Re: [Jmol-users] Full presentation in jmol
Saravanan, I don't know if this is what you're looking for, but I have used a plug-in for PowerPoint called LiveWeb that allows you to embed html web pages in a Powerpoint presentation. See: http://skp.mvps.org/liveweb.htm. Or you can do your presentation entirely in html like a presentation I did for the American crystallographic Association meeting in 2009. See: http://macxray.chem.upenn.edu/aca09/index.html Pat -------- Patrick J. Carroll, Ph.D. Director, X-ray Facility Department of Chemistry University of Pennsylvania -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2dcopy2 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Help with Firefox 4
Just installed Firefox 4 on Windows 7 system. Now Java doesn't work! There was a message during installation that the Java plug-in is incompatible with Firefox 4. So what do I do? Pat Patrick J. Carroll, Ph.D. Director, X-ray Crystallography Facility Department of Chemistry University of Pennsylvania Philadelphia, PA Phone: 215-898-3505 Web: http://macxray.chem.upenn.edu -- Create and publish websites with WebMatrix Use the most popular FREE web apps or write code yourself; WebMatrix provides all the features you need to develop and publish your website. http://p.sf.net/sfu/ms-webmatrix-sf ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Making movies
Arjan, I have used Eric Martz' MORPH2 to calculate intermediate co-ordinates from a beginning and a final PDB file. MORPH2 is a part of pdbtools, available from: http://www.umass.edu/microbio/rasmol/pdbtools.htm#martz Go all the way to the bootom of the page to download pdbtools. Pat -- Patrick J. Carroll, Ph.D. Director, X-ray Facility Department of Chemistry University of Pennsylvania -- SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. The future of the web can't happen without you. Join us at MIX09 to help pave the way to the Next Web now. Learn more and register at http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] trouble accessing through Firefox
Frieda, The exploringdna page works for me with firefox on windows - and it's beautiful! Pat Carroll Chem dept U Penn - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] van der Waals radii in Jmol
I remember a discussion a couple years ago about the van der Waal's radii used in Jmol. There was a feeling that the values in Jmol are somewhat "over-estimated". Is there a way that a user can input his own radii? (other than using the explcit "spacefill 1.70" every time he wants to draw a van der Waals carbon atom). Or, alternatively, can the values in JmolConstants.jave be changed to those in, e.g., A. Bondi, J. Phys. Chem, vol.68, p.441 (1964) - which, I think, are widely accepted. Pat Carroll U of Penn Phila, PA - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] What's New for Jmol
Bob, Of course, I would like you to highlight the unit cell capabilities of Jmol! Here's an example where you can construct a packing diagram in order to investigate hydrogen bonding: http://macxray.chem.upenn.edu/cells/7014SG.html I don't know of any other web program where the user can build a unit cell! Pat Carroll Chem dept U of Penn - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Unit Cell Packing Diagrams
Bob, Jmol version 11.1.41 has repaired my problems with atoms at special positions. It took a little playing around with "hide" and "display" to get all the bonds drawn corectly, but (so far) all of my cells with special positions work correctly! See, e.g., http://macxray.chem.upenn.edu/gam/9129b.html and http://macxray.chem.upenn.edu/lgs/6130b.html Thanks for all your help! Pat Carroll UPenn X-ray Facility - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Drawing Bonds Between Different symops in Unit Cell
Bob,
I've been playing with your code suggestions that involve using
the "translateselected" command. The problem I'm having is that it seems
there can't be more than one occurrence of a symmetry operation but with
different translations. E.g., it seems to be impossible to have both a
-x,-y,-z translated 0,0,0 AND a -x,-y,-z translated 1,1,1. Once I have
displayed -x,-y,-z 1,1,1, if I select -x,-y,-z 0,0,0 the atoms that have
already been translated are selected and if I translate them, the molecule
at -x,-y,-z 1,1,1 is gone.
So I went back to playing with "load 9129.cif {444 666 0}". If I
load first with this command and then select -x, -y, -z 0,0,0 the correct
fragment is chosen, except for the Ni atom which is chosen in the x,y,z
0,0,0 fragment (this is the original problem I was having). See
http://macxray.chem.upenn.edu/gam/9129d.html
If I load first with "load 9129.cif {444 555 0}", and select
-x,-y,-z 0,0,0 then the correct fragment is chosen, including the Ni! See
http://macxray.chem.upenn.edu/gam/9129c.html
Can this be "fixed"? Because it looks like the only way to have
multiple occurences of the same symop is to pre-load all possible symops
{444 666 0} and then select. AND again, this all seems to work fine for all
those cases in which no atoms sit directly on a symmetry element.
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Re: [Jmol-users] Drawing Bonds Between Different symops in Unit Cell
Thanks Bob! That looks like a much more efficient way of doing things. - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Drawing Bonds Between Different symops in Unit Cell
Bob, I'm trying to work through your suggestions about using "display", but meanwhile, I've noticed some other strange behavior. On that same page, http://macxray.chem.upenn.edu/gam/9129b.html when I try to add a molecule by using symmetry operation no. 3 (center of symmetry), when I try to select symop = 3555, the green Ni atom in symop = 1555 is instead selected. This is the atom that lies on the symmetry element (at .5, .5,.5). I have seen this behavior in other cells whenever an atom lies directly on a symmetry operation and I select a symop that should be the symmetry-related molecule, the atoms in the central molecule (1555) that lie directly on the symmetry element are selected, instead. See, for example http://macxray.chem.upenn.edu/lgs/3160b.html In this case, several of the atoms in 1555 lie on a mirror plane at y=.25. When I try to select symop = 4555, these atoms in 1555 that lie on the mirror plane are selected instead. Pat Carroll UPenn X-ray Facility - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Help for a Complete Beginner
Steve, I have been using Jmol and javascript to design web pages that will enable users to build crystal packing diagrams. See, for example: http://macxray.chem.upenn.edu/cells/7014SG.html Pat Carroll U Penn X-ray Facility - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Packing diagram - study H bonding with Jmol 11
Thought you might like to see a webpage that uses Jmol 11 to build a packing diagram in order to interactively investigate hydrogen bonding in a small organic molecule: http://macxray.chem.upenn.edu/cells/7014SG.html Pat Carroll Chem Dept U of Penn - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Building unit cells with Jmol 11 - Success!
Here's my latest attempt at a web page that allows the user to construct a unit cell packing diagram using a variety of strategies: http://macxray.chem.upenn.edu/cells/3159SG.html I still have some things to do - make it general with respect to the no. of symmetry options and play with the crystallographic logic. Thanks to Tim Driscoll and Angel Herraez for some javascript tips and, of course, to Bob Hanson, for including all this confusing crystallography stuff in the Jmol code. BTW, Bob, could we label the origin of the unit cell with a 0 (zero)? Pat Carroll Chem Dept U of Penn - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Javascript help with sysop!
I am trying to construct a webpage that will allow the user to build up a unit cell packing diagram by a variety of options and I need some (more) javascript help. I've written a script using radio buttons (using a tip from T. Driscoll) and menus to choose the symop, but when I try to use this symop in, e.g., a jmolButton, it always uses the default symop that was active when the page first loaded! How do I get a "current" symop chosen by a javascript script into a jmolButton? To see what I've done so far, take a look at: http://macxray.chem.upenn.edu/cells/3159SG.html Actually, the script I'm dealing with is in 3159SG_menu.html (the webpage is a frame). Thanks, Pat Carroll Chem Dept U of Penn - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Building unit cells with Jmol 11
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 selecting a new symop which is the old symop with a translation. Do I make myself clear? I don't want to just use the "translate selected" command because that removes the first molecule. Pat Carroll Chem Dept U of Penn - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Building unit cells with Jmol 11
Bob, Your new 10.9.79 is great! It has everything needed to allow the user to build a unit cell using whatever strategy he desires. Now I just need to learn enough Javascript to get it done. First humble attempt: http://macxray.chem.upenn.edu/cells/3159SG.html You'll notice that it isn't very elegant - it needs to be general to handle any number of symop's and those translation radio buttons, right now, only work on symop no. 1 (told you I need to learn more Javascript); but as far as the Jmol Java code, it's all there! Thanks! Pat Carroll Chem Dept U of Penn - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Building unit cells in Jmol 11
Bob,
Just downloaded Jmol 10.9.79 with the new load "" {ijk i'j'k'
doNormalize} command - VERY NICE! But now the selection of individual
symops has changed: select 1000 used to select only symop #1 (x.y,z); now
it selects eight different symops #1, all those translated by +1 along a OR
b OR c!
And how do I select symops along negative directions, e.g.,
-1+x,y,z (which is in unit cell 455)?
Pat Carroll
Chem Dept
U of Penn
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Re: [Jmol-users] Selecting molecules in unit cell -Jmol 11
Bob, That all looks very exciting! Are these symop=nijk capabilities in Jmol 10.9.70? Another question: Does an instruction "select symop=2000" really put the atom at the base location for symmetry operation 2? What I'm getting at is: if symop 2 is -X, 1/2+Y, 1/2-Z, the coordinates produced will be in a neighboring unit cell (along -a if the original X is positive). I noticed that when I tried selecting molecule no. 2 which should be in that neighboring cell, Jmol moved it so that all the co-ordinates were positive. I would prefer that symop 2000 be the "real" base location even if one (or more) of the co-ordinates are negative! Do I make myself clear? Now, of course, I need to carve out some time to play with this - that's always a problem! But I think you've hit a home run here! Pat Carroll Chem dept U of Penn - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys -- and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Selecting molecules in unit cell -Jmol 11
Bob, This problem of selecting molecules in the unit cell is a general problem - I would like the user to be able to interactively build up the packing diagram (of any compound) based on, e.g., hydrogen bonding like I did using a big PDB file in : http://macxray.chem.upenn.edu/cells/99027cellFrame.html This can be done, as above, with a PDB file that includes all of the molecules that you will eventually want to display. But, of course, this requires that you figure out everything beforehand, write the PDB file and then write a script to (kind of) re-trace the process. I would like it to be more interactive. But you have given me some ideas to play with -- thanks. Pat Carroll Chem Dept U of Penn - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys -- and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Selecting molecules in unit cell -Jmol 11
Bob, The difficulty I have in selecting molecules in the unit cell is that I would like to be able to, e.g., select the molecule produced by the symmetry operation X, 1/2-Y, 1/2+Z and THEN select the one produced by 1+X, 1/2-Y, 1/2+Z, which is the same symmetry operation, just translated +1 in a. But when I select symop=2, all of the symop=2 molecules (1+X, 1/2-Y, 1/2+Z, X, 3/2-Y, 1/2+Z, X, 1/2-Y, 3/2+Z, etc) are selected. I, maybe, could select by molecule no., if I knew the relationships between the molecule nos. and the sym op's (and I am ignoring, for now, the problem of the Jmol "molecule" not being the same as the "crystallographic molecule", usually called, BTW, the "asymmetric unit"). Pat Carroll Chem Dept U of Penn - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys -- and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Use of Jmol 10.2 to display unit cells
Bob,
I know how to build a unit cell with Jmol 11.0 using load
"file.cif" {1 1 1} and how to display just the first molecule, but how do
I, e.g., select the molecule that's produced by the symmetry operation X,
1/2-Y, 1/2+Z so I display the two molecules related by the c-glide plane
as I did in:
http://macxray.chem.upenn.edu/cells/3159glideFrame.html
?
Pat
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[Jmol-users] Use of Jmol 10.2 to display unit cells
I thought those of you who have been working on the unit cell capabilities of Jmol (and those I've bothered in the past for such capabilities!) might be interested to see some of the unit cell pages I've written. Take a look at: http://macxray.chem.upenn.edu/cells The last example is the most ambitious. These pages use Jmol 10.2. Will I need to make any changes in order to use version 11.0? The major advantage is the ability to label the unit cell axes! Keep up the great work! Patrick J. Carroll, Ph.D. Director, X-ray Facility Department of Chemistry University of Pennsylvania Philadelphia PA - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Jmol sandbox - WOW!
Back on May 5, Bob Hanson demonstrated a capability he called a "Jmol sandbox". I finally had a chance to try it - it is fairly impressive! Bob, I cut and pasted one of my SHELXL .res files into your webpage and there it was! Complete with unit cell and symmetry related positions! I have several questions about the symmetry positions - have you programmed them into the Jmol applet via java or are they in the scripting (forgive my ignorance - I'm not a programmer!) Have you started to do anything with letting the user build up the cell one sym posn at a time - all the examples you seem to have do ALL the sym posn's at a time. At what point can users get what you've done and build their own "Jmol sandboxes" (whether scripting or java applet)? Pat Carroll Chem Dept X-ray Facility U of Penn Phila, PA --- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Jmol application and PowerPoint?
Can the Jmol application be used inside a PowerPoint presentation? I know that the applet can be used with LiveWeb, but only on a PC. For Mac users, is this possible. Apparently RasMol can be run from a PPT presentation by running a script; is it possible for Jmol? Patrick J. Carroll, Ph.D. Director, X-ray Facility Department of Chemistry University of Pennsylvania Philadelphia, PA e-mail: [EMAIL PROTECTED] phone: (215)-898-3505 --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] No bonds drawn to metals from shelxl .res file
SHELXL .res files do not have any charge info (as several respondents have remarked). Generally, to draw bonds to metals, the covalent radius is used and usually there is a rather large tolerance to what is considered bonding distance (maybe 20-25% of the sum of the covalent radii). For the most part, this enables the correct drawing of the great majority of bonds (and this also takes into account differences in covalent radii due to charge). But it appears that Jmol does not use the covalent radii to decide bonding distances - the covalent radii stored in Jmolconstants.java are reasonable (a no. of them are even overestimated). For example, I have a Europium compound with Eu-O bond distances of 2.2 - 2.3 Angstroms; the covalent radii for Eu and O in Jmolconstants are 1.99 + 0.68 = 2.67 ! There must be something else going on! Pat Carroll --- SF email is sponsored by - The IT Product Guide Read honest & candid reviews on hundreds of IT Products from real users. Discover which products truly live up to the hype. Start reading now. http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] No bonds drawn to metals from shelxl .res file
When reading a shelxl .res file, Jmol 10.00 does not draw bonds to transition metals. Where are the covalent radii stored? I'd like to re-build Jmol with correct metal radii. Patrick J. Carroll, Ph.D. Director, X-ray Facility Department of Chemistry University of Pennsylvania Philadelphia, PA e-mail: [EMAIL PROTECTED] phone: (215)-898-3505 --- SF email is sponsored by - The IT Product Guide Read honest & candid reviews on hundreds of IT Products from real users. Discover which products truly live up to the hype. Start reading now. http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Re: Jmol-users digest, Vol 1 #282 - 1 msg
From: "RichBall" <[EMAIL PROTECTED]> As long as the student is aware that the esds presented by this calculation are, to a greater or lesser extent, an underestimation of the true esd for that parameter I can see some value to this. (to more closely approximate the true esd for the calculated quantity Jmol would need to add the error contribution from the cell parameters; except for the most problematic structures that additional step would make the estimate more reliable) Do other image-rendering programs do these esd calculations? I've always just used the straight distance (angle, torsion) calculation to get a list of desired quantities and then did the "real" calculations elsewhere. Rich The only stand-alone rendering program I know of that calculates esd's is CrystMol (see www.crystmol.com). And, yes, cell constant errors should be considered (tho for a good quality crystal, those errors are less of a determining factor) AND with this capability, Jmol would allow a student to report parameters with esd's without having to have access to a structure determination package. Pat --- This SF.Net email is sponsored by: IBM Linux Tutorials Free Linux tutorial presented by Daniel Robbins, President and CEO of GenToo technologies. Learn everything from fundamentals to system administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Reading CIF's in Jmol
My interest in Jmol reading CIF's is not that it be able to parse the bond length and bond angle data present in the CIF, but rather that when a user measures bond lengths and other geometric parameters, that Jmol reports the parameter along with its estimated standard deviation which can be calculated by Jmol from the esd's of the x, y, z co-ordinates which are supplied in the CIF. This is most applicable when measuring a non-bonding distance, for example, the ones involved in hydrogen bonds and other forms of intermolecular interactions. This is also important in the referencing of torsion angles and dihedral angles. The situation now in our facility is that if a student has had an X-ray structure done and needs some of these "extra" geometric parameters for a publication or for inclusion with his thesis, he would need to download the CIF and then use a program on his desktop computer to calculate the parameters (and there are only a few available programs that will do these calculations with the esd's included). Or he has to ask me to do the calculation. It would be a very convenient utility to be able to do these calculations in a browser environment. Pat --- This SF.Net email is sponsored by: IBM Linux Tutorials Free Linux tutorial presented by Daniel Robbins, President and CEO of GenToo technologies. Learn everything from fundamentals to system administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Scripting with Jmol 10
Fellow Jmol'ers! I've finally gotten some time to learn how to do scripting with Jmol using JmolAppletControl - it is Way Cool!!! Look at this page that I've written for my crystallography course, demonstrating unit cell symmetry: http://macxray.chem.upenn.edu/cells/cell457total.html It also indicates the sort of unit cell building I would like to be able to do with Jmol. I've also got a page on "shape" in Chemistry that uses DNA as an example: http://macxray.chem.upenn.edu/cells/tutorial And I have some scripting questions: Is there documentation on JmolAppletControl? Are there other things you can do than the sort of button demonstrated on the Jmol website? In Jmol 10, how do you designate the color of the unit cell edges, Or change their thicknesses in the script? Pat --- This SF.Net email is sponsored by: IBM Linux Tutorials Free Linux tutorial presented by Daniel Robbins, President and CEO of GenToo technologies. Learn everything from fundamentals to system administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] reading CIF's with Jmol 10 pre8
Miguel, I like very much that Jmol 10pre8 can read CIF's. Here's a small section from a CIF that shows how bond distances are listed: loop_ _geom_bond_atom_site_label_1 _geom_bond_atom_site_label_2 _geom_bond_distance _geom_bond_site_symmetry_2 _geom_bond_publ_flag Ga1 O2 1.959(3) . ? Ga1 O4 1.965(3) . ? Ga1 O1 1.968(3) . ? Ga1 O3 1.975(3) . ? Ga1 O6 1.990(3) . ? Ga1 O5 1.995(3) . ? AND, now with this CIF capability, Jmol could be enhanced to include the calculation of the estimated standard deviations on bond distances, bond angles, torsion angles, etc. When a crystallographic paper references, e.g., a bond distance, it will list it like those bond distances in the CIF selection above. The Ga1 O2 bond distance is 1.959(3) Angstroms - the "(3)" means the estimated standard deviation (or standard error) in that individual bond distance is 0.003 Angstrom. These errors are calculated from the errors in the crystal coordinates, which are depicted in the same fashion, as nos. inside parentheses. Pat --- This SF.Net email is sponsored by: IBM Linux Tutorials Free Linux tutorial presented by Daniel Robbins, President and CEO of GenToo technologies. Learn everything from fundamentals to system administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] van der Waals radii in Jmol
Miguel, I've noticed that Jmol draws space-filling models with what look like rather larger van der Waal's radii than you would expect. If you look at: http://macxray.chem.upenn.edu/tutorial/basepair.html and change all the atoms to 100% VDW, the H's are really totally buried in the atoms to which they are hydrogen bonded. If I use the same PDB file in rasmol, I get a more reasonable looking display. The VDW radii displayed in the "Atom Properties" item on the "edit" menu in the Jmol application up to version 9 are reasonable, but the display looks "wrong". BTW, that menu item is "gone" from Jmol 10? (it would be nice to be able to adjust Atom Properties). Pat --- This SF.Net email is sponsored by: IBM Linux Tutorials Free Linux tutorial presented by Daniel Robbins, President and CEO of GenToo technologies. Learn everything from fundamentals to system administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Comments on Jmol 10 pre7
Miguel, Just downloaded Jmol 10 pre7: (1) I'm getting the same "java.util.NoSuchElementException " error as Robert Grossman, But I notice that the frame_1.res file supplied in the samples folder of earlier full releases of Jmol works !! Files that used to work with Jmol 9 now do not. (2) I tried the measurement by double clicking, but it only seems to give distances - if I double click on a 3rd atom, I get another distance. How do you get bond angles and torsion angles. (3) My two cents on the Jmol colors: I like most of them, but carbon is too dark - when you have an organic molecule with a lot of C's, it's kind of overpowering. Can we have back the rasmol grey? (I do know I can set the carbon color with a script command, but I would like a lighter default.) Pat --- This SF.Net email is sponsored by: IBM Linux Tutorials Free Linux tutorial presented by Daniel Robbins, President and CEO of GenToo technologies. Learn everything from fundamentals to system administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Just downloaded Jmol 9
Egon, Just downloaded Jmol 9 - very nice! I can draw a nice unit cell using a SHELXL .res file with the Jmol application - cell angle problem is fixed. Have you had a chance yet to put a choice into the Jmol applet to draw "the original atoms only" and to increase the size of the "Bond Box" so that bonds are drawn to atoms that are on the other side of the unit cell edge? And, apparently, Jmol 9 does not have the unit cell drawing capability with PDB files? Pat --- 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! http://ads.osdn.com/?ad_id=1356&alloc_id=3438&op=click ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] How to fill unitcell and nomenclature
Fellow Jmol'ers: As an example of filling a unit cell, see: http://macxray.chem.upenn.edu/cells/cell3148b.html The researcher who had this structure done (it's a double carborane cage bonded to a niobium atom which has a chlorine attached, if anyone's interested) wanted to see if there were any interactions between CL's on neighboring molecules (sometimes these kind of molecules form dimers by forming a CL-CL bond). The model was built in a crystallographic program that constructs all the molecules with coordinates between x = -0.5 to +1.5, y = -0.1 to +1.1, z = -0.5 to +1.5 and then writes a PDB file. The limits on x, y and z can be adjusted interactively and, of course, the space group symmetry operations are used to build additional molecules starting with the asymmetric unit. The advantage of Jmol is that if I drew a hard copy paper representation of the packing diagram, the researcher may not "see" just what he's looking for, but by rotating the display in real time, it's easy for him. Also, certainly, the same thing could be done with many applications (RasMol, CrystMol, WebLabViewer), but then I need to get individual researchers trained in using whichever of those programs they have AND I have to deal with what kind of computer they have, etc. By just putting it on my webpage, I avoid all those problems. I also saw a question about nomenclature of the molecules in an extended unit cell drawing. The very popular graphics program ORTEP invented a nomenclature many years ago to do this. This nomenclature has three parts: XXXYYYZZ. The no. XXX is the number of the atom in the asymmetric unit, YYY is a unit cell designation - the "central" unit cell is 555; the unit cell translated one unit cell length in the negative x direction is 455; the unit cell translated two unit cell lengths in the positive y direction and one unit cell in the negative z direction is 574. Finally, the ZZ no. is the number of the symmetry related position in the space group. Thus, for example, atom no. 36 that was produced by the third symmetry operation and then moved into the above unit cell is 3657403. BTW, in constructing that packing diagram on my webpage, I'm unable to select boron atoms or niobium atoms using script commands in order to change their colors; I am able to select chlorines! Pat -- --- 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! http://ads.osdn.com/?ad_id=1356&alloc_id=3438&op=click ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Examples of unit cells with Jmol
I have some example unit cells on my website with the Jmol applet: http://macxray.chem.upenn.edu/pack131.html http://macxray.chem.upenn.edu/smith.html http://macxray.chem.upenn.edu/cells/cell457.html http://macxray.chem.upenn.edu/cells/cell9903.html That last one is very cool when you switch to 100% vanderWaals. Jmol does indeed rock!! Pat --- 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! http://ads.osdn.com/?ad_id=1356&alloc_id=3438&op=click ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Re: crystal cell terminology
Miguel,
About your unit cell terminology, I prefer "unit cell" and
"multi cell" ("supercell" means something else to a crystallographer).
But I also wanted to address a bigger question - how to deal
with space group symmetry in order to "fill up" the unit cell. I've
seen some discussions about the 230 different space groups and how to
incorporate this information into Jmol. If the input file is a SHELXL
.res file, all the space group info is present in the "LATT" line and
the "SYMM" lines. If LATT is 1, the cell is centrosymmetric (for
every atom at x,y,z there is a symmetry related atom at -x,-y,-z); if
LATT is -1, the cell is non-centrosymmetric and the space group does
not have the -x,-y,-z symmetry operation. The SYMM lines list the
other symmetry operations.
Thus, for the popular space group P2(1)/c, the LATT and SYMM lines are:
LATT 1
SYMM -X, .50+Y, .50-Z
The combination of LATT and SYMM in this case, leads to four
symmetry-related positions:
x,y,z
-x,-y,-z
-x, 1/2+y, 1/2-z
x, 1/2-y, 1/2+z
which is all the info needed to "populate" the cell. Of course,
depending on the particular co-ordinates, these expressions can lead
to molecules in the "next cell over" and it may be necessary to use,
e.g., that third symmetry operation as 1-x, 1/2+y, 3/2-z to get the
molecule into the central unit cell (it is always legal to add or
subtract 1 from the crystal coordinates).
So there is no need to "teach" Jmol about all those space groups!
Pat
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[Jmol-users] hbonds and unit cells in Jmol 10
As per Miguel's questions about my wanting to use hbonds to draw unit cells: I realized I could do a better job with normal bonds and script commands to draw the unit cell edges thin and I can also have the applet display come up immediately with non-default atom and bond sizes by using script commands like: select all; cpk on; cpk 0.40; wireframe on; wireframe 0.15; select oxygen; cpk 0.1; wireframe 0.1 Take a look at: http://macxray.chem.upenn.edu/cell457b.html Of course, the better way to draw unit cells would be the capability to read shelxl .res files (which was introduced into Jmol with version 7). These files have all the necessary information. Unfortunately, Jmol 7 has a bug that reads the cell angles incorrectly (Jmol reports alpha, beta, gamma as beta, gamma, alpha). Jmol 8 has an additional bug in that it represents the cell angles in radians rather than degrees. So the Jmol 7 application will only display a correct unit cell for orthogonal cells (all cell angles 90 degrees). But the Jmol 7 applet does not have the capability of displaying "original atoms only" (as the application can) and so it will not draw any atoms that are outside the boundaries of the cell. So for drawing unit cells right now, I don't need anything added to the hbond functionality, but it would be nice to fix the shelxl.res bugs. Pat --- The SF.Net email is sponsored by EclipseCon 2004 Premiere Conference on Open Tools Development and Integration See the breadth of Eclipse activity. February 3-5 in Anaheim, CA. http://www.eclipsecon.org/osdn ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] H-bond capability in Jmo 10 is cool!
The H-bond capability in Jmol 10 is very cool! For an applet example of a fairly intricate small molecule H-bond example, see http://macxray.chem.upenn.edu/1162hb.html The H-bond capability can even be used to fake a unit cell packing diagram. E.g, see http://macxray.chem.upenn.edu/cell457.html Is there any way to vary the appearance of the dashed H-bonds, e.g., to make them solid lines or dotted lines? Is it possible to preset some of the atom and bond size parameters so the applet display comes up with non-default values, immediately? As part of the development of the full version 10, are some of the problems with reading shelxl .res files being worked on? E.g., the mis-reading of the unit cell angles. Version 7 reads the angles as gamma, alpha, beta rather than alpha, beta, gamma and version 8 displays the cell angles as radians rather than degrees. Pat --- The SF.Net email is sponsored by EclipseCon 2004 Premiere Conference on Open Tools Development and Integration See the breadth of Eclipse activity. February 3-5 in Anaheim, CA. http://www.eclipsecon.org/osdn ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Re: Jmol-users digest, Vol 1 #188 - 3 msgs
Miguel, I use babel to convert a shelxl .res file to a PDB file. Actually, I don't mind having to fix my PDB files to conform (it doesn't happen that often) in order to have that H-bonding capability. I've attached a copy of the offending PDB file. Pat HEADERPROTEIN COMPND3224.pdb AUTHORGENERATED BY BABEL 1.6 ATOM 1 C 1 3.101 4.016 10.872 1.00 0.00 ATOM 2 C 1 4.604 4.193 10.226 1.00 0.00 ATOM 3 B 1 3.999 5.452 11.216 1.00 0.00 ATOM 4 B 1 3.087 4.597 12.473 1.00 0.00 ATOM 5 B 1 3.144 2.856 12.128 1.00 0.00 ATOM 6 B 1 4.099 2.616 10.651 1.00 0.00 ATOM 7 B 1 5.695 4.921 11.300 1.00 0.00 ATOM 8 B 1 4.742 5.166 12.787 1.00 0.00 ATOM 9 B 1 4.216 3.554 13.358 1.00 0.00 ATOM 10 B 1 4.841 2.325 12.221 1.00 0.00 ATOM 11 B 1 5.752 3.179 10.959 1.00 0.00 ATOM 12 B 1 5.832 3.752 12.635 1.00 0.00 ATOM 13 C 1 1.872 4.102 9.967 1.00 0.00 ATOM 14 H 1 1.749 3.239 9.543 1.00 0.00 ATOM 15 H 1 1.096 4.263 10.526 1.00 0.00 ATOM 16 C 1 1.899 5.145 8.898 1.00 0.00 ATOM 17 H 1 1.897 6.036 9.165 1.00 0.00 ATOM 18 C 1 1.925 4.896 7.599 1.00 0.00 ATOM 19 H 1 1.979 4.003 7.345 1.00 0.00 ATOM 20 C 1 1.877 5.900 6.500 1.00 0.00 ATOM 21 C 1 1.608 7.237 6.769 1.00 0.00 ATOM 22 H 1 1.422 7.508 7.639 1.00 0.00 ATOM 23 C 1 1.617 8.169 5.738 1.00 0.00 ATOM 24 H 1 1.437 9.063 5.917 1.00 0.00 ATOM 25 C 1 1.896 7.764 4.438 1.00 0.00 ATOM 26 H 1 1.902 8.387 3.747 1.00 0.00 ATOM 27 C 1 2.165 6.427 4.169 1.00 0.00 ATOM 28 H 1 2.352 6.156 3.299 1.00 0.00 ATOM 29 C 1 2.156 5.495 5.200 1.00 0.00 ATOM 30 H 1 2.336 4.600 5.021 1.00 0.00 ATOM 31 H 1 4.621 4.387 9.284 1.00 0.00 ATOM 32 H 1 3.672 6.381 10.755 1.00 0.00 ATOM 33 H 1 2.134 5.036 12.832 1.00 0.00 ATOM 34 H 1 2.258 2.272 12.249 1.00 0.00 ATOM 35 H 1 3.827 1.957 9.830 1.00 0.00 ATOM 36 H 1 6.453 5.589 10.877 1.00 0.00 ATOM 37 H 1 4.943 6.020 13.482 1.00 0.00 ATOM 38 H 1 4.061 3.323 14.417 1.00 0.00 ATOM 39 H 1 5.082 1.315 12.513 1.00 0.00 ATOM 40 H 1 6.542 2.759 10.300 1.00 0.00 ATOM 41 H 1 6.758 3.680 13.225 1.00 0.00 CONECT123456 13 CONECT21367 11 31 CONECT312478 32 CONECT413589 33 CONECT51469 10 34 CONECT6125 10 11 35 CONECT7238 11 12 36 CONECT83479 12 37 CONECT9458 10 12 38 CONECT 10569 11 12 39 CONECT 11267 10 12 40 CONECT 12789 10 11 41 CONECT 131 14 15 16 CONECT 14 13 CONECT 15 13 CONECT 16 13 17 18 CONECT 17 16 CONECT 18 16 19 20 CONECT 19 18 CONECT 20 18 21 29 CONECT 21 20 22 23 CONECT 22 21 CONECT 23 21 24 25 CONECT 24 23 CONECT 25 23 26 27 CONECT 26 25 CONECT 27 25 28 29 CONECT 28 27 CONECT 29 20 27 30 CONECT 30 29 CONECT 312 CONECT 323 CONECT 334 CONECT 345 CONECT 356 CONECT 367 CONECT 378 CONECT 389 CONECT 39 10 CONECT 40 11 CONECT 41 12 MASTER00000000 410 410 END
[Jmol-users] Jmol 10 prerelease 5
I just downloaded Jmol 10 pre 5 and am using the applet on my webpage. The graphics are beautiful!! I especially like the atom labelling. There is, tho, one feature I don't understand - some of the bonds are drawn as "dashed" bonds. Is this intentional, perhaps having to do with the bond length? And you can't change the width of the dashed bonds. Pat -- --- The SF.Net email is sponsored by EclipseCon 2004 Premiere Conference on Open Tools Development and Integration See the breadth of Eclipse activity. February 3-5 in Anaheim, CA. http://www.eclipsecon.org/osdn ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Jmol reads ubit cell angles incorrectly
When the capability to display the unit cell was added to Jmol by reading a Shelx type file, a bug was introduced - Jmol displays the cell angles incorrectly (and perhaps reads them in incorrectly?) The "crystal properties" item in the "extras" menu displays alpha as beta, beta as gamma and gamma as alpha. In addition, in v.8, the cell angles are displayed in radians, rather than degrees. Pat --- This SF.net email is sponsored by: IBM Linux Tutorials. Become an expert in LINUX or just sharpen your skills. Sign up for IBM's Free Linux Tutorials. Learn everything from the bash shell to sys admin. Click now! http://ads.osdn.com/?ad_id=1278&alloc_id=3371&op=click ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Bug in unit cell display in Jmol?
I think I've found a problem with the unit cell display in Jmol 7 when reading a SHELXL .res type file. I had not noticed it as long as I was displaying unit cells that had cell angles of 90 degrees, but I had a problem with a triclinic cell. The cell angles in the .res file are alpha=112, beta=103, gamma=92, BUT Jmol lists the angles as alpha=92, beta=112, gamma=103 and the molecules were not displayed correctly. Pat --- This sf.net email is sponsored by:ThinkGeek Welcome to geek heaven. http://thinkgeek.com/sf ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] A Crystallographer's Wish List for the Jmol
I am using Jmol version 7, both the application and the applet, and have a short wishlist that would make Jmol very useful for X-ray crystallographers like me: As far as I can tell, the Jmol applet is the only applet in the known world that will display a unit cell on a webpage (by using a shelxl.res file as input). And it is beautiful! But, for showing unit cells of molecular compounds (rather than just ionic compounds), it is necessary that you be able to draw all the molecules that extend into neighboring cells and, apparently, this can't be done in the applet (though it can be done using the Jmol application by choosing "original atoms only" under "Crystal Properties" on the "Extras" menu - tho in the application, it would be nice if all the bonds outside the cell would also be drawn automatically instead of by adjusting the "Bond Box"). To see an example of what I'm trying to do, go to the following page on my website: macxray.chem.upenn.edu/sneddon.html Here I display a cell using the chemsymphony applets (I had to build a PDB file that included "bonds" for the cell edges). I would like to use the Jmol applet to do this. My wish for Jmol would also include another type input file - the CIF. This is a "Crystallographic Information File" which is the most popular way of archiving X-ray crystallographic structures - most chemical journals require submission of the CIF with any publication that includes an X-ray structure. With the CIF as input, Jmol would have available to it the estimated errors in the atom coordinates, so when the Jmol application is used to measure a bond distance or angle, it could display the estimated error (which is very important in crystallographic publications) as a number like "1.542(3) A", where the "(3)" indicates the estimated error is .003 A. Finally, if the Jmol applet could also include the ability to measure distances and angles, that would be very useful. I include the PDB file and the CIF on my website for all users' structures. So if the Jmol applet had these facilities, a user could explore all the important geometrical features of his structures - bond distances, bond angles, hydrogen bonding, crystal packing diagrams, etc. And he could do this using just his web browser without acquiring any other software! AND there is very little software available for individual X-ray structure users to do these sorts of calculations even on there local machine without the use of the web!! I have noticed one "bug" in the Jmol application - I'm not able to change any of the "atom properties" available on the "Edit" menu. One of the things I would like to do is draw the hydrogen atoms smaller than they are done now. This could be done by adjusting the van der Waals radius in "atom properties". Thank you and keep up the good work - Jmol is amazing! Pat Carroll --- This sf.net email is sponsored by:ThinkGeek Welcome to geek heaven. http://thinkgeek.com/sf ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Jmol 6.1 applet
I just downloaded Jmol 6.1 applet and am impressed with the unit cell drawing ability when reading a shelx file! Is there any way to pass some of the parameters to the applet that are available in the menus of the Jmol application. Specifically, can you tell the applet to draw the atoms that were originally in the .res file, rather than only the ones that occur inside the unit cell? This can be done in the application by selecting "original atoms only" in the "Crystal Properties" dialog of "Extras". Are there plans to use space group symmetry in drawing the cell? I notice in the code for drawing the cell, only symmetry 1 is used. Thanks, Pat Carroll --- This SF.net email is sponsored by: Etnus, makers of TotalView, The best thread debugger on the planet. Designed with thread debugging features you've never dreamed of, try TotalView 6 free at www.etnus.com. ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Jmol applet 5 - read shelx97 file?
Is it possible to extend the capabilities of the Jmol applet to read shelx97 files as the version 5 application can? It looks like the Jmol-applet.jar has the ShelxReader.class in it! How about the various measurement capabilities? And it would be nice if the measurements could take into account the uncertainties in the atomic co-ordinates (this info is available in the shelx file) so Jmol could calculate the uncertainties in the geometrical parameters. This would be very valuable to chrystallographers like myself especially if it were available in the Jmol applet and users of facilities like mine could do those calculations over the web!! Thanks, Pat Carroll Patrick J. Carroll, Ph.D. Director, X-ray Facility Department of Chemistry University of Pennsylvania Philadelphia, PA e-mail: [EMAIL PROTECTED] phone: (215)-898-3505 fax: (215)-573-2112 --- This SF.NET email is sponsored by: SourceForge Enterprise Edition + IBM + LinuxWorld = Something 2 See! http://www.vasoftware.com ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
