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

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] 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] 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

[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] 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

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] 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] 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

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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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

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] 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] 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] 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] 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] 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?

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] 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

[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] 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

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] 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] 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] 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] 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

[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] 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 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] 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

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] 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

[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

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

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] 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] 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] 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] 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

[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] 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

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

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

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] 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

[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] 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

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

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

? > > 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 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] 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

[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] 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

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] 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] 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] 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] 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

[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] "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

[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] 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

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] 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 4:49 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] 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

[Jmol-users] Fwd: Re: Chime's superset of RasMol script commands & reference manuals

like tweening and key frames, for example, that would be a wonderful paradigm shift in molecular animations. regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization <http://www.molvisions.com/> usa:north carolina:wake forest

Re: [Jmol-users] JmolApplet Wish List

oftware. that being said, I do support software applying default rules in the absence of data from a file. I just don't think it should override. I don't know enough about JMol yet to know what it does, but I cc'd your message to the developer list. regards, :tim -- ti

Re: [Jmol-users] nucleic acid bases wanted

t. for example, compare the RNA in 1CX0 and the DNA in 1d66. in addition, there are structures for many DNA:RNA hybrids, and it would quite useful to be able to easily distinguish between the two nucleic acids within the same file. regards, :tim (who is building his first JMol We

[Jmol-users] JMol applet from javascript - a few comments

with the data stream. these are invaluable hooks for developing dynamic mol vis Web sites. any chance to implement something similar in JMol? regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization <http://www.molvisions.com/>

Re: [Jmol-users] JMol applet from javascript - a few comments

. > 'yet' implies it will be at some point? that would be cool. > > I strongly recommend that you switch to using Jmol v10pre1. > I did, and I updated my site. thanks, :tim -- timothy driscoll molvisions - molecular graphics & visualization <http://www.molvisions.com/&

Re: [Jmol-users] JMol applet from javascript - MessageCallback

edu/microbio/chime/chimehow/fs_cmdln.htm > IIRC, if you send a long script to Chime, the messages returning are scrambled (IOW, not in the same order as they went to Chime). I don't recall the details, and maybe this has no bearing on JMol - maybe Paul can say more? regards, :tim --

Re: [Jmol-users] help needed with 1HIV.pdb file format

all > the HOH molecules which also make up a chain (from a file format > perspective). > possible tests for validity: is it one of the standard residues? does it have a CA? is it in the correct position in the atom records? is it defined in the SEQRES rec

[Jmol-users] using latest applet build?

who spends too much time in interpreted languages. :-) :tim -- timothy driscoll molvisions - molecular graphics & visualization <http://www.molvisions.com/> usa:north carolina:wake forest --- This SF. Net email is sponsored by:

Re: [Jmol-users] callbacks do not work on OSX

t started converting major resources from Chime to JMol is the OSX problem. regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization <http://www.molvisions.com/> usa:north carolina:wake forest --- This S

Re: [Jmol-users] How to get the latest development version ...

again > > cd your-favorite-path-to/Jmol-HEAD > cvs up -dP > > 'up' stands for 'update' > '-dP' says 'look for new directories and Prune unused stuff' > > I see a dir called appletweb with various applet files like JmolApplet.prop

Re: [Jmol-users] JMol applet from javascript - MessageCallback

he distribution - a routine that parses the psbheader info. is that better? [...] > Down the road we will have the chance to define/build one or more 'Jmol > scripting langages' that are better suited for web application > development ... in JavaScript and/or PHP and/or Python an

Re: [Jmol-users] what is a ligand?

has vitamin B6 (group PLP) bound to a Lys in chain A: <http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1D2F> regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization <http://www.molvisions.com/> usa:north carolina:wake forest -

Re: [Jmol-users] JMol applet from javascript - MessageCallback

here a student must click on an atom in the 3D structure to answer the question (for example, click on the backbone of any polar amino acid). being able to access atom properties directly from pickcallback would be very helpful here. I have also used pickcallback to modify the currently s

[Jmol-users] JMol button without javascript - how?

:tim -- timothy driscoll molvisions - molecular graphics & visualization <http://www.molvisions.com/> usa:north carolina:wake forest --- This SF. Net email is sponsored by: GoToMyPC GoToMyPC is the fast, easy and secure way to access you

[Jmol-users] Re: [Jmol-developers] JMol button without javascript - how?

e any such beast for the JMol button? I tried state="true" but that did not work. thanks, :tim -- timothy driscoll molvisions - molecular graphics & visualization <http://www.molvisions.com/> usa:north carolina:wake forest at 6:12 pm EDT on (Tuesday) 18 November 2003

Re: [Jmol-users] chime2jmol

odate entire scripts post haste). you should see the effect on the 3D structure, and the response of JMol in the output textarea (sorry but this does not yet work in OSX browsers - it will very soon, I hope). if any commands don't work, you can request that they be supported. hope that help

[Jmol-users] Re: immediate button behavior

ng? > would it be different from changing the type from "immediate" to "button"? regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization <http://www.molvisions.com/> usa:north carolina:wake forest

Re: [Jmol-users] scale3d questions

support implementing them as script commands. (I assume the chime2jmol.pl script would take these from the embed tag and add them to the script param?) :tim -- timothy driscoll molvisions - molecular graphics & visualization <http://www.molvisions.com/> usa:north carolina:wake forest

[Jmol-users] Re: [Jmol-developers] JMol button without javascript - how?

mail. > no problem - send it along and I will confirm it works. this type of implementation would be an *enormous* help to OSX users until Apple fixes LiveConnect. thank you!! regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization <http://www.molvisions.com/&

[Jmol-users] debugging jmol in Safari

. regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization <http://www.molvisions.com/> usa:north carolina:wake forest --- This SF.net email is sponsored by: SF.net Giveback Program. Does SourceForge.net help y

Re: [Jmol-users] primitives RasMol script compatibility

tor: *;B (no wildcard) > Model: */1 (no wildcards but /0) > Wildcards: **:*./0 > > The Insertion code is really important and I'm very sad about the lack of a primitive for it, but RasMol in contrary to Jmol > is able to deal with it (there must be an inter

Re: [Jmol-users] primitives RasMol script compatibility

hi Egon, at 11:46 am EDT on (Thursday) 20 November 2003 E.L. Willighagen said: > On Thursday 20 November 2003 11:28, timothy driscoll wrote: > > > > There is currently not a good mechanism in Jmol to support > > > > alternate locations. Therefore, I will modify the

Re: [Jmol-users] primitives RasMol script compatibility

is is true, don't they belong in a separate structure file altogether? sorry; the insertion code property is not familiar to me (or maybe it is, but the terminology is not). can you please explain it a little more? thanks, :tim -- timothy driscoll molvisions - molecular graphics & visualizati

Re: [Jmol-users] primitives RasMol script compatibility

. ;-) > - nobody is paying me any money > - I am doing this for fun :-) > I hope it still is! I just got here... > - I would *love* to have someone maintain the priority list for me > I will be happy to volunteer, based on my own experience and feedback from the user and developer

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