Re: [Jmol-users] Re: color schemes
According to Miguel: Q: Should the color scale be red - blue ? Since we are talking about 'temperature' I guess that makes sense. But it seems strange (unfortunate) to me that both charge temp are using red/blue. You're correct. In Rasmol, the ONLY difference between the charge and temperature colour schemes is that increasing temperature values proceed from blue to red, whereas increasing charge values go from red to blue. It would be nice to be able to set the color scheme gradient, i.e: red-white-blue gradient, where blue is the highest value, going through white (Rasmol goes through green).. Jaim -- Dr Jaime Prilusky | [EMAIL PROTECTED] RD Bioinformatics and Data Management | Weizmann Institute of Science | fax: 972-8-9344113 76100 Rehovot - Israel | tel: 972-8-9344959 info URL http://bip.weizmann.ac.il/staff/jaime_prilusky.html OCA is at http://bip.weizmann.ac.il/oca/ --- This SF.Net email is sponsored by OSTG. Have you noticed the changes on Linux.com, ITManagersJournal and NewsForge in the past few weeks? Now, one more big change to announce. We are now OSTG- Open Source Technology Group. Come see the changes on the new OSTG site. www.ostg.com ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] default for jmolApplet
How can I start an applet in wireframe mode? It seems that always Jmol.js starts a model as ballstick, independently of the requested mode. On executing either one of these jmolApplet(300, 1pgb.pdb); jmolApplet(300, 1pgb.pdb,wireframe on); it just draws as ball sticks. Jaim -- Dr Jaime Prilusky | [EMAIL PROTECTED] RD Bioinformatics and Data Management | Weizmann Institute of Science | fax: 972-8-9344113 76100 Rehovot - Israel | tel: 972-8-9344959 info URL http://bip.weizmann.ac.il/staff/jaime_prilusky.html OCA is at http://bip.weizmann.ac.il/oca/ --- This SF.Net email is sponsored by OSTG. Have you noticed the changes on Linux.com, ITManagersJournal and NewsForge in the past few weeks? Now, one more big change to announce. We are now OSTG- Open Source Technology Group. Come see the changes on the new OSTG site. www.ostg.com ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] default for jmolApplet
How can I start an applet in wireframe mode? It seems that always Jmol.js starts a model as ballstick, independently of the requested mode. On executing either one of these jmolApplet(300, 1pgb.pdb); jmolApplet(300, 1pgb.pdb,wireframe on); it just draws as ball sticks. The 'balls' are controlled separately from the 'sticks'. You need to say 'spacefill off; wireframe on' Miguel --- This SF.Net email is sponsored by OSTG. Have you noticed the changes on Linux.com, ITManagersJournal and NewsForge in the past few weeks? Now, one more big change to announce. We are now OSTG- Open Source Technology Group. Come see the changes on the new OSTG site. www.ostg.com ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] dummy atoms included/excluded
Rene Kanters wrote: I am using JMol to look at Gaussian 03 output and wanted to know whether in a future version JMol will also show dummy atoms. Since I am using z-matrix optimizations, several of the angles that are important to me are defined using a dummy atom. It looks like JMol uses the standard orientation to parse for the multiple structures in a log file, which has the dummy atoms stripped. If it were to look for the Z-Matrix orientation: it would find the cartesian coordinates of all the atoms. The added advantage of using the Z-Matrix orientation is that it will also not flip my molecule around (which the standard orientation sometimes does). Thanks, Rene On this subject: There are two sides to this: Jmol *is* showing dummy atoms when they appear in XYZ files, and I didn't find a simple command to *exclude* them from the display. Did I overlook something? It would be convenient if they could be addressed by the element name 'dummy' or by the atom type X / Xx / XX. Miguel: a dummy atom is a point in space on a position where there is no atom, but which is convenient to include in the definition of the positions of real atoms, or a group of real atoms. Example: one can write the structure of cyclopropane very efficiently in internal coordinates ( z-matrix) using the center of the ring as the origin, i.e. by placing a dummy atom there. Or: to measure the distance to a benzene ring, one could take the center of the ring as a reference point. Hens Borkent --- This SF.Net email is sponsored by OSTG. Have you noticed the changes on Linux.com, ITManagersJournal and NewsForge in the past few weeks? Now, one more big change to announce. We are now OSTG- Open Source Technology Group. Come see the changes on the new OSTG site. www.ostg.com ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] dummy atoms included/excluded
Hens wrote: There are two sides to this: Jmol *is* showing dummy atoms when they appear in XYZ files, and I didn't find a simple command to *exclude* them from the display. Did I overlook something? It would be convenient if they could be addressed by the element name 'dummy' or by the atom type X / Xx / XX. You should be able to select them using the element name unknown. I don't really like 'dummy' because Jmol turns any unrecognized element into 'unknown'. However, if you think that something other than 'unknown' is more appropriate, then please let me know. -- 1 minute later -- Actually, I forgot that I could easily add 'dummy' as an alias for 'unknown', so it is not a problem. I just made the change and it will be in the next release. You should also be able to select them as 'select elemno=0' Note that I have not tried either of these things. If they do not work then let me know. Miguel: a dummy atom is a point in space on a position where there is no atom, but which is convenient to include in the definition of the positions of real atoms, or a group of real atoms. Example: one can write the structure of cyclopropane very efficiently in internal coordinates ( z-matrix) using the center of the ring as the origin, i.e. by placing a dummy atom there. Or: to measure the distance to a benzene ring, one could take the center of the ring as a reference point. OK. Thanks. Miguel --- This SF.Net email is sponsored by OSTG. Have you noticed the changes on Linux.com, ITManagersJournal and NewsForge in the past few weeks? Now, one more big change to announce. We are now OSTG- Open Source Technology Group. Come see the changes on the new OSTG site. www.ostg.com ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Re: color schemes
On [2004-Aug-08] Miguel [EMAIL PROTECTED] wrote: Jaime one of his colleagues replied off-list suggesting that we have both relative and absolute coloring. Rather than make this a 'setting' and adding more hidden state to the system, it seems to me that we would be better off making a new script command. That'd be fine. By default, RasMol uses relative values. Q: Is there another name that we can use? color atoms absoluteTemperature color atoms byTempFactorRelative color atoms byTempFactorValue ?? Q: Should the color scale be red - blue ? Since we are talking about 'temperature' I guess that makes sense. But it seems strange (unfortunate) to me that both charge temp are using red/blue. Red is commmonly taken to mean warning -- these atoms are the most mobile (hottest) and their positions may be unreliable whereas as blue, denotes cold and therefor not very mobile. Rich --- This SF.Net email is sponsored by OSTG. Have you noticed the changes on Linux.com, ITManagersJournal and NewsForge in the past few weeks? Now, one more big change to announce. We are now OSTG- Open Source Technology Group. Come see the changes on the new OSTG site. www.ostg.com ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] vibrational frequencies
Hi, I downloaded Jmol10pre12 and tried to open a gaussian98 output file (frequency job). I am running the stand alone Jmol application. I don't see anything in the menu to visualize the frequencies. What should I do? Thank you. Valentin Valentin Gogonea Assistant Professor of Chemistry Department of Chemistry Cleveland State University Tel: 216-875-9717 Fax: 216-687-9298
[Jmol-users] Why use jmolAppletInline jmolLoadInline?
I have received several questions about jmolAppletInline and jmolLoadInline. I have a question: Why does anyone want to use these functions? I am beginning to wonder whether or not I should remove them from the library ... just kidding ;-) Seriously, I think that people would be *much* better off if they accessed the data models through a URL. That is, you can pass in a URL as your molecular model ... it does not need to be a file name. That URL can run a CGI/ASP/JSP/PHP/whatever in order to return the model. scriptJmolApplet(300, /cgi-bin/myCgi.pl?model=someMolecule)/script OR scriptJmolApplet(250, /molecules/someMolecule.jsp?id=1ABC)/script I honestly think that this approach will simplify things and will avoid many problems. No race conditions, much simpler HTML code, cleaner database interface, ... Now, I realize that I am not the one building the applications ... you folks are. But I can honestly only think of one case where people should even consider using jmolAppletInline or jmolLoadInline. That is, if one is building a very high volume database application and is generating *all* of the HTML code on the web server (via server-side scripting), then one *might* want to use the inLine routines. Otherwise, I think that they are too complicated and not worth messing with. I may be mistaken ... let me know what you think :-) Miguel --- This SF.Net email is sponsored by OSTG. Have you noticed the changes on Linux.com, ITManagersJournal and NewsForge in the past few weeks? Now, one more big change to announce. We are now OSTG- Open Source Technology Group. Come see the changes on the new OSTG site. www.ostg.com ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] vibrational frequencies
I downloaded Jmol10pre12 and tried to open a gaussian98 output file (frequency job). I am running the stand alone Jmol application. I don't see anything in the menu to visualize the frequencies. Oops ... that was pretty silly of me. You are right ... there is no way to control the vibrations from the menus ... a *small* oversight :-) I will put it on our list-of-things-to-do :-) What should I do? For the present time you need to type in scripting commands to see the vibrations. File - Script ... vibration on frame 1 # to show vibration 1 frame 2 # to show vibration 2 frame all # to show all vibrations ... probably has no practical value Miguel --- This SF.Net email is sponsored by OSTG. Have you noticed the changes on Linux.com, ITManagersJournal and NewsForge in the past few weeks? Now, one more big change to announce. We are now OSTG- Open Source Technology Group. Come see the changes on the new OSTG site. www.ostg.com ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
RE: [Jmol-users] Why use jmolAppletInline jmolLoadInline?
Miguel, Well, personal preferences aside ;-)... Your inference is exactly correct. We have a database application (please don't kill me: it is ASP ggghhh!!!) which renders the entire user interface using templates and ASP. Having said that there is no technical reason we couldn't provide a URL for sourcing the MOL content directly. But, we like having the MOL data embedded in the page, because it allows us to use copy/paste to local MOL editing software on the user's machine (we unforunately live mostly in the Windoze world). Since the data is already there, jmolLoadInline() works well for us. So please don't whack it! Cheers, David --- This SF.Net email is sponsored by OSTG. Have you noticed the changes on Linux.com, ITManagersJournal and NewsForge in the past few weeks? Now, one more big change to announce. We are now OSTG- Open Source Technology Group. Come see the changes on the new OSTG site. www.ostg.com ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] vibrational frequencies
Egon wrote: I will put it on our list-of-things-to-do :-) I'll do it... (now). Thanks Egon! Miguel --- This SF.Net email is sponsored by OSTG. Have you noticed the changes on Linux.com, ITManagersJournal and NewsForge in the past few weeks? Now, one more big change to announce. We are now OSTG- Open Source Technology Group. Come see the changes on the new OSTG site. www.ostg.com ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] mixed occupancy
Okay, thanks! Karin At 01:19 PM 8/7/2004 +0200, you wrote: Karen wrote: a crystal contains many atoms and if the crystal has high symmetry, many of the atoms sit on positions that are related. OK ... I follow that. So, if I put in the positions of atoms, I only have to tell the software the position of 1 atom and that it sits on, let's say a 16d position. The software will then generate 16 symmetrically equivalent positions from this 1 atom. Now in many cases all 16 atoms in this 16d position are the same kind - no problem there. OK In some cases, you want to see what happens if you put 8 atoms A and 8 atoms B on those 16 positions and let them mix randomly. The software gives you a chance to define the site occupancy for atom A in a 16d position as 50% and the site occupancy of atom B in a 16d position as 50% - and there is your mix. OK ... understood It would be nice now, if an input like this would create a structure image with this random mix of 2 kinds of atoms on those positions. It only accepts the atom you enter first though and fills all 16 positions with that. Alright, I now gather that you are using Jmol v9 ... correct? If I understand what you are saying, then this functionality does not yet exist in the prerelease Jmol v10 code. I guess one could not use the automatic generation of equivalent positions and instead define each atom individually and try to reach a random mix that way, but it would be more convenient, if the structure representation would translate the structure information directly. Any way to do this? Having the software randomly choose between the atoms seems simple. And it seems to me that it should be straightforward to implement at some point. However, it will have to wait a bit. We are in the process of trying to release Jmol v10. It is a complete rewrite of Jmol and offers some significant performance and functionality improvements. However, v10 has taken a step backwards in some areas of crystallography. In particular, some of the crystal construction and space group functionality is not in the v10 code. The v10 code is currently in code freeze and we are only doing bug fixes. Because of the release of v10, I suspect it will be at least several months before we can add this functionality for you. Stay tuned :-) Miguel --- This SF.Net email is sponsored by OSTG. Have you noticed the changes on Linux.com, ITManagersJournal and NewsForge in the past few weeks? Now, one more big change to announce. We are now OSTG- Open Source Technology Group. Come see the changes on the new OSTG site. www.ostg.com ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users --- SF.Net email is sponsored by Shop4tech.com-Lowest price on Blank Media 100pk Sonic DVD-R 4x for only $29 -100pk Sonic DVD+R for only $33 Save 50% off Retail on Ink Toner - Free Shipping and Free Gift. http://www.shop4tech.com/z/Inkjet_Cartridges/9_108_r285 ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Vibrational frequencies
Hi Jmol users, I am trying to visualize the vibrational frequencies for a molecule for which I ran a compound job opt+freq with gaussian98. I get an error when I try to read in the file. I tried to 're-arrange' the file basically cutting out the optimization part, but it doesn't work. Is there a solution except for running another frequency calculation? Thank you for your help. Valentin --- SF.Net email is sponsored by Shop4tech.com-Lowest price on Blank Media 100pk Sonic DVD-R 4x for only $29 -100pk Sonic DVD+R for only $33 Save 50% off Retail on Ink Toner - Free Shipping and Free Gift. http://www.shop4tech.com/z/Inkjet_Cartridges/9_108_r285 ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Vibrational frequencies
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On Tuesday 10 August 2004 04:19, Valentin Gogonea wrote: I am trying to visualize the vibrational frequencies for a molecule for which I ran a compound job opt+freq with gaussian98. I get an error when I try to read in the file. I tried to 're-arrange' the file basically cutting out the optimization part, but it doesn't work. Is there a solution except for running another frequency calculation? It might be possible that there is a bug in the gaussian98 reader... can we see the file, private, or if possible, redistributable? In the former case, send to file in a private email to Miguel or me... Egon - -- [EMAIL PROTECTED] PhD on Molecular Representation in Chemometrics Nijmegen University http://www.cac.sci.kun.nl/people/egonw/ GPG: 1024D/D6336BA6 Again a chemist did something useful with a computer -BEGIN PGP SIGNATURE- Version: GnuPG v1.0.7 (SunOS) iD8DBQFBGFyFd9R8I9Yza6YRAq7/AJ42aidL4BxMfiQHFewKMoUPLcCmdACeIy8g XrDbdoFNnGJ7sfwyyYBty4g= =hyee -END PGP SIGNATURE- --- SF.Net email is sponsored by Shop4tech.com-Lowest price on Blank Media 100pk Sonic DVD-R 4x for only $29 -100pk Sonic DVD+R for only $33 Save 50% off Retail on Ink Toner - Free Shipping and Free Gift. http://www.shop4tech.com/z/Inkjet_Cartridges/9_108_r285 ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
