Answers below ! Hervé
-----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Miguel Sent: jeudi 23 mars 2006 01:43 To: [email protected] Subject: RE: [Jmol-users] Support of V3000 Mol format Herve wrote: > 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. Just for my own edification ... Q: Are they all 2D files, or are some of the 3D files? [Hervé Azoulay] Well ... I don't think I can answer this one. What I can tell you is that all the molecules described in the file I sent you are correctly displayed in 3D by the MDL plug-in Q: When Chime reads a 2D file does it display it using the RasMol 3D engine? Or do they have a separate 2D renderer built into Chime? [Hervé Azoulay] Dont know .... > 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. Yes. I have the MDL ctfile specification. [Hervé Azoulay] OK this is where I took all the knowledge I have ... > 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. I understand that 'Chime string' is an encryptedversion of a 'mol description' But I am not clear what a 'mol description' is. Q: Are you using the term 'mol description' to refer to the molecular model file format? In this case .mol/V2000/V3000 ? [Hervé Azoulay] yes > 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 ... I am still somewhat confused :-( Let's try a different approach. You sent me a file that contains 8 molecular models. They contain different molecules, not different conformations of the same molecule. When Jmol opens this file it should: 1. read and display only the first molecular model [Hervé Azoulay] yes. I've sent you an SD file but basically I would like to display only one molecule at a time. 2. read all of the atoms in all of the molecular models into the same Jmol model and display them all at the same time ... essentially merging all of the files together. [Hervé Azoulay] No, see my previous answer 3. read the molecular models independently into individual Jmol 'models' [Hervé Azoulay] No, see my previous answer 4. do something else Q: Which of the 4 choices above best describes your desire? [Hervé Azoulay] The first one :-)! Don't worry about SD file. If I can open a mol file whether it's V2000 or V3000 I'm the king of the world :-) ! 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
