at 11:22 am EDT on (Tuesday) 4 November 2003 Sebastian Lisken said: > Hi again, the recent discussion I joined was about .pdb files and > the "set connect" script command. Miguel said that when there is > bond information in a file, Jmol should stick to it, and I wonder > if this would apply to all formats. Back in the days of CaGe > development, the suggestion was made to indicate in a molecule > convention that the data should be taken "as is", even in the > case of "unchemical" molecules. >
hi Sebastian, my 2c: I have always believed that data should be stored in the data file, and not in the software. if you want to create an "unchemical" molecule, rendering software should not second-guess you. of course, that might give rise to strange and funky results, but data files are much easier to "fix" than software. that being said, I do support software applying default rules in the absence of data from a file. I just don't think it should override. I don't know enough about JMol yet to know what it does, but I cc'd your message to the developer list. regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization <http://www.molvisions.com/> usa:north carolina:wake forest > I got a colleague who is still working with CaGe to send me two > samples of the CML format that I made our program send to the Jmol > applet. Note the "convention" in the third lines. I wonder what a > current version of the applet would make of them? What the display > should be with the "unchemical" file I don't know, I'm afraid - this > is not a question of the "what do you see" style but rather one > for the developers: what would Jmol make of the data in these > files, and would you be willing to make it adhere strictly to the > bonds and atom positions? > > Sebastian > > > ----- > <?xml version="1.0" encoding="ISO-8859-1"?> > <!DOCTYPE molecule SYSTEM "cml.dtd" []> > <molecule convention="MathGraph"> > <atomArray> > <stringArray builtin="id">a1 a2 a3 a4 a5 a6 a7 a8 a9 a10 a11 a12 a13 a14 > a15 a16 a17 a18 a19 a20 a21 a22 a23 a24 a25 a26 a27 a28 a29 a30 a31 a32 a33 > a34 a35 a36 a37 a38 a39 a40 a41 a42 a43 a44 a45 a46 a47 a48 a49 a50 a51 a52 > a53 a54 a55 a56 a57 a58 a59 a60</stringArray> > <stringArray builtin="elementType">C C C C C C C C C C C C C C C C C C C C > C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C > C</stringArray> > <floatArray builtin="x3">-3.17 -3.182 -3.186 -2.388 -1.581 -0.277 0.537 > 1.848 2.358 3.171 3.182 3.186 2.388 1.581 0.277 -0.537 -1.848 -2.358 -3.162 > -2.345 -1.53 -0.22 0.587 1.891 2.382 1.57 1.558 0.247 -0.264 -1.572 -2.371 > -3.177 -3.165 -2.351 -1.534 -0.225 0.266 -0.552 -1.86 -2.382 -1.891 -0.587 > 0.22 1.53 2.345 3.162 3.166 3.177 2.371 1.572 0.264 -0.247 -1.558 -1.57 -0.266 > 0.225 1.534 2.351 1.86 0.551</floatArray> > <floatArray builtin="y3">-1.401 -0.799 0.596 0.946 2.089 2.052 2.822 2.413 > 2.517 1.401 0.799 -0.596 -0.946 -2.089 -2.052 -2.822 -2.413 -2.517 -0.608 > -1.233 -0.463 -0.872 0.271 0.234 1.312 2.428 3.03 3.439 3.335 2.882 2.533 1.39 > 0.788 1.558 0.933 1.386 2.465 3.09 2.637 -1.312 -0.234 -0.271 0.872 0.463 > 1.233 0.608 -0.788 -1.39 -2.533 -2.882 -3.335 -3.439 -3.03 -2.428 -2.465 > -1.386 -0.933 -1.558 -2.637 -3.09</floatArray> > <floatArray builtin="z3">0.138 -1.126 -1.237 -2.332 -2.275 -2.784 -1.945 > -1.673 -0.374 -0.138 1.126 1.237 2.332 2.275 2.784 1.945 1.673 0.374 1.291 > 2.24 3.079 3.351 3.409 2.899 2.154 1.918 0.654 0.382 -0.918 -1.121 -0.026 > -0.083 1.181 2.019 2.969 3.172 2.427 1.478 1.274 -2.154 -2.899 -3.409 -3.351 > -3.079 -2.24 -1.291 -1.181 0.083 0.026 1.121 0.918 -0.382 -0.654 -1.918 -2.427 > -3.172 -2.968 -2.019 -1.274 -1.478</floatArray> > </atomArray> > <bondArray> > <stringArray builtin="atomRef">a1 a1 a1 a2 a2 a3 a3 a4 a4 a5 a5 a6 a6 a7 > a7 a8 a8 a9 a9 a10 a10 a11 a11 a12 a12 a13 a13 a14 a14 a15 a15 a16 a16 a17 a17 > a18 a19 a19 a20 a21 a21 a22 a23 a23 a24 a25 a26 a26 a27 a28 a28 a29 a30 a31 > a31 a32 a33 a34 a34 a35 a36 a37 a38 a40 a40 a41 a42 a42 a43 a44 a44 a45 a46 > a47 a47 a48 a49 a49 a50 a51 a52 a52 a53 a54 a55 a55 a56 a57 a58 > a59</stringArray> > <stringArray builtin="atomRef">a18 a19 a2 a3 a40 a32 a4 a5 a41 a30 a6 a7 > a43 a29 a8 a9 a45 a27 a10 a11 a46 a25 a12 a13 a48 a24 a14 a15 a50 a22 a16 a17 > a51 a20 a18 a53 a20 a33 a21 a22 a35 a23 a24 a36 a25 a26 a27 a37 a28 a29 a38 > a30 a31 a32 a39 a33 a34 a35 a39 a36 a37 a38 a39 a41 a54 a42 a43 a56 a44 a45 > a57 a46 a47 a48 a58 a49 a50 a59 a51 a52 a53 a60 a54 a55 a56 a60 a57 a58 a59 > a60</stringArray> > </bondArray> > </molecule> > > ----- > <?xml version="1.0" encoding="ISO-8859-1"?> > <!DOCTYPE molecule SYSTEM "cml.dtd" []> > <molecule convention="MathGraph"> > <atomArray> > <stringArray builtin="id">a1 a2 a3 a4 a5 a6 a7 a8 a9 a10 a11 a12 a13 a14 > a15 a16 a17 a18 a19</stringArray> > <stringArray builtin="elementType">X X C X C Si Si X X C Si S C X C Si C C > Si</stringArray> > <floatArray builtin="x3">-0.51 -0.242 -0.454 -1.19 -0.474 -1.315 -1.296 > -0.371 0.503 0.433 0.453 0.544 0.431 0.475 0.391 -0.458 0.455 1.331 > 1.293</floatArray> > <floatArray builtin="y3">-0.878 0.042 -0.767 -0.529 -0.687 0.216 0.461 > 0.731 -0.716 -1.634 -1.217 -0.321 1.071 1.058 1.476 1.191 0.291 0.114 > 0.098</floatArray> > <floatArray builtin="z3">-0.36 0.931 1.034 0.24 -1.099 -0.681 0.364 -0.857 > -0.687 0.077 1.135 1.282 1.211 -0.036 -0.776 0.085 -1.589 -0.388 > 0.114</floatArray> > </atomArray> > <bondArray> > <stringArray builtin="atomRef">a1 a1 a1 a1 a1 a1 a1 a1 a2 a2 a2 a2 a2 a2 > a2 a2 a2 a2 a2 a3 a4 a4 a4 a4 a4 a5 a6 a7 a8 a8 a8 a8 a8 a9 a9 a9 a9 a9 a9 a9 > a10 a11 a12 a12 a12 a13 a14 a14 a14 a15 a18</stringArray> > <stringArray builtin="atomRef">a2 a3 a4 a5 a6 a7 a8 a9 a9 a10 a11 a12 a13 > a14 a8 a15 a16 a4 a3 a4 a16 a8 a7 a6 a5 a6 a7 a8 a16 a15 a14 a17 a9 a17 a14 > a18 a19 a12 a11 a10 a11 a12 a19 a14 a13 a14 a19 a18 a17 a16 a19</stringArray> > </bondArray> > </molecule> ------------------------------------------------------- This SF.net email is sponsored by: SF.net Giveback Program. 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