My mistake. I dropped a line of code in the JVXL file reading section. The JVXL file is ok, but Jmol 11.1.30 is just skipping the color. I'll get this up at St. Olaf momentarily. That's probably the white/orange issue as well, because orange is the default color now. The zip file is
http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/Jmol-11_1.zip It will show up as 11.1.31, and if Nico can get that released, it's fine with me. 11.1.31 fixes a bug that 11.1.29/30 were not reading the color of JVXL file data. 11.1.31 adds better property data loading: ------------------------------------------- propertyDataField = 3 # data will be in the third column propertyAtomNumberField = 2 # atom numbers will be in the 2nd column propertyDataField = 0 # data are not in columns, just white-space separated. With propertyDataField = 0, all nonnumeric information is ignored. It's just a stream of numbers. With propertyDataField = 3, data is read line by line, but only the third white-space-delimited field is read for data. With propertyAtomNumberField = 1, data is matched to the atom number contained in the first field. In all cases you need to select the desired atoms upon which to map the data prior to issuing the data "property_x @x" command. So, for example, if the file "my.data" looks like this: atomno data1 data2 -------- ------ ----- 3 2.4 -5.4 4 6.5 -9.5 6 5.2 -5.3 Then x = load("my.data") propertyAtomNumberField = 1 propertyDataField = 2 select 1.2 #second model in the first file data "property_x @x" will create data for atoms 3, 4, and 6 only -- 2.4, 6.5, and 5.2, respectively. (if other atoms have been assigned this property already, values will be set to 0) For the same data, propertyAtomNumberField = 0 propertyDataField = 2 select *.CA/1.2 # alpha carbons in second model in the first file data "property_x @x" disregards the atom number idea and fills the property for the first three alpha carbons in that model. For the same data, propertyAtomNumberField = 0 propertyDataField = 0 select * data "property_x @x" fills the property for the first nine atoms loaded (starting in frame 1) 3 2.4 -5.4 4 6.5 -9.5 6 5.2 -5.3 Note, too, that label %{property_x} labels the atoms with that property. -------------- Seems to me this should do the trick. I look forward to seeing applications of this. Note that the "free-format" PQR files that some programs produce can thus be read for charge data after the fact. One would first load the regular full-featured PDB file, then add the charge data later from column 9 or 10, depending upon whether the chain_ID field is there or not. Bob Bob Angel Herraez wrote: >I've being mad all morning trying to get some surfaces color-mapped >by MEP. I've got the mep in a dx file, and it works correctly. >However, when I save to JVXL, I cannot recover the mapping, only get >a plain orange surface. >In the end, it seems that it is a difference in the latest versions >(11.1.30 and 11.1.29 at least), since I test in 11.1.5 and it works. >See >http://biomodel.uah.es/Jmol/surfaces/test/ > >I've tried with at least 2 different dx files, prepared by different >means. > >Is this a change in syntax/behaviour that I cannot figure out, or a >bug? I find no way to colormap the jvxl surface (when I create it >first, it is colored, but not after saving to jvxl) > >Thanks > > >------------------------------------------------------------------------- >This SF.net email is sponsored by DB2 Express >Download DB2 Express C - the FREE version of DB2 express and take >control of your XML. No limits. Just data. Click to get it now. >http://sourceforge.net/powerbar/db2/ >_______________________________________________ >Jmol-users mailing list >[email protected] >https://lists.sourceforge.net/lists/listinfo/jmol-users > > ------------------------------------------------------------------------- This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
