Re: [Jmol-developers] 20,000 commits

Wow! On Mon, Apr 13, 2015 at 5:42 PM, Robert Hanson wrote: > Just noticed that we are at revision # 20,448. > > -- > Robert M. Hanson > Larson-Anderson Professor of Chemistry > Chair, Department of Chemistry > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr > > > If natur

Re: [Jmol-developers] Fwd: Any way to speed up Jmol Android?

> The Canvas in Android only uses the phone's CPU and not GPU. The Canvas code is only used to blit a pre-formed RGB image to the screen. The issue is probably that Jmol itself consumes CPU while rendering the frames. > It would be a massive rewrite of Jmol to fully implement OpenGL. I agree tha

Re: [Jmol-developers] speed tests

Chrome Version 24.0.1312.56 Mac OS X http://chemapps.stolaf.edu/jmol/jsmol/j2s/test/test_replace.htm Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko) Chrome/24.0.1312.56 Safari/537.17 5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.17 (KHTML, like Gecko)

Re: [Jmol-developers] high priority problem

Hmmm ... very strange. When you say "compiled on a PC" ... Q: Do you know if the build is taking place in Eclipse? I'm not sure what kind of effect this would have, but it is a factor *** 2 minutes later *** Here is my theory: Jmol uses an independently-developed implementation of javax.Poin

Re: [Jmol-developers] surfaces... volume too?

On Tue, Jun 7, 2011 at 12:52 PM, Egon Willighagen wrote: > Hi Miguel! > > On Tue, Jun 7, 2011 at 6:18 PM, Miguel Howard wrote: >> Actually, I did the original marching cubes implementation. > > Oops, sorry! No problem :) > (and cool that you are still listening in!

Re: [Jmol-developers] surfaces... volume too?

Actually, I did the original marching cubes implementation. With all the work that Bob did on surfaces he may have ended up redoing it. My recollection is that it did *not* calculate volume. However, it seems to me that it would be straightforward to do. I suspect that any "partial" boxes could be

Re: [Jmol-developers] Jmol applet not running in Chrome 8.0.552

Kevin & Angel, That is the same thing that I see on Mac Snow Leopard + Chrome. I tried to post a screenshot, but my image size was too big. Miguel On Thu, Jan 27, 2011 at 3:40 PM, Kevin Rosso wrote: > Hi Angel, > I can see the middle 2 displayed on the page. > > The first one (inserted by Jmo

Re: [Jmol-developers] Is is time to update the vecmath library we use?

On Tue, Jul 13, 2010 at 1:23 AM, Robert Hanson wrote: > note that we only load a selected subset of that package. I agree. *** 2 minutes later *** Bob & Nico, we used to use a 3rd party implementation of javax.vecmath that followed the javax.vecmath API. That was necessary because javax.vecmath

Re: [Jmol-developers] Slab transparency options

On Tue, Jul 13, 2010 at 2:13 AM, wrote: > Hi, > > The Jmol slab function can be confusing for casual users, because it displays > only one half of the model. It demands great effort from the user to > understand > what's looking at. Quite true. I always had a great deal of trouble visualizing a

Re: [Jmol-developers] Java 1.5

On Tue, Apr 27, 2010 at 5:17 PM, Robert Hanson wrote: > Does it matter that Jmol 12 will require Java 1.5? Java 1.5 was released in Sept 2004 Requiring 1.5 should not be an issue for anyone. Miguel --

Re: [Jmol-developers] Based on response at ACS I have a demo that we might want to use on the Jmol web site...

On Mon, Mar 29, 2010 at 4:47 PM, Jonathan Gutow wrote: > Dear All, > > The demo of Jmol capabilities available at the link below got Ooohs > and Aaahs at the National ACS meeting I just presented at. Excellent work! Miguel ---

Re: [Jmol-developers] terminology questions

Tim wrote: > just to make sure I understand, you need separate class names for the > following: > > 1. a single molecule that could be part of a polymeric chain, but isn't. > (AA, nuc, sugar, etc.) this does not include 'plain old' molecules like > water, ligands, etc. > > 2. a dimer of two molec

Re: [Jmol-developers] XML parsers

Joerg wrote: >> An honest question ... What is the value in giving people a choice of >> XML library? > What is more complex ? > 1. To write a parser for all arbitrary chemical file formats, nearly > every program introduces proudly it's own format (why, just why ?)! or > 2. To write a complex pars

Re: [Jmol-developers] Re: Display of properties

Daniel wrote: > In our > very first looks at using Jmol we saw two problems. The first is > essentially what is described above. we needed a way to label > pharmacophore points and have the label be displayed, even if the atom > was dummy atom. OK, there is now the basic infrastructure in place to

[Jmol-developers] XML parsers

Egon (& others) I have a question about the XML parsers that are used in the CML code. Be advised that to data I have no experience with any of this stuff. There are several parsers that are referenced in the cdk.io.CMLReader code. Q: Since JAXP is bundled with Java 1.4 or later, can we just as

Re: [Jmol-developers] load dadml://any/pdbid?1CRN

>> * We will have to make some modifications to the present code to get >> it >> to work with the JmolApplet. The applet security model will only allow >> the JmolApplet to retrieve URLs from its home server. Therefore, all >> URLs which are fetched by the unsigned JmolApplet must be routed >> thr

Re: [Jmol-developers] load dadml://any/pdbid?1CRN

>> I get a CML not supported error :( Can this be the reason of the >> FileNotFound exception? [snip] > I am not sure why. I will try to take a look at it. Egon, This seems to be working now. I changed several things ... and I honestly don't know what I modified to make it start working. But it

Re: [Jmol-developers] load dadml://any/pdbid?1CRN

> This has now been added to Jmol, Great! > but it is not fully working yet... but > that's ok in a developers release. > > Try in HEAD: > > load dadml://any/CAS-NUMBER?50-00-0 > > This can be resolved into a URL and is then tried to be loaded, but this > fails... Miguel, I get a FileNotFound,

[Jmol-developers] SPGR record in ShelX .res files

Egon, I am looking at the shelx reader. Comments in the file say that PLATON adds a SPGR record. Q: What is the format of that line? Q: Is there only one token after the SPGR record tag? Q: Can you check in a sample .res file that has a SPGR record into jmol/samples? Thanks, Miguel

[Jmol-developers] Re: [NPE in unit cell rendering -> FIXED

Egon wrote: > i now get this error when trying to display the unit cell: > > java.lang.NullPointerException > at > org.openscience.jmol.viewer.g3d.Graphics3D.drawString(Graphics3D.java:307) > at > org.openscience.jmol.viewer.datamodel.UccageRenderer.render(UccageRenderer.java:62) > at

[Jmol-developers] Re: Display of properties

sending an EditBus command "showChemFile()" (or so) does not >> work in the current HEAD (stackTrace attached). If I walk down this >> hierarchy, I do indeed not find any code for handling cdk.ChemFiles. >> It worked in b6. > &

Re: [Jmol-developers] font setting + echo control

>>I have implemented a new scripting command that gives one more >>explicit control over fonts. [snip] > tried to compile with the newest HEAD and it failed with lot of these > errors: > > > [javac] > /Users/driscoll/Documents/dev/Jmol-HEAD/src/org/openscience/jmol/viewer/ > script/Eval.java:

[Jmol-developers] font setting + echo control

I have implemented a new scripting command that gives one more explicit control over fonts. font [label|measure|axes|echo] {SansSerif|Serif|Monospaced} {Plain|Bold|Italic|BoldItalic} I have also implemented the following extension to the echo command. It allows one to pipe the output of the echo

Re: [Jmol-developers] NeSC meeting - Toward a common data and command representation for quantum chemistry

Peter wrote: > I attach details of a meeting next month on communal tools for quantum > chemistry. I shall highlight the contribution made by open efforts like > Jmol and the rest of the software. I shall promote the use of Jmol as a > visualiser for quantum chemistry. I think the meeting will be q

Re: [Jmol-developers] cmlrss_distrib

>>Jmol causes an uknown exception without debugging ability: >> >>2. java -DproxyHost=www-cache.informatik.uni-tuebingen.de >> -DproxyPort=3128 -Dcdk.debugging=true -jar jmol.jar >> >>Exception in thread "main" >>it seems to crash during/after creating the menu bar. > > Egon is away and I;m not s

[Jmol-developers] Desirable monitor/label color behavior?

Tim wrote: > my opinion is that color monitors should apply to the selected set, like > most other commands. that way, if you want to color a monitor, select > one of the involved atoms and issue a "color monitor [color]" command. This makes sense to me. I would also propose that the default mo

Re: [Jmol-developers] Commands 'monitor' and 'color monitor'

Eric wrote: > In Chime (and RasMol), both monitor lines and labels follow the colors > of the respective atoms by default. Each monitor line by default is two > colors: half the color of each of the two atoms it connects. The > distance number seems to be colored arbitrarily by the color of the

[Jmol-developers] Re: RasMol selection syntax

>> by the way, I can't do >> select 1.ca >> as I'm used from RasMol > > This does not work because '1.' is the way that one denotes a floating > point number :-( > > I will see if I can come up with some hack to make it work. Done. The selection: select 1.ca now works. As does: select 1-5.ca

[Jmol-developers] RasMol selection syntax

> by the way, I can't do > select 1.ca > as I'm used from RasMol This does not work because '1.' is the way that one denotes a floating point number :-( I will see if I can come up with some hack to make it work. (I am starting to hate this scripting *language* more and more :-) Miguel -

Re: [Jmol-developers] Commands 'monitor' and 'color monitor'

Sergey, I added you to both jmol-developers and jmol-users This is probably a better question for the jmol-users mailing list. > I am developing the web site that allows to see interactively > macromolecular structures. I use Jmol/JmolApplet for this purpose and > I'm very impressed by the progr

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-developers] Re: speed test pages

Tim wrote: > ok, I just turned off all callbacks and debug script at my animation > page: > > > > but of course, I can't see any difference (I have never seen the speed > problems, maybe because I am on the local network.) Local net

[Jmol-developers] Re: speed test pages

Miguel wrote: > The performance problems on some platforms is caused by the callbacks. [snip] > Remove the callbacks and the problem goes away. This picture may not be as ugly as the one I painted. Mozilla seems much happier if you just turn off debugscript. It is then happier still if you shut

[Jmol-developers] Re: speed test pages

will allow us to accomplish thing we want to accomplish without using the callback mechanism so heavily. Stay tuned ... Miguel > at 7.07p EDT on 2004 March 08 Monday Miguel Howard said: > >> I can reproduce this problem running locally on my local web server. >> >>

[Jmol-developers] B factor

Egon, Do you know what file types support B factor? (other than .pdb) 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! htt

Re: [Jmol-developers] Standard syntax for pulling from remote databases

DanZ wrote: > Our web pages get ~1.5 million hits/year from ~40K disitinct IP > addresses. OK, broad user base running a wide variety of systems. > We recognize that using CML (and > XML in general) can have resource and performance issues, but I haven't > seen any other technology that > will get

Re: [Jmol-developers] CGI stuff

Tommi wrote: >> This makes me a little nervous ... :-) > > Even if this looks bad, it isn't so; please let me explain :) > >> If you want to pass pack all that data then you are probably going to >> want to feed it back to Jmol. That implies that Jmol can store this >> data, do something with it,

Re: [Jmol-developers] Jmol <-> JOELib connection

Joerg wrote: > It's a graph based representation of chemical compounds. OK > A regular expression syntax for subgraph searching known as > SMARTS is included. That sounds very useful > Please read for more informations: > http://www-ra.informatik.uni-tuebingen.de/software/joelib/index.html Wi

Re: [Jmol-developers] Jmol <-> JOELib connection

Joerg wrote: > Hi Egon, > > your previews for the Jmol 10 release are really promising, seems that > there is a hard-working Jmol developer team :-) > > O.k., let's go into detail. I'm definitely interested in a Jmol<->JOELib > connection. That is very good to hear. Unfortunately, I know absolut

Re: [Jmol-developers] Standard syntax for pulling from remote databases

DanZ wrote: > it seems that CML and loadInLine > are not yet supported. Is this true and if so what are the issues? CML === CML is probably a good thing for Egon to work on. We have code to support it in previous versions of Jmol and in the CDK (Chemistry Development Kit). One of the major barrie

Re: [Jmol-developers] CGI stuff

Tommi wrote: >> A few small fields for your parameters ... plus one BIG field for the >> data file. > > Ok, I see. We in have two possibilities: > > 1) pass the extra parameters in extra fields (see above). > 2) pass the extra parameters as a part of the data file. Good point. > Actua

Re: [Jmol-developers] Applet v9 or v10pre? Which one to use?

Egon said: > yesterday I released Jmol 9, both the application and the applet. I was > asked about the applet and there was a tiny bit of confusion about the > functionality of the applet. Here's an short overview: Egon, thanks for putting this together! > (using fixed font): > >

Re: [Jmol-developers] CGI stuff

Tommi wrote: > Ok, thanks, I think this is getting a bit clearer now. I found an > example of sending a POST request using Java, and it seems that the > classes to be used are URL and URLConnection (at least). The idea is > that we have a "form" as you explained: > >> Let's say that we have a form

[Jmol-developers] CGI stuff

Tommi, > So far I have known that I might be given a number of chars that I > need (or can) read from the input. But I don't know what "splitting > up" and "un-escaping" means ; could you give some practical examples > of these? Let's say that we have a form with two fields. One called 'name' an

Re: [Jmol-developers] Interface to fetch model data

Tommi wrote: > So far I have known that I might be given a number of chars that I need > (or can) read from the input. But I don't know what "splitting up" and > "un-escaping" means ; could you give some practical examples of these? Sure, I will tell you exactly what you need to do. What language

Re: [Jmol-developers] Interface to fetch model data

Tommi wrote: > I have started to make the cgi-program according the last week's plans. > The input already works (command-line) but I still need to work with > output. When I think it's usable I'll post instructions how you can > download it and try it (tomorrow or Wednesday I hope). Sounds very g

[Jmol-developers] Interface to fetch model data

Tommi (& Egon) I have done some work on the interface you should use to fetch the data from Jmol. After giving it some thought I realized that one api, the JmolModelAdapter, should be used for both importing data into Jmol and exporting data out of Jmol. So, I added a method JmolViewer.getExpo

Re: [Jmol-developers] Re: [Cdk-devel] Re: IO porting work

>> How and where may I store these information ? : >> - Vibrations associated with a molecule. > > This has not been defined yet. > > Miguel, have you given thoughts to this? Can you tell me what file to look at that has this information? (I think you may have told me this but I forgot) What is t

Re: [Jmol-developers] ghemical-cgi

>> That will be a good thing. Just set aside a few hours to install >> apache and then play with it. > > Well, apt-get install apache does not take that long :) That is true :-) But I want him to _play_ with it for a few hours. Tommi doesn't seem to have much experience with web servers. And the

Re: [Jmol-developers] ghemical-cgi

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! > http://ads.osdn.com/?ad_id=1356&alloc_id=3438&op=click > ___ > Jmol-developer

Re: [Jmol-developers] ghemical-cgi

>> So, there is no 'command line' version. > > There is no command line version, yet. But it is easy to do, and it will > have smaller size than that of the GUI app. The command line app will > just link to libghemical that contained the functionality but no file > I/O. OK, good. >> Since it has

Re: [Jmol-developers] a question about JmolEditBus

Egon wrote: >> On Thu, 19 Feb 2004, Miguel Howard wrote: >> > Can you tell me a little about the ghemical? > > Will you be using the Ghemical Reader in CDK? Probably. If Tommi sends the data back in Ghemical format. > BTW, the link is: http://bioinformatics.org/ghemical/

[Jmol-developers] ghemical-cgi

Tommi wrote: >> Can you tell me a little about the ghemical? > > It's a molecular modelling program written in C++. Currently it is split > in 2 parts: > > libghemical : only contains the core functionality (no graphics [snip] > ghemical : contains a GUI part for gnome. So, there is no 'command li

Re: [Jmol-developers] jmolcdk.jar vs. jmol2cdk.jar

>> So, does that mean that the Jmol build now depends upon having CDK >> installed and compiled locally? > > No, not at all... OK --- SF.Net is sponsored by: Speed Start Your Linux Apps Now. Build and deploy apps & Web services for Linux wi

Re: [Jmol-developers] jmolcdk.jar vs. jmol2cdk.jar

Egon wrote: > I've just removed one of the jmolcdk.jar, which was there also named as > jmol2cdk.jar, as it is found in CDK cvs. Overthere it was renamed, to > allow different jars for the b6 branch (jmolcdk.jar) and the HEAD > branch (jmol2cdk.jar). > > The build.xml for Jmol is also adapted to

Re: [Jmol-developers] a question about JmolEditBus

Egon, [snip - Miguel's ranting about JmolModelAdapter] I truly apologize ... I should have looked at the JmolEditBus code before I started lecturing about good design. The method that you are using ... JmolViewer.openClientFile() ... is just fine. The way that you implemented it is good. Becaus

Re: [Jmol-developers] a question about JmolEditBus

Tommi, Can you tell me a little about the ghemical? What is the input format? > I'll learn about cgi and web servers before I start anything at the > server side. Good. > I can start from client side by first figuring out how to > get and set atoms and bonds from/to Jmol classes. Be advised t

Re: [Jmol-developers] a question about JmolEditBus

Tommi, > On Thu, 19 Feb 2004, Miguel Howard wrote: > >> If Ghemical does not have a server then I recommend that you access it >> through a .cgi on a web server. > > There is no such server yet. However, the latest version in CVS works as > a bonobo component (bonobo is

Re: [Jmol-developers] a question about JmolEditBus

>> 500:remote.server.net >> >> where "500" is the port number and "remote.server.net" is the IP >> address of the remote server. In this case there should be a server >> process listening the port 500 in the remote system, which would >> receive the requests from plugins and provide the servi

Re: [Jmol-developers] a question about JmolEditBus

>> Passing the structure back to Jmol means that you need to implement >> the JmolModelAdapter interface. That is the API for feeding structures >> to Jmol. > > Miguel, the plugins use the CDKEditBus interface for this... Jmol's > jmol/app/JmolViewer.java provides this interface to plugins... > >>

Re: [Jmol-developers] a question about JmolEditBus

Tommi wrote: > Perhaps I could describe my plugin plan a bit. The plugin would make > some comp.chem. methods available into Jmol. It would read the current > atoms/bonds from Jmol, This sounds like good functionality. I think that Jmol should provide iterators for this purpose. > send them to a

Re: [Jmol-developers] a question about JmolEditBus

Egon wrote: >> Could you please tell me about the status of the JmolEditBus class? > > Which Jmol version are you refering too? Jmol HEAD, or Jmol from the b6 > branch? (If you just did cvs co Jmol, then it would be the default = > HEAD...) > > I'll have alook at the source code how difficult this

[Jmol-developers] supercell

right. Every one of these types is actually an array. Each of these 'shapes' needs to be able to 'checkpoint' itself so that it knows where the end of its 'real' data is. Then, later on, it can 'rollback' to that previous setting. OK ... I need to go in a

[Jmol-developers] unitcell issues

Egon, Thanks for the discussion this morning ... it was very enlightening for me. Two items we need to discuss. 1. connected sets I now understand that I need to determine connected sets prior to shifting to the unit cell. This means that, in cases where the file does not contain bonding infor

[Jmol-developers] Re: how to store crystal info in HEAD

ntation in Chemometrics > Nijmegen University > http://www.cac.sci.kun.nl/people/egonw/ > GPG: 1024D/D6336BA6 > > -BEGIN PGP SIGNATURE- > Version: GnuPG v1.0.7 (SunOS) > > iD8DBQFAMg2gd9R8I9Yza6YRAhtmAJ4/CWlhUAPwWRhTPSSu4r9aJKUZJwCfeygQ > GoGQZmz5SNZYB8xUkAtEc5

[Jmol-developers] Re: ## and #! (no, I'm not cussing)

SUMMARY === Per Eric's request, I have implemented some special commenting conventions for Jmol v10. These allow better interoperability between RasMol, Chime, and Jmol scripts. #jx denotes a command that Jmol will eXecute #jc denotes a special type of Jmol Comment DETAIL == Normally, a

[Jmol-developers] Re: compatible *restrict* behavior

>> Q: Is it the case that 'restrict' applies to *all* graphic shapes ... >> cartoons, strands, etc? > > The intention is that RasMol's restrict command applies to all graphics > representations. The documentation was written when there were only a > handful of representations used by RasMol, and (

[Jmol-developers] compatible *restrict* behavior

This question refers to the 'restrict' scripting command. I have received several complaints that the Jmol implementation of 'restrict' is not correct. The RasMol doc says: This command is very similar to the RasMol 'select' command, except 'restrict' disables the 'wireframe', 'spacefill' and

[Jmol-developers] IO porting work -> Jmol vibrations

>> How and where may I store these information ? : >> - Vibrations associated with a molecule. > > This has not been defined yet. > > Miguel, have you given thoughts to this? So far I have not given it much thought. But clearly I need to do so. At this point, I think that I would rather work on v

Re: [Jmol-developers] 'protein' set and modified residues

>> This might make it somewhat easier ... in fact, most of the data >> structures to support this are already in place. >> > then perhaps we don't need to read the MODRES at all. I think that would be good. Esp if MODRES records are often missing from .pdb file. > as long as Jmol > can separate m

[Jmol-developers] DNA/RNA

> 3. Jmol does not recognize DNA as a predefined set, which is easily > fixed. Then you should do this. I have been holding off on nucleic stuff because 1) I didn't have anyone to help me with it, and 2) my outstanding grant proposal with Brian White You are now here to help/tutor me ... and we

[Jmol-developers] 'protein' set and modified residues

> 2. I need some advice on how to proceed with fixing the predefined set > 'protein'. should I try to include all of the known modified residue > names in the JmolConstants file? seems like an awful kludge, though > maybe that's the only way. > > some background info, from the PDB FAQ: [snip] >

[Jmol-developers] adding WAT as alternate identifier for HOH

> 1. I've added WAT to the list of Jmol constants and tested it. do you > want me to send you the files, or just check them in to SF? You should: - make sure that everything you have is up-to-date cvs up -dP - do a clean build ant clean main - then check it in cvs ci - update the so

Re: [Jmol-developers] Standard syntax for pulling from remote databases

> First of all let me point out that this is > especially timely considering the new NIH roadmap initiatives (See > http://nihroadmap.nih.gov). The particularly applicable group is the > Molecular Libraries and Imaging one. I am very interested in having NIH use Jmol as part of this effort. [snip

Re: [Jmol-developers] unitcell & boundbox

> The user may wish to select a particular atom (or point derived from a > group of atoms - e.g. centroid of a molecule and to rotate about that. Yes, this works today and will continue to work. I am concerned about the 'default' center of rotation. > I think the displayed corners of the unitcell

[Jmol-developers] unitcell & boundbox

This question involves: - boundbox - unitcell If there is no crystal unitcell data present in the file: * the corners of the boundbox are defined by the min and max values of the atom centers along the x,y,z axes * the center of rotation is the center of the boundbox When unitcell data is

[Jmol-developers] NSC index

Daniel, >>> After searching the web I figured out that 'NSC number' is >>> from >>> the National Safety council and is used within the CAMEO database >>> system. >>> >>> Q: Is this 'NSC' number used by anyone in the Jmol community? >> >> I don't think there are many databases which use the NSC ind

Re: [Jmol-developers] unitcell help needed

>> Your job, should you choose to accept it, is to do the angle >> calculations. > > I'll take it... it's all in CrystalGeometryTools... I've tried to > understand how Fabian's code in b6 works, but I failed... Thanks! Miguel --- The SF.Ne

[Jmol-developers] unitcell help needed

Egon, Fabian, etc. I need someone to implement unitcell cartesian coordinate calculations in Jmol v10. Perhaps I should be able to do it from the cdk, Jmol, and RasMol source code ... but I can't. Your job, should you choose to accept it, is to do the angle calculations. The infrastructure is al

[Jmol-developers] basic unit cell geometry questions

I have some very basic questions about unit cells: As I understand it, the unit cell is defined by three lengths (a, b, c) and three angles (alpha, beta, gamma) You then do transformations of these to define the other vertices. Q: Are there always 8 vertices and 12 edges? Q: Is the origin of th

Re: [Jmol-developers] Standard syntax for pulling from remote databases

> This would allow things in Java like: > > URI uri = new URI("dadml://nist/cas?50-00-0") > String protocol = uri.getScheme(); > String service = uri.getAuthority(); > String index = uri.getPath(); > String query = uri.getQuery(); Good idea ... let Java do the parsing. Miguel --

Re: [Jmol-developers] Standard syntax for pulling from remote databases

>> Q: Are there other large, publically available databases on the web? > > Yes, see: > > http://www.woc.sci.kun.nl/super.xml > > This lists 9 databases... All links refer to URL+database.xml, e.g. > > http://www.woc.sci.kun.nl/database.xml for the first entry... Very good. >> Q: Is this 'NSC' nu

Re: [Jmol-developers] Standard syntax for pulling from remote databases

> CAS is short for CAS rigestry number... it's a simple index used for a > very big database of published structures, I think... see: > > http://www.cas.org/EO/regsys.html This is *very* helpful. As I understand it, this is the 'registry' only. I see that the cactus database (http://cactus.nci.n

Re: [Jmol-developers] Standard syntax for pulling from remote databases

> where the syntax is as follows: > > PROTOCOL://SERVICE[/INDEXTYPE]/INDEX I should have read ahead :-) Miguel --- The SF.Net email is sponsored by EclipseCon 2004 Premiere Conference on Open Tools Development and Integration See the bread

Re: [Jmol-developers] Standard syntax for pulling from remote databases

>> unless 'pdb' in the above context refers to the actual db from whence >> the structure cometh? > > My intention was indeed that pdb was denoting the actual PDB database... > The DADML protocol would know how to resolve it into a URL and as such > into a HTTP request... I agree. - //pdb/ was i

Re: [Jmol-developers] Standard syntax for pulling from remote databases

> I don't think Peter is refering to the RSS work... JCP also has a system > called DADML: database access definition markup language... I wasn't aware of that. > It uses XML files to download from databases, and is very well suited > for downloading from databases like the PDB... > > See CDK's

Re: [Jmol-developers] Standard syntax for pulling from remote databases

> I like the URL syntax, too. the only trouble I can see is if a > structure DB changes the syntax for remote apps accessing their DB. Regardless of what syntax we choose (even if it looks like a URL), we will pull out the key components and substitute them into a pattern to construct the 'true'

Re: [Jmol-developers] Standard syntax for pulling from remote databases

> I am sure you know that Egon has done something like this in CDK/JCP. While I was aware of the RSS and plug-in work, I did not make the association between the two ... Thanks! > So it's important to keep consistency... Agreed. > I favour the use of symbolic addresses which are set in configu

Re: [Jmol-developers] Standard syntax for pulling from remote databases

> how about > > load someID(someDB,someFlag) > > instead? I think of the ID as the central element here, and I'd like to > be able to say simply > > load someID > > and have Jmol use the default database from its pref file. Well, you have an interesting point. But I am concerned that it would res

[Jmol-developers] Standard syntax for pulling from remote databases

>> Q: Do you think that there is value in specifying a 'standard' syntax >> for pulling files from the pdb? Something like: 'load [pdb]1ezn' >> >> That way, you could externalize the location of the server (and the >> specific URL) and get it out of the RasMol script. >> >yes - esp if there is also

[Jmol-developers] Babel generates invalid CONECT in PDB

Summary --- It looks like Babel generates invalid CONECT records for bonds in .pdb files. The fields that are set aside for Hydrogen bonds and salt bridges in the CONECT record are not being respected. I do not know if OpenBabel has the same problem. Detail -- New functionality to suppo

[Jmol-developers] Re: MICE is a signed applet from SDSC/RCSB

> One of the options on the View Structure page of RCSB's Structure > Explorer is MICE. I just tried clicking it for the first time. > Although > I was afraid to proceed with all the downloads (wondering if they would > interfere with Jmol), it announced that MICE is a signed applet and > reque

Re: [Jmol-developers] Re: [Open Babel] resolving color differences

Phillip, > Although I like the idea of using colors suggestive of the 'native > state', grey for Si is not particularly enticing. ... > until ground up into > sand where it generally has a yellowish color. When I think silicon I think of a sandy beach ... so do you want a tan color? > Same issu

[Jmol-developers] Re: JmolApplet - prerelease test

> http://www.liv.ac.uk/chemistry/jmol/test2.html you say that naphos2.pdb is OK with the modified CONECT records ja91.pdb has a central atom that is hot pink. In fact, it is OK. The atom is correctly recognized as Yb. The problem is that we do not yet have a color identified for this element. I a

[Jmol-developers] Jmol 10 prerelease 5

Jmol10pre5 is not available at http://jmol.sourceforge.net/betatest This release includes: - full support for ssbonds - RasMol/Chime compatible support for protein backbone hbonds - cpk color scheme switch to RasMol/Chime - menu system changes under Display styles - support for pdb ins

[Jmol-developers] [Fwd: Re: Standard Element Colors?]

ments? (I am aware of the few defined by CPK) > >Is this something that IUPAC has considered or is considering? > > >Thank you for your time, >Miguel > > > > >Thank you for contacting IUPAC! >We will respond to your message as soon as possible. -

Re: [Jmol-developers] resolving color differences

> Seems to me to be reasonable for Jmol to leave one color, say 'hot > pink', for any atoms not identified when atomic symbols are parsed and > the unique colors assigned. Should help in seeing when a data file or > the parser misbehave. Agreed. There is a special 'element' (with atomic number 0

[Jmol-developers] Re: [ jmol-Bugs-869549 ] Lanthanide complexes as PDB - problems

> Certain PDBs still give problems > > 3 of the first 4 on http://www.liv.ac.uk/Chemistry/jmol/test2.html Nick, Thanks very much for putting together this page which displays Jmol problems with some interesting molecular models. I am going to send you another email (offlist) with a new JmolAppl

[Jmol-developers] resolving color differences

There differences in the RasMol and OpenBabel coloring schemes. Not sure what the mechanism should be to try to resolve the differences ... It seems to me that the differences fall into three groups. undisputed inorganic atoms: are 'hot pink' in the RasMol scheme are essentially 'unassigned'

[Jmol-developers] RasMol vs. OpenBabel color scheme

I have put together another color comparison table so that we can look at element colors. Geoff Hutchison send me a molecular model file of the periodic table. It looks pretty cool :-) http://jmol.sourceforge.net/colors Miguel --- The

  1   2   >