Actually, this didn't work. I took the output from a couple of ABINIT runs I had sitting around. Both loaded nicely into Jmol when I parsed the output file. However, when I saved the file as CML, and re-loaded it into Jmol, it didn't work.
Looking at the resulting CML (attached) there doesn't appear to be any crystal specific information in the file. Which is what I was looking for in the first place.
I'm grateful for any help anyone can offer...
Here is a CML file with crystal info I have generated from a crystal structure (CIF). [Apologies for the size but I don't like posting attachments to lists.] Please feel free to add it to the Jmol distribution.
IIRC the <crystal> element cause problems with Jmol and the molecule didn't display. This may have been fixed. I think the file conforms to the Schema - but it will be better to use <symmetry> elements in <crystal> - I haven't got around to converting the letters to matrices.
Note that each atom has both fractional and Cartesian coords.
P.
<molecule>
<crystal>
<scalar dictRef="cml:a">10.0321</scalar>
<scalar dictRef="cml:b">33.0634</scalar>
<scalar dictRef="cml:c">7.4379</scalar>
<scalar dictRef="cml:alpha">90.00</scalar>
<scalar dictRef="cml:beta">93.193</scalar>
<scalar dictRef="cml:gamma">90.00</scalar>
<list id="symm" title="symmetry">
<scalar dictRef="cml:symmpos">x, y, z</scalar>
<scalar dictRef="cml:symmpos">-x, y+1/2, -z+1/2</scalar>
<scalar dictRef="cml:symmpos">-x, -y, -z</scalar>
<scalar dictRef="cml:symmpos">x, -y-1/2, z-1/2</scalar>
</list>
</crystal>
<atomArray>
<atom id="a1" elementType="Cl" xFract="0.59866" yFract="0.01974" zFract="-0.21423" x3="5.996493415258073" y3="0.6526715160000004" z3="-1.9279424524947295"/>
<atom id="a2" elementType="N" xFract="0.6121" yFract="0.09690" zFract="-0.2956" x3="6.13111552380227" y3="3.2038434600000008" z3="-2.5406744213655896"/>
<atom id="a3" elementType="C" xFract="0.6765" yFract="0.12959" zFract="-0.3561" x3="6.776179793909877" y3="4.284686006" z3="-3.026653007830128"/>
<atom id="a4" elementType="H" xFract="0.6268" yFract="0.15406" zFract="-0.3617" x3="6.278358455022485" y3="5.093747404" z3="-3.040533724036843"/>
<atom id="a5" elementType="N" xFract="0.8009" yFract="0.13187" zFract="-0.4089" x3="8.02223562001836" y3="4.360070558" z3="-3.488886754789578"/>
<atom id="a6" elementType="C" xFract="0.8633" yFract="0.09631" zFract="-0.3946" x3="8.64726683825927" y3="3.184336054000001" z3="-3.417392854904286"/>
<atom id="a7" elementType="C" xFract="0.8095" yFract="0.06004" zFract="-0.3361" x3="8.108377743045152" y3="1.9851265360000006" z3="-2.9522131700938488"/>
<atom id="a8" elementType="C" xFract="0.6788" yFract="0.06244" zFract="-0.2877" x3="6.799217803556577" y3="2.0644786960000006" z3="-2.519185849132433"/>
<atom id="a9" elementType="N" xFract="0.9023" yFract="0.02918" zFract="-0.3404" x3="9.03791134965984" y3="0.9647900120000006" z3="-3.0360512187259787"/>
<atom id="a10" elementType="C" xFract="1.0081" yFract="0.04700" zFract="-0.3999" x3="10.097659793408052" y3="1.5539798000000007" z3="-3.5377255286320057"/>
<atom id="a11" elementType="H" xFract="1.0891" yFract="0.03303" zFract="-0.4170" x3="10.908998394009235" y3="1.0920841020000005" z3="-3.710175055800137"/>
<atom id="a12" elementType="N" xFract="0.9919" yFract="0.08745" zFract="-0.4355" x3="9.935392073287815" y3="2.8913943300000007" z3="-3.79346248119838"/>
<atom id="a13" elementType="C" xFract="1.0892" yFract="0.11720" zFract="-0.4945" x3="10.910000046602569" y3="3.875030480000001" z3="-4.286668184117628"/>
<atom id="a14" elementType="H" xFract="1.0484" yFract="0.13283" zFract="-0.5969" x3="10.501325788521974" y3="4.391811422000001" z3="-5.025510790581088"/>
<atom id="a15" elementType="H" xFract="1.1108" yFract="0.13638" zFract="-0.3949" x3="11.126357006762884" y3="4.509186492000001" z3="-3.557923060695796"/>
<atom id="a16" elementType="C" xFract="1.2125" yFract="0.09858" zFract="-0.5493" x3="12.145037694184369" y3="3.259389972000001" z3="-4.763163069584672"/>
<atom id="a17" elementType="C" xFract="1.3146" yFract="0.08546" zFract="-0.5939" x3="13.167724991979194" y3="2.825598164000001" z3="-5.151945171743513"/>
<atom id="a18" elementType="H" xFract="1.3970" yFract="0.07486" zFract="-0.6299" x3="13.993086728887064" y3="2.475126124000001" z3="-5.465753305356525"/>
<atom id="a19" elementType="Cl" xFract="0.56889" yFract="0.14440" zFract="0.17211" x3="5.698301438222306" y3="4.77435496" z3="0.9622508086224961"/>
<atom id="a20" elementType="N" xFract="0.6249" yFract="0.06816" zFract="0.2443" x3="6.259327055749124" y3="2.2536013440000007" z3="1.4678953639954957"/>
<atom id="a21" elementType="C" xFract="0.7077" yFract="0.03607" zFract="0.2479" x3="7.088695403030333" y3="1.1925968380000005" z3="1.4484045571125177"/>
<atom id="a22" elementType="H" xFract="0.6726" yFract="0.01178" zFract="0.2944" x3="6.73711534276982" y3="0.3894868520000005" z3="1.8138801965520408"/>
<atom id="a23" elementType="N" xFract="0.8324" yFract="0.03379" zFract="0.1951" x3="8.33775618691882" y3="1.1172122860000004" z3="0.9860031752005931"/>
<atom id="a24" elementType="C" xFract="0.8733" yFract="0.06930" zFract="0.1319" x3="8.74743209759275" y3="2.2912936200000007" z3="0.4930736633465619"/>
<atom id="a25" elementType="C" xFract="0.7991" yFract="0.10492" zFract="0.1197" x3="8.004205873338334" y3="3.4690119280000005" z3="0.44379299492526936"/>
<atom id="a26" elementType="C" xFract="0.6717" yFract="0.10245" zFract="0.1793" x3="6.7281004694298066" y3="3.3873453300000005" z3="0.9582808114094648"/>
<atom id="a27" elementType="N" xFract="0.8724" yFract="0.13584" zFract="0.0473" x3="8.738417224252737" y3="4.491332256000001" z3="-0.1356697717960143"/>
<atom id="a28" elementType="C" xFract="0.9874" yFract="0.11843" zFract="0.0186" x3="9.89031770658775" y3="3.9156984620000004" z3="-0.4133975669112616"/>
<atom id="a29" elementType="H" xFract="1.0593" yFract="0.13245" zFract="-0.0313" x3="10.610505921195465" y3="4.379247330000002" z3="-0.8247252871876639"/>
<atom id="a30" elementType="N" xFract="0.9949" yFract="0.07850" zFract="0.0664" x3="9.96544165108786" y3="2.5954769000000004" z3="-0.06205682072312568"/>
<atom id="a31" elementType="C" xFract="1.1057" yFract="0.04971" zFract="0.0484" x3="11.07527272450281" y3="1.6435816140000006" z3="-0.257852196503729"/>
<atom id="a32" elementType="H" xFract="1.1354" yFract="0.03938" zFract="0.1690" x3="11.372763544723243" y3="1.3020366920000006" z3="0.6225626832012897"/>
<atom id="a33" elementType="H" xFract="1.0737" yFract="0.02643" zFract="-0.0258" x3="10.754743894635677" y3="0.8738656620000007" z3="-0.791863314906443"/>
<atom id="a34" elementType="C" xFract="1.2185" yFract="0.06855" zFract="-0.0348" x3="12.205136849784456" y3="2.266496070000001" z3="-0.9397162186341628"/>
<atom id="a35" elementType="C" xFract="1.3116" yFract="0.08223" zFract="-0.1033" x3="13.137675414179151" y3="2.718803382000001" z3="-1.5012350822187674"/>
<atom id="a36" elementType="H" xFract="1.3866" yFract="0.09326" zFract="-0.1585" x3="13.888914859180245" y3="3.0834926840000008" z3="-1.9537159003374067"/>
<atom id="a37" elementType="Cl" xFract="1.37176" yFract="0.31091" zFract="0.18674" x3="13.740269614329362" y3="10.279741694000004" z3="0.622437037978335"/>
<atom id="a38" elementType="N" xFract="1.3361" yFract="0.23243" zFract="0.1856" x3="13.383080299546174" y3="7.6849260620000015" z3="0.6338840399958106"/>
<atom id="a39" elementType="C" xFract="1.2613" yFract="0.19923" zFract="0.2095" x3="12.63384415973175" y3="6.587221182000001" z3="0.8534468314794671"/>
<atom id="a40" elementType="H" xFract="1.3041" yFract="0.17404" zFract="0.1916" x3="13.062551469679041" y3="5.754354136000001" z3="0.6963925015930966"/>
<atom id="a41" elementType="N" xFract="1.1348" yFract="0.19723" zFract="0.2550" x3="11.366753629163236" y3="6.521094382000001" z3="1.262557353106239"/>
<atom id="a42" elementType="C" xFract="1.0819" yFract="0.23368" zFract="0.2747" x3="10.83687940728913" y3="7.726255312000001" z3="1.4386436130592526"/>
<atom id="a43" elementType="C" xFract="1.1472" yFract="0.27040" zFract="0.2548" x3="11.49095855073675" y3="8.94034336" z3="1.254140861737291"/>
<atom id="a44" elementType="C" xFract="1.2788" yFract="0.26772" zFract="0.2103" x3="12.809133363565337" y3="8.851733448000001" z3="0.8496184459184514"/>
<atom id="a45" elementType="N" xFract="1.0616" yFract="0.30230" zFract="0.2852" x3="10.633543930842167" y3="9.99506582" z3="1.5280848615100315"/>
<atom id="a46" elementType="C" xFract="0.9503" yFract="0.28438" zFract="0.3226" x3="9.518704594460543" y3="9.402569692000002" z3="1.8684548888780925"/>
<atom id="a47" elementType="H" xFract="0.8722" yFract="0.29891" zFract="0.3497" x3="8.736413919066068" y3="9.882980894000001" z3="2.113662944838969"/>
<atom id="a48" elementType="N" xFract="0.95527" yFract="0.24320" zFract="0.3195" x3="9.56848672834928" y3="8.041018880000001" z3="1.8426202464987638"/>
<atom id="a49" elementType="C" xFract="0.8484" yFract="0.21391" zFract="0.3507" x3="8.498020601852387" y3="7.072591894000001" z3="2.1343998844019505"/>
<atom id="a50" elementType="H" xFract="0.8182" yFract="0.20140" zFract="0.2345" x3="8.195521518665279" y3="6.658968760000001" z3="1.2869911562843892"/>
<atom id="a51" elementType="H" xFract="0.8845" yFract="0.19217" zFract="0.4309" x3="8.859617188046247" y3="6.353793578000001" z3="2.710747391787512"/>
<atom id="a52" elementType="C" xFract="0.7345" yFract="0.23259" zFract="0.4315" x3="7.357138298044058" y3="7.6902162060000006" z3="2.799027608024791"/>
<atom id="a53" elementType="C" xFract="0.6405" yFract="0.24657" zFract="0.4953" x3="6.415584860309351" y3="8.152442538" z3="3.3260912464668193"/>
<atom id="a54" elementType="H" xFract="0.5645" yFract="0.25787" zFract="0.5470" x3="5.654328889374908" y3="8.526058958" z3="3.753098197760374"/>
</atomArray>
<bondArray>
<bond atomRefs2="a1 a8" order="1"/>
<bond atomRefs2="a2 a3" order="2"/>
<bond atomRefs2="a2 a8" order="1"/>
<bond atomRefs2="a3 a4" order="1"/>
<bond atomRefs2="a3 a5" order="1"/>
<bond atomRefs2="a5 a6" order="2"/>
<bond atomRefs2="a6 a7" order="1"/>
<bond atomRefs2="a6 a12" order="1"/>
<bond atomRefs2="a7 a8" order="1"/>
<bond atomRefs2="a7 a9" order="2"/>
<bond atomRefs2="a9 a10" order="1"/>
<bond atomRefs2="a10 a11" order="1"/>
<bond atomRefs2="a10 a12" order="1"/>
<bond atomRefs2="a12 a13" order="1"/>
<bond atomRefs2="a13 a14" order="1"/>
<bond atomRefs2="a13 a15" order="1"/>
<bond atomRefs2="a13 a16" order="1"/>
<bond atomRefs2="a16 a17" order="3"/>
<bond atomRefs2="a17 a18" order="1"/>
<bond atomRefs2="a19 a26" order="1"/>
<bond atomRefs2="a20 a21" order="2"/>
<bond atomRefs2="a20 a26" order="1"/>
<bond atomRefs2="a21 a22" order="1"/>
<bond atomRefs2="a21 a23" order="1"/>
<bond atomRefs2="a23 a24" order="2"/>
<bond atomRefs2="a24 a25" order="1"/>
<bond atomRefs2="a24 a30" order="1"/>
<bond atomRefs2="a25 a26" order="1"/>
<bond atomRefs2="a25 a27" order="2"/>
<bond atomRefs2="a27 a28" order="1"/>
<bond atomRefs2="a28 a29" order="1"/>
<bond atomRefs2="a28 a30" order="1"/>
<bond atomRefs2="a30 a31" order="1"/>
<bond atomRefs2="a31 a32" order="1"/>
<bond atomRefs2="a31 a33" order="1"/>
<bond atomRefs2="a31 a34" order="1"/>
<bond atomRefs2="a34 a35" order="3"/>
<bond atomRefs2="a35 a36" order="1"/>
<bond atomRefs2="a37 a44" order="1"/>
<bond atomRefs2="a38 a39" order="2"/>
<bond atomRefs2="a38 a44" order="1"/>
<bond atomRefs2="a39 a40" order="1"/>
<bond atomRefs2="a39 a41" order="1"/>
<bond atomRefs2="a41 a42" order="2"/>
<bond atomRefs2="a42 a43" order="1"/>
<bond atomRefs2="a42 a48" order="1"/>
<bond atomRefs2="a43 a44" order="1"/>
<bond atomRefs2="a43 a45" order="2"/>
<bond atomRefs2="a45 a46" order="1"/>
<bond atomRefs2="a46 a47" order="1"/>
<bond atomRefs2="a46 a48" order="1"/>
<bond atomRefs2="a48 a49" order="1"/>
<bond atomRefs2="a49 a50" order="1"/>
<bond atomRefs2="a49 a51" order="1"/>
<bond atomRefs2="a49 a52" order="1"/>
<bond atomRefs2="a52 a53" order="3"/>
<bond atomRefs2="a53 a54" order="1"/>
</bondArray>
</molecule>
Rick
On Thursday, October 9, 2003, at 02:54 PM, Fabian Dortu wrote:
I have to find the time to generate a CML file from the last version of ABINIT. It is expected this file will be readable by jmol.
Fab
On Thu, 2003-10-09 at 21:49, Miguel wrote:Rick Muller [EMAIL PROTECTED]
------------------------------------------------------- This SF.net email is sponsored by: SF.net Giveback Program. SourceForge.net hosts over 70,000 Open Source Projects. See the people who have HELPED US provide better services: Click here: http://sourceforge.net/supporters.php _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
