > I have looked at the page on my Mac (Snow Leopard). It does not work with > Safari, Camino, or omniweb, but does work with Firefox and Chrome. I get the > same black image with the web GL message. I think the browser-compatiobility > page is o

Re: [Jmol-users] OSX Java vulnerability

it didn't come through. sorry about that. cheers, tim > On Apr 5, 2012, at 10:11 AM, Timothy Driscoll wrote: > >> <http://arstechnica.com/apple/news/2012/04/flashback-trojan-reportedly-controls-half-a-million-macs-and-counting.ars> >> >> Flashback trojan reporte

[Jmol-users] OSX Java vulnerability

Flashback trojan reportedly controls half a million Macs and counting By Jacqui Cheng | Published about 16 hours ago Variations of the Flashback trojan have reportedly infected mo

Re: [Jmol-users] "Jmol" for iPads?

> On Mar 23, 2012, at 3:33 PM, Eric Martz wrote: > >> I just heard a segment on NPR about hundreds of high schools that are >> abandoning textbooks and giving every student an iPad instead. As we >> all know, iPads will not run java and so will not run Jmol. What are >> people's thoughts on por

Re: [Jmol-users] Jmol.app default dir in OS X?

On Jan 18, 2011, at 12:34 PM, Fco. Javier Modrego wrote: > May this is of some help, > I use to bundle the jar into double clickable mac app using the instructions > in http://www.devdaily.com/apple/mac/java-jar-bundler/ nevertheless this does > not solve the working dir issue. > I think that t

Re: [Jmol-users] Fwd: Java 1.5

On Apr 28, 2010, at 10:10 AM, Egon Willighagen wrote: > On Wed, Apr 28, 2010 at 3:59 PM, Robert Hanson > wrote: >> I propose that Jmol 12.0 officially require Java 1.5. This will >> allow easy >> expansion of several features, including parallel processing, which >> we just >> introduced fo

Re: [Jmol-users] displaying multiple models

On Dec 2, 2009, at 1:33 pm, Brian Moldover wrote: > So do you load the pdb file multiple times? I’m reading the > documentation but obviously not clear on how to do this or I > wouldn’t have asked J > yes, you can load the same pdb file in multiple applets, and restrict to different models i

[Jmol-users] Jmol in BioHealthBase

Just found Jmol running on a nice Web site here: http://www.biohealthbase.org/ tim -- earth:usa:virginia:blacksburg I am behindtherabbit: del.icio.us | last.fm | mojo | twitter | www | brightkite - This SF.net email is spon

Re: [Jmol-users] memory allocation

pper.tanukisoftware.org/doc/english/properties.html> (fair warning: while the link was working 5 minutes ago, it is currently offline ) > not sure if I helped or not. :-) tim -- Timothy Driscollem: [EMAIL PROTECTED] Virginia Bioinformatics Instit

Re: [Jmol-users] Exploring the limits

, you could make this more sophisticated.) just a thought. tim -- Timothy Driscollem: [EMAIL PROTECTED] Virginia Bioinformatics Institute ph: 540-231-3007 Bioinformatics I: M-1 im: molvisions Washington St., Blacksb

Re: [Jmol-users] Loading several models at once

;t speak to other systems; sorry. tim -- Timothy Driscollem: [EMAIL PROTECTED] Virginia Bioinformatics Institute ph: 540-231-3007 Bioinformatics I: M-1 im: molvisions Washington St., Blacksburg, VA 24061 04-16-07

Re: [Jmol-users] using color scheme with external data file

On Oct 30, 2007, at 5:06 PM, Timothy Driscoll wrote: > hi, > > I am using an external data file to apply a roygb color scheme to a > set of atoms. a snippet from an example data file looks like this: > apologies; please ignore. this is a duplicate message. tim -- T

Re: [Jmol-users] do color schemes fail with large data ranges?

On Oct 31, 2007, at 11:33 AM, Angel Herraez wrote: > El 31 Oct 2007 a las 10:37, Timothy Driscoll escribió: >> Bob, can you explain how Jmol assigns colors in the case of an >> external data set? for example, the roygb scheme. I assume Jmol >> breaks up the entire da

Re: [Jmol-users] do color schemes fail with large data ranges?

On Oct 31, 2007, at 4:09 AM, Bob Hanson wrote: > Timothy Driscoll wrote: > >> hi, >> >> I am using an external data file to apply a roygb color scheme to a >> set of atoms. a snippet from an example data file looks like this: >> snip >> >> my Jmol

[Jmol-users] do color schemes fail with large data ranges?

o 5-10 categories first. perhaps even log-transform them. this will require a bit of work, though, so I thought I would float it on the list first. can anyone confirm this hypothesis? thanks! tim -- Timothy Driscollem: [EMAIL PROTECTED] Virginia Bioinfor

Re: [Jmol-users] Jmol 11.3.9 -- symmetry "range" and applet synchronization

ing, desired behavior). the only glitch I have found so far is that 'spin' turns on spinning in both applets, but the right-hand applet quickly falls out of synch with the left (within 15-20 seconds or so). issuing a 'spin off' stops the left side, but does *no

Re: [Jmol-users] mouse synch command vs structure alignment

sier to compare multiple characteristics between structures. tim -- Timothy Driscollem: [EMAIL PROTECTED] Virginia Bioinformatics Institute ph: 540-231-3007 Bioinformatics I: M-1 im: molvisions Washington St., Blacksb

Re: [Jmol-users] mouse synch command

? > > How does one recognize which applet is the controller applet, and > which are followers? > > What happens when a new file gets loaded in one of the applets? > > > Timothy Driscoll wrote: > >> >> hmm. are you listing these as programming issues that must

Re: [Jmol-users] mouse synch command

On May 23, 2007, at 6:59 PM, Bob Hanson wrote: > Timothy Driscoll wrote: >> >>> But if you can figure out a scheme that would be reasonable in >>> terms of >>> setting up this function wihtin Jmol -- I would want it to be >>> possible >>> to

Re: [Jmol-users] mouse synch command

hen I can see if I can implement it. Maybe some interesting > issues there. I can think about it, sure. I don't really see a problem with synching all applets on a page; that would be much simpler anyway. best, tim -- Timothy Driscollem: [EMAIL PROTECT

Re: [Jmol-users] mouse synch command

e events to another target Chime plug-in true - send mouse events to another target Chime plug-in " > Timothy Driscoll wrote: > >> hi, >> >> does Jmol implement an equivalent to the Chime synch parameter? in >> Chime, synch gave the user mouse control of *al

[Jmol-users] mouse synch command

even though I seem to remember recent discussion on this topic, I found nothing relevant. many thanks, tim -- Timothy Driscollem: [EMAIL PROTECTED] Virginia Bioinformatics Institute ph: 540-231-3007 Bioinformatics I: M-1 im

Re: [Jmol-users] Reg. loading Ligand pdb files directly from pdb

RROR: java.io.IOException >> >> load >> "=111.pdb" << >> Script completed >> Jmol script terminated/_ >> // >> Please help me.... >> also, looking at the error message, you don't need to pass the extension

Re: [Jmol-users] apply matrix to 3D coords

for real. I'm trying to get from the original coords and the matrix, to the transformed coordinates. (in this particular case, I do know the transformed coordinates, but only because I'm trying to work out the equations. normally I will not know them in advance.) tim -- Tim

Re: [Jmol-users] apply matrix to 3D coords

think that... > Unless they also applied a zoom > but I have no other data from the operation other than the matrix, and the two coordinate sets. tim -- Timothy Driscollem: [EMAIL PROTECTED] Virginia Bioinformatics Institute ph: 540-231-3

Re: [Jmol-users] apply matrix to 3D coords

0.521-0.484 0.703 0.626-0.342 -0.7 > > Timothy Driscoll wrote: > >> On May 10, 2007, at 3:54 PM, Bob Hanson wrote: >> >> >>> This is always a royal pain to get right. Certainly looks like a >>> rotation matrix to me. >>&g

Re: [Jmol-users] apply matrix to 3D coords

e on transformation matrices but most of them are 4x4, not 3x3? anyway, I'll keep looking. tim > > Timothy Driscoll wrote: > >> hi, >> >> I have two structures that I have aligned using a program called >> MUSTANG. the program gives me a 3x3 transfo

[Jmol-users] apply matrix to 3D coords

the coordinate system of the first, I am told that I should apply this matrix to the xyz coords of the second. I thought this could be done via a simple matrix multiplication, but apparently not. can anyone please suggest a reference that deals with this? thank you, tim -- Timothy Driscoll

Re: [Jmol-users] 11.1.36

; zoomTo 2.0 (His89) 0 > > it zooms to the "natural" zoom setting for that group. > this works quite well. I've tried it in a number of different structures. nice! tim -- Timothy Driscollem: [EMAIL PROTECTED] Virginia Bioinformatic

Re: [Jmol-users] slab/depth in more than one direction

On May 4, 2007, at 4:23 PM, Bob Hanson wrote: > Timothy Driscoll wrote: > >> On May 4, 2007, at 1:40 PM, Bob Hanson wrote: >> >> >>> You can slab and depth ATOMS in any number of directions based on >>> miller >>> planes or any other sort

Re: [Jmol-users] slab/depth in more than one direction

surface point with the nearest atom and handle it that way? tim -- Timothy Driscollem: [EMAIL PROTECTED] Virginia Bioinformatics Institute ph: 540-231-3007 Bioinformatics I: M-1 im: molvisions Washington St., Blac

Re: [Jmol-users] forget 11.1.30 -- 11.1.31 is better -- Re: color-mapping fails in 11.1.30

sounds fantastic. this feature will be immensely useful for my current project! I'll let you know when it is ready for primetime. thanks Bob, tim -- Timothy Driscollem: [EMAIL PROTECTED] Virginia Bioinformatics Institute ph: 540-2

Re: [Jmol-users] color from external dataset FOLLOWUP

dat file is written, it can't be used >> for any other set of atoms. I think your idea above would be an >> excellent refinement that would solve both of these problems. >> > > Sure, I see. Then we definitely need those atom numbers in the file. > Do you like the idea o

Re: [Jmol-users] color from external dataset FOLLOWUP

it can't be used for any other set of atoms. I think your idea above would be an excellent refinement that would solve both of these problems. thanks Bob, tim -- Timothy Driscollem: [EMAIL PROTECTED] Virginia Bioinformatics Institute

[Jmol-users] link echo to frame?

, have the echo display only when that frame is visible? if it matters, I am loading multiple files using: load files "file1" "file2" ... thanks! tim -- Timothy Driscollem: [EMAIL PROTECTED] Virginia Bioinformatics Institute

Re: [Jmol-users] color from external dataset FOLLOWUP

explicit atomno:value syntax in the data file, and have Jmol ignore values for atoms that are not in the selected set. kudos for great work, tim -- Timothy Driscollem: [EMAIL PROTECTED] Virginia Bioinformatics Institute ph: 540-231-3007 Bioinf

Re: [Jmol-users] signed applets

t files in the applet tag. as far as signing it, I don't know how that is done. sorry; I'm not much help. tim -- Timothy Driscollem: [EMAIL PROTECTED] Virginia Bioinformatics Institute ph: 540-231-3007 Bioinformatics I: M-1

Re: [Jmol-users] signed applets

On May 2, 2007, at 8:14 PM, Bob Hanson wrote: > I looking for someone who is using the signed applet. > hi Bob, I have used it, though rarely. tim -- Timothy Driscollem: [EMAIL PROTECTED] Virginia Bioinformatics Institute ph: 540-23

[Jmol-users] color by occupancy

hi, is there a Jmol command to apply a color scheme using the occupancy column of a pdb file? something akin to color temperature I looked through the script doc but didn't see anything immediately apparent. thanks, tim -- Timothy Driscollem: [

Re: [Jmol-users] color from external dataset

s ""), I guess I can load different datasets - I'll give this a try in the morning... definitely intrigued to see this in action. especially applied to cavity isosurfaces, my "Jmol Feature of the Month" for March. regards, tim -- Timothy Driscoll

[Jmol-users] color from external dataset

e-3 > -2.54 3 6 > etc. I grasp how to load the external dataset into Jmol, but how do I associate a particular charge with the correct atom? for example: atomnum charge 1-0.33 2 0.32 3 0.55 4 -0.55 5 0 thanks for any help, tim -- Timothy Driscol

Re: [Jmol-users] 11.1.28 javascript command option could be useful

r's point of view. Jmol (thanks to its dedicated developer group!) has internalized some of what I used to do in javascript, but still. this is a very useful ability indeed. tim -- Timothy Driscollem: [EMAIL PROTECTED] Virginia Bioinformatics Instit

Re: [Jmol-users] Jmol button experiments

. and the cavities are generated separately for each model in the animation - fantastic! I like the clickable text. that is a great feature for users. is there any chance at a mouseover event option as well? it would be icing on the cake. :-) tim -- Timothy Driscoll

Re: [Jmol-users] two more minor issues

, I routinely run Jmol with a max heap size of 1024mb: java -Xmx1024m -jar /local/java/jmol/Jmol/build/Jmol.jar I don't know how to do this for applets; sorry. hope that helps, tim -- Timothy Driscollem: [EMAIL PROTECTED] Virginia Bioinformatics Institute

Re: [Jmol-users] page design: flexible size, scrollable, no frames

ng. this is mostly an issue with the float property; the divs are forced into strange positions. I have access to a projector so I can investigate this issue on monday. regards, tim -- Timothy Driscollem: [EMAIL PROTECTED] Virginia Bioinformatics Institute

Re: [Jmol-users] isosurfaces and the new translucency

I noticed this, too, and logged it as a bug a few days ago. select nucleic should work instead, if you want a quick fix. regards, tim -- Timothy Driscollem: [EMAIL PROTECTED] Virginia Bioinformatics Institute ph: 540-231-3007 Bioi

Re: [Jmol-users] Jmol 11.1.21 better translucency

instead of by size. in addition, one can now set levels of translucency relative to distance form the protein surface - giving a tunneling effect. can't wait to play around with this more! thanks, Bob (and Miguel, and all). tim -- Timothy Driscoll

[Jmol-users] a 3D search engine?

icle quotes Henry Rzepa, which means it must be on-topic as well as authoritative. :-) tim -- Timothy Driscollem: [EMAIL PROTECTED] Virginia Bioinformatics Institute ph: 540-231-3007 Bioinformatics I: M-1 im: molvisions Wa

Re: [Jmol-users] investigating the top menu on app

save a script from the app?) just a thought, prompted by Bob's comment that he only uses the app for script development: it would be cool if Jmol had a built-in script editor - a user could open a script file in Jmol, edit it, run it, run only pieces of it, even debug it, all in Jmol. t

Re: [Jmol-users] jme mole files ? in Jmol?? or code?

can post? or can you send me the source php off-list? best, tim -- Timothy Driscollem: [EMAIL PROTECTED] Virginia Bioinformatics Institute ph: 540-231-3007 Bioinformatics I: M-1 im: molvisions Washington St., B

Re: [Jmol-users] jme mole files ? in Jmol?? or code?

6 7 1 0 > M END > ">';; > > > > jmolInitialize("java/jmol"); > jmolApplet(300); > jmolLoadInline(mol); > > > > Paul > > Research Technician > Mass Spectrometry >o The > / > o Scripps > \ >o Research >

Re: [Jmol-users] jme mole files ? in Jmol?? or code?

off the cuff, you may need some quotes around the value for mol, like this: > var mol = > if ($data['molfile']) > echo '\' \n/", "|", > $data['molfile']) . '">\';'; > ?>; > > var mol = >

Re: [Jmol-users] image flash with moveto

thing similar from Chime. in any case, a quick fix might be to issue 'restrict none' immediately after the 'load' command. regards, tim -- Timothy Driscollem: [EMAIL PROTECTED] Virginia Bioinformatics Institute ph: 540-231-3007 B

Re: [Jmol-users] some advice regarding Jmol, Javascript & PHP

On Oct 26, 2006, at 1:38 PM, Angel Herraez wrote: > Timothy Driscoll answered to Rajarshi Guha: > >>> * Since Jmol cannot show multiple structures, I need to convert >>> my SDF >>> to PDB and concatenate it to the protein PDB. Is this correct? >>> &

Re: [Jmol-users] some advice regarding Jmol, Javascript & PHP

ates, like this: this has worked for me in the past. just be sure to append each line with a bar (|) to fit the syntax for loadinline. hope that helps, tim -- Timothy Driscollem: [EMAIL PROTECTED] molvisions - see. grasp. learn. ph: 919-368-

Re: [Jmol-users] Validate with Jmol

ng. an idea: is it possible for Jmol to echo error messages to the applet space itself? that would be the most obvious, in my opinion, and certainly less annoying than a popup. tim -- Timothy Driscollem: [EMAIL PROTECTED] molvisions - see. gras

Re: [Jmol-users] Building unit cells with Jmol 11

On Oct 20, 2006, at 3:46 PM, Patrick J. Carroll wrote: > > I need a small (?) amount of javascript help. Is there a way to > tell which > menu item in a jmolMenu has been selected? I am dealing with > selecting a > symop from a jmolMenu and then applying a translation to that symop by > selecti

Re: [Jmol-users] Validate with Jmol

On Oct 20, 2006, at 10:14 AM, [EMAIL PROTECTED] wrote: >> Thank You for this one!!! And half way on the road. >> There is a slight drawback with this solution. Each time >> my generated script contains an error, detected by Jmol, >> the execution stops with a compileError: >> >> --* console start *

Re: [Jmol-users] 10.9.80 fails if the Hall or H-M symbol contains underscores?

;it just works". But without that effort the program > wouldn't be > any where near as functional. Your work is deeply appreciated. > hear, hear! heartily seconded. tim -- Timothy Driscollem: [EMAIL PROTECTED] Virginia Bioinformatics I

Re: [Jmol-users] issue with message callbacks and internationalization

On Oct 13, 2006, at 11:29 AM, Bob Hanson wrote: > Let's think about this: > > 1) We want translations, certainly. > 2) Lots of us hack the message stream or message reports to respond to > user or other events. > 3) We have an established set of pages we don't want to break. > > Options: > > 1) no

Re: [Jmol-users] Selecting Amino Acids?

e, you can: select (leu, ala, val, ile, met) # or select :A and (leu, ala, val, ile, met) hope that helps! tim -- Timothy Driscollem: [EMAIL PROTECTED] molvisions - see. grasp. learn. ph: 919-368-2667 <http://www.molvisi

Re: [Jmol-users] pause/resume

sume) command via javascript or the Console, by itself, and it will pause (quit, exit,resume) the loop. is that right? tim -- Timothy Driscollem: [EMAIL PROTECTED] Virginia Bioinformatics Institute ph: 540-231-3007 Bioinformatics I: M-

Re: [Jmol-users] new command-line options; jmol writes JVXL files directly

On Sep 26, 2006, at 5:48 PM, Bob Hanson wrote: > new command: > > write JPEG|PNG|PDF "filename.xxx" > > so you have that in your script file, you do NOT use the "noDisplay" > option, and there you go! > > Any objection to "write"? > sorry; late to this corner of the party. should this not be 'exp

Re: [Jmol-users] Jmol - deuterium and tritium - colors

On Sep 23, 2006, at 8:35 AM, Angel Herraez wrote: > Hi > > After Eric's post on Jmol "lots of bugs", Bob has added support for > deuterium and tritium --in fact, for any isotopes--. He has chosen > to assign > them helium and lithium colors. > I have proposed on jmol-developers that unique color

Re: [Jmol-users] Lots of bugs in Jmol: fix some before v11?

On Sep 23, 2006, at 9:59 AM, Bob Hanson wrote: > >> Jmol fails to connect some atoms with covalent bonds where there >> should be >> connections. >> >> > This is an intended feature, not a bug. In many PDB/mmCIF files, the > author has explicitly defined quite a number of bond connections using >

Re: [Jmol-users] Prerelease 10.9.62

. :-( the two pages look the same to me. perhaps a local caching issue? tim -- Timothy Driscollem: [EMAIL PROTECTED] molvisions - see. grasp. learn. ph: 919-368-2667 <http://www.molvisions.com/>im: molvisions usa:vir

Re: [Jmol-users] Amino acids in "protein"-selection

inition, I'm all ears. But my understanding it's a > catch-all > term mostly meaning "greasy". > Miguel and I discussed lipid when we implemented the special atoms for other molecule types, but we could not hit upon a 'standard'

Re: [Jmol-users] Amino acids in "protein"-selection

On Sep 21, 2006, at 1:01 PM, Timothy Driscoll wrote: > if I recall correctly, Jmol does not use the group name to determine > membership in the pre-defined set 'protein.' it uses a minimum set > of atoms (i.e., N, C, O, CA). so as long as modified residues still > use the

Re: [Jmol-users] Amino acids in "protein"-selection

, O, CA). so as long as modified residues still use the standard nomenclature for backbone atoms, they should be included in 'protein' already. is this not happening? or am I wrong about Jmol's behavior here? best, tim -- Timothy Driscoll

Re: [Jmol-users] [Jmol-developers] [Fwd: updated Jmol.js library documentation]

ards compatible with Jmol.js, of course. best, tim -- Timothy Driscollem: [EMAIL PROTECTED] molvisions - see. grasp. learn. ph: 919-368-2667 <http://www.molvisions.com/>im: molvisions usa:virginia:blacksburg

Re: [Jmol-users] save orientation (Was: Problems with "load "";")

I agree with Angel's comments above. also, possible to implement a "moveto orientation" function? seems like a natural outgrowth of restore. best, tim -- Timothy Driscollem: [EMAIL PROTECTED] molvisions - see. grasp. learn. p

[Jmol-users] save orientation (Was: Problems with "load "";")

worth checking out. I'll try to look it up in the next day, unless someone else is faster... tim -- Timothy Driscollem: [EMAIL PROTECTED] molvisions - see. grasp. learn. ph: 919-368-2667 <http://www.molvisions.com/>

Re: [Jmol-users] jmol and space groups

uot; does it of course. (I knew it was a dumb question >> - sorry). Alan. >> >> >> > actually, not. True "unrestrict" is not possible, since "restrict" > wipes > out any previous spacefill and wireframe size information. I'm still > thinking

Re: [Jmol-users] Mac Safari Question

rary/Internet Plug-Ins folder and for some reason, that mucked up my applets (all plug-ins, actually). I deleted the Plug- Ins folder in my user library and everything worked fine. so, you might try that. hope it works! tim -- Timothy Driscollem: [EMAIL

Re: [Jmol-users] Mac Safari Question

I am running 10.4.7 on a MacBook, and I can load Jmol in Safari without trouble (from http://jmol.sourceforge.net/). it sounds like a site issue; can you provide a url to test that does not work for you? regards, tim -- Timothy Driscollem: [EM

Re: [Jmol-users] centering with motion

desire. 3. in the Jmol Console, issue the command: show orientation. 4. copy and paste the 'moveto' part of the response to 3 in your script. the moveto will move the molecule from any position to the position defined in 2 using a smooth motion. hope that helps, tim -- Timothy Dri

Re: [Jmol-users] Hydrogens in pentose: sidechain or backbone?

uot;, // 59 - 3' terminus hydrogen so all of these hydrogens should be selected if you say select nucleic and backbone protein backbone Hs are determined in similar fashion. is it possible that your pdb file did not use these atom identifiers? tim -- Timothy Driscoll

Re: [Jmol-users] Hydrogens in pentose: sidechain or backbone?

uish backbone from non- backbone hydrogens, without resorting to work-arounds like the one above. I would hence vote for assigning H atoms to backbone set when they are bound to backbone C, N, O atoms. Opinions? so this is also a problem with the protein set as well? I

Re: [Jmol-users] save orientation?

set; rotate x -35.1; rotate y -58.6; rotate z 18.5;" Bob, I knew if I mentioned your name often enough, you would provide a better solution. :-) I would certainly recommend the above in lieu of callbacks; although I have never had trouble with callbacks myself, they are problemat

Re: [Jmol-users] save orientation?

L PROTECTED] On Behalf Of Timothy Driscoll Sent: Monday, May 22, 2006 10:50 PM To: jmol-users@lists.sourceforge.net Subject: Re: [Jmol-users] save orientation? On May 22, 2006, at 10:23 p, Samuel Flores wrote: Hi Guys, I'm trying to write some code to let the viewer rotate the molecule to their

Re: [Jmol-users] save orientation?

Bob's arsenal). the command gives a well-formed string that is easily parsable. hth, tim -- Timothy Driscollem: [EMAIL PROTECTED] Virginia Bioinformatics Institute ph: 540-231-3007 Bioinformatics Iim: molvisions

Re: [Jmol-users] FirstGlance 0.991 Released

lue >= 2. yes, I encountered this a while ago as well. it is returned as an Object, not a string. and, a word to the wiser ;-), you *must* force it to a string using the + operator, as Eric describes. no other method works. best, tim -- Timothy Driscoll

Re: [Jmol-users] offset for echo?

On May 10, 2006, at 2:07 a, Bob Hanson wrote: Timothy Driscoll wrote: hi all, anyone know if there is an offset for echo, akin to labeloffset? I found nothing in the script doc, and I tried some obvious commands without success (well, obvious to me anyway ;-). thanks! tim no

[Jmol-users] offset for echo?

hi all, anyone know if there is an offset for echo, akin to labeloffset? I found nothing in the script doc, and I tried some obvious commands without success (well, obvious to me anyway ;-). thanks! tim -- Timothy Driscollem: [EMAIL PROTECTED] Virginia

Re: [Jmol-users] bug or not a bug -- select within()

On May 9, 2006, at 5:21 p, Nicolas Vervelle wrote: Timothy Driscoll wrote: On May 9, 2006, at 4:08 p, Nicolas Vervelle wrote: as one example, it makes scripting multi-model animations much easier. for instance, I can use this script: select all spacefill 30% wireframe 0.25 select within

Re: [Jmol-users] bug or not a bug -- select within()

with just a few script commands, how the binding site for a ligand behaves across different models. this would be more difficult if within were restricted by model. not impossible, but not as elegant in my opinion. best, tim -- Timothy Driscollem: [

Re: [Jmol-users] bug or not a bug -- select within()

ld do just what it does now. in other words, I don't think it is a bug. :-) tim -- Timothy Driscollem: [EMAIL PROTECTED] molvisions - see. grasp. learn. ph: 919-368-2667 <http://www.molvisions.com/>im: molvisions

Re: [Jmol-users] troubles rendering DNA backbone in Jmol

o the script doc, perhaps where the predefined atoms sets are discussed. unless it is in there already and I just missed it. :-) thanks again, tim -- Timothy Driscollem: [EMAIL PROTECTED] molvisions - see. grasp. learn. ph: 919-

Re: [Jmol-users] trouble selecting an atom [was] Re: [Jmol-users] selecting atom IDs such as 1h47

On May 7, 2006, at 2:21 p, Bob Hanson wrote: Timothy Driscoll wrote: can Jmol support both versions (HG11 and 1HG1) without converting between them? If by "can" you mean "could" -- Yes, absolutely. It all has to do with recognizing what's a number and what'

Re: [Jmol-users] trouble selecting an atom [was] Re: [Jmol-users] selecting atom IDs such as 1h47

macromolecules, while it should not necessarily be promoted, it should be supported. (someone please feel free to correct me, of course.) I'm pretty sure that is what Miguel is saying above; I just wanted to add my comments. best, tim -- Timothy Driscoll

Re: [Jmol-users] trouble selecting an atom

way you might expect to finish off a name -- ack. I did expect that... before tonight, that is. ;-) select T*.;color yellow #does NOT work. You have to use ?s ok, very good. thanks, Bob. tim -- Timothy Driscollem: [EMAIL PROTECTED] molvisions - see. grasp

Re: [Jmol-users] trouble selecting an atom

On May 6, 2006, at 11:41 p, Bob Hanson wrote: Timothy Driscoll wrote: would it be possible to add to the script doc a brief description of how to use 'wildcard' characters (*, ?, others) in atom expressions? this might prove useful for others as well. If I knew how to use

Re: [Jmol-users] trouble selecting an atom

On May 6, 2006, at 11:14 p, Bob Hanson wrote: Timothy Driscoll wrote: hi all, I seem to have run into a slew of problems lately. sorry for so many pleas for help. I have a pdb file (ATP) that contains several atom records in the following format: HETATM 42 1HN6 ATP 1

Re: [Jmol-users] trouble selecting an atom

On May 5, 2006, at 10:52 p, Timothy Driscoll wrote: I have a pdb file (ATP) that contains several atom records in the following format: HETATM 42 1HN6 ATP 1 5.276 3.765 1.510 1.00 0.00 as far as I can tell, this is valid pdb format. I should be able to select the above

Re: [Jmol-users] trouble selecting an atom

t it takes. :-( best, tim -- Timothy Driscollem: [EMAIL PROTECTED] Virginia Bioinformatics Institute ph: 540-231-3007 Bioinformatics Iim: molvisions Washington St., Blacksburg, VA 24061 "Anyone who considers arith

[Jmol-users] trouble selecting an atom

format. I should be able to select the above atom with this kind of expression: select *.1HN6 but Jmol throws a script error (end of expression expected). can anyone tell what I am doing wrong? many thanks for any help, tim -- Timothy Driscollem: [EMAIL

[Jmol-users] troubles rendering DNA backbone in Jmol

anks, tim -- Timothy Driscollem: [EMAIL PROTECTED] molvisions - see. grasp. learn. ph: 919-368-2667 <http://www.molvisions.com/>im: molvisions usa:virginia:blacksburg tx: [EMAIL PROTECTED] "

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