Tried this and the latest release and I'm afraid there's still a problem. I've experimented quite a bit and it looks like an assembly that is generated by using *only* the identity operation is causing the problem. e.g. in the cae of 3fsx:
loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,F,G,H,I,J,Z,C,N,P,BA,B,K,L,M,O,AA # <-- here symop 1 is 1_555 x,y,z ... 2 1,2,3 D,Q,R,S,T,U,DA 3 '1,2,3' E,V,W,X,Y,CA load =3fsx.cif filter "ASSEMBLY 1" fails (with the error reported below in Jsmol - the java applet just 'hangs'), while load =3fsx.cif filter "ASSEMBLY 2" and load =3fsx.cif filter "ASSEMBLY 3" are OK. Sorry for not being able to report back sooner (i.e. before you put out 13.3.8 - though this is a relatively minor bug as most people seem to work with pbb files rather than mmcifs :-) Cheers Simon Quoting Robert Hanson <[email protected]>: > could be. I had some compiling errors. Please try > http://chemapps.stolaf.edu/jmol/zip/Jmol.zip > > > > > On Sun, Oct 27, 2013 at 6:40 AM, <[email protected]> wrote: > >> Thanks, but I now get the error: >> >> File Error:ERROR creating model: TypeError: c.get(...).get(...) is null >> script ERROR: ERROR creating model: TypeError: c.get(...).get(...) is null >> >> when calling load =3fsx.cif filter "ASSEMBLY 1" >> >> However, I am also unable to use the java applets at all >> (I'm getting class not found exceptions - under windows and linux), >> so could it just be a problem with the packaging of >> jmol-13.3.8_2013.10.24.zip? >> >> Cheers >> >> Simon >> >> >> >> >> >> Quoting Robert Hanson <[email protected]>: >> >> CIF reader bug fixed >>> >>> http://chemapps.stolaf.edu/**jmol/zip/jmol-13.3.8_2013.10.**24.zip<http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.8_2013.10.24.zip> >>> >>> >>> >>> >>> On Thu, Oct 24, 2013 at 4:34 PM, Robert Hanson <[email protected]> >>> wrote: >>> >>> definitely a Jmol bug. Will check it out. >>>> >>>> >>>> On Wed, Oct 23, 2013 at 5:41 AM, <[email protected]> wrote: >>>> >>>> Calling: >>>>> >>>>> load =3fsx.cif filter "ASSEMBLY 1" >>>>> >>>>> gives the following error: >>>>> >>>>> for file >>>>> http://www.rcsb.org/pdb/files/**3fsx.cif<http://www.rcsb.org/pdb/files/3fsx.cif> >>>>> type MMCIF_PDBX >>>>> script ERROR: Error reading file at line 14991: >>>>> 2 1,2,3 D,Q,R,S,T,U,DA >>>>> null >>>>> >>>>> Am I doing something wrong, or is Jmol (version 13.3.4), or perhaps the >>>>> PDB? >>>>> >>>>> Cheers >>>>> >>>>> Simon >>>>> >>>>> >>>>> ------------------------------**------------------------------** >>>>> ------------------ >>>>> October Webinars: Code for Performance >>>>> Free Intel webinars can help you accelerate application performance. >>>>> Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most >>>>> from >>>>> the latest Intel processors and coprocessors. See abstracts and >>>>> register > >>>>> >>>>> http://pubads.g.doubleclick.**net/gampad/clk?id=60135991&iu=** >>>>> /4140/ostg.clktrk<http://pubads.g.doubleclick.net/gampad/clk?id=60135991&iu=/4140/ostg.clktrk> >>>>> ______________________________**_________________ >>>>> Jmol-users mailing list >>>>> [email protected].**net <[email protected]> >>>>> https://lists.sourceforge.net/**lists/listinfo/jmol-users<https://lists.sourceforge.net/lists/listinfo/jmol-users> >>>>> >>>>> >>>> >>>> >>>> -- >>>> Robert M. Hanson >>>> Larson-Anderson Professor of Chemistry >>>> St. Olaf College >>>> Northfield, MN >>>> http://www.stolaf.edu/people/**hansonr<http://www.stolaf.edu/people/hansonr> >>>> >>>> >>>> If nature does not answer first what we want, >>>> it is better to take what answer we get. >>>> >>>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 >>>> >>>> >>>> >>> >>> -- >>> Robert M. Hanson >>> Larson-Anderson Professor of Chemistry >>> St. Olaf College >>> Northfield, MN >>> http://www.stolaf.edu/people/**hansonr<http://www.stolaf.edu/people/hansonr> >>> >>> >>> If nature does not answer first what we want, >>> it is better to take what answer we get. >>> >>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 >>> >>> >> >> > > > -- > Robert M. Hanson > Larson-Anderson Professor of Chemistry > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > ------------------------------------------------------------------------------ Android is increasing in popularity, but the open development platform that developers love is also attractive to malware creators. Download this white paper to learn more about secure code signing practices that can help keep Android apps secure. http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/4140/ostg.clktrk _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
