Hi Miguel, Thanks again for your cooperation.
I'm not fully happy with the Chime plug-in :-)! Again, it's Windows/IE only, and the display is not as *nice* as with JMOL. I don't want to say "look they do better than you" because actually I think the opposite way! But my users require support from information coming from MDL products i.e. mol description in V2000 AND V3000. No way for me to force them to get only V2000. File containing more than one molecule The sample file contains more than one molecule because it's an "SD file". SD file is basically a grouping of mol descriptions in a file with some extra information (the information you want btw ...). All the molecules are separated with a specific string: $$$$. Ok ... it's basic but it seems to be widely used in industry as a way to exchange mol description. What does Chime do? MDL provides a number of products dealing with chemistry. They provide chemical entity recognition component and a name to structure component. The name to structure sent back either a mol description or a chime string. A chime string is an MDL encrypted, compressed version of a mol description (MDL proprietary algorithm). Chime strings are also properly displayed by the MDL chime plug-in. But chime strings does not seem to be standard. By dealing with mol descriptions, much more things can be done: SD file generation for post processing ... and display with another component ...like JMOL! Hope this clarifies ... Hervé -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Miguel Sent: jeudi 23 mars 2006 00:30 To: [email protected] Subject: RE: [Jmol-users] Support of V3000 Mol format > Per my previous e-mail, I have a Windows solution that works (free MDL > Chime plug-in). If you are happy with Chime then you should use it. > The file I sent you is properly displayed by this plug-in > even in 3D. I have added preliminary test code to Jmol which supports the V3000 format. I did not realize that you file was 2D until I tested your file. I am not very familiar with Chime. I do not know what Chime's behavior is when it reads a 2D .mol/.sdf file. Jmol will treat it as a 3D molecule where all the Z coordinates are 0.0 ... just as it is written in the file. This presents problems with files that do not have connectivity information because the distances are incorrect, causing problems for the 'autobond' code. In addition, some 2D files store coordinates as integer pixel counts ... which Jmol interprets as angstroms. These do not seem to be problems in the sample file that you sent. There is a connection table and the distances look reasonable. I have been told by several experts that this is not a good way to represent 2D data, because it can give the wrong impression that the molecule is flat. That is the primary reason why I suggested that you may want to consider a proper 2D viewer. I have some questions about the format ... The sample file contains more than one molecule in the file ... Q: What is the proper behavior if more than one molecule is present in the file? Q: What does Chime do? Miguel ------------------------------------------------------- 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_______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users ------------------------------------------------------- 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&kid0944&bid$1720&dat1642 _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
