Re: [Jmol-users] mmcif reading problem?

The difference is that the mmCIF reader was split off from the CIF reader. In the past, the CIF reader included all the macromolecule code, and somewhere along the way of reading it all Jmol determined that it was mmCIF and not CIF. That is a difference recently introduced. Actually it doesn't matt

Re: [Jmol-users] mmcif reading problem?

Sorry - I was looking at the script console. Indeed Jmol 14.3.12 and Jmol 13.3.7 both 'think Cif' Console output is below for both: 1) From Jmol 14.3.12_2015.02.25c: cacheGet file:/srv/www/htdocs/publcryst/cifmoldb/gui/tests/4QQS.cif false FileManager opening 1 file:/srv/www/htdocs/publcryst

Re: [Jmol-users] mmcif reading problem?

> Using Jmol application I dont get any 'resolver' messages in the console, I thought I've seen that... I meant it just as a diagnostic tool, not a solution. Ah, it is at least in the "Jmol Java Console" (accesible form Jmol application top menu > Help ) Jmol 14.3.12_2015-02-19 load http://ci

Re: [Jmol-users] mmcif reading problem?

Using Jmol application I dont get any 'resolver' messages in the console, and using the Jmol application to open a file via the menus you dont get an option to say 'this is an mmcif'. Fair enough I can pre-process the CIF or script Jmol to make sure it will be recognized by Jmol (application or

Re: [Jmol-users] mmcif reading problem?

Simon, usually the console tells you what file format is being assumed on loading. Something like "resolver thinks: pdb" Can you see that? -- Dive into the World of Parallel Programming The Go Parallel Website, sponsore

Re: [Jmol-users] mmcif reading problem?

Thanks for the info - the original problem was the second example I gave - I only added the blank lines in order to try and figure out what the problem was. In the case of the second example, Jmol-13.3.7 had no problem with reading the CIF, while Jmol 14+ doesnt offer cartoons as an option etc., b

Re: [Jmol-users] mmcif reading problem?

So don't add blank lines. ;) Jmol needs to identify the file as mmCIF in the first 16 lines, exclusive of comments. If you are adding lines, add one along with those blank lines starting like one of these: private final static String[] mmcifLineStartRecords = { "MMCif",* "_entry.id

Re: [Jmol-users] mmcif reading problem?

-- Angel got it -- exactly. On Fri, Feb 27, 2015 at 10:21 AM, Robert Hanson wrote: > So don't add blank lines. ;) > > Jmol needs to identify the file as mmCIF in the first 16 lines, exclusive > of comments. > If you are adding lines, add one along with those blank lines starting > like one of th

Re: [Jmol-users] mmcif reading problem?

Aha, there it is: http://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol/src/org/jmol/a dapter/smarter/Resolver.java line 573: // Test 4. One of the first 16 lines starts with one of these strings [snip] private final static String[] mmcifLineStartRecords = { "MMCif", "_entry.id", "_database_PD

Re: [Jmol-users] mmcif reading problem?

Hi Simon As far as know, Jmo reads the fisrt N lines of every file in search for tokens that will tell what format the file is in. Your insertion of lines is probably making ti not reach the relevant, information-richs lines. There was a similar problem recently reported with PDB files from a

Re: [Jmol-users] mmcif reading problem?

I'm afraid I'm still having some problems: If I add 13 blank lines after the start of a data block, Jmol seems to not handle the secondary structure again, e.g. data_UNNAMED # loop_ _atom_site.group_PDB ... Furthermore, its not just blank lines, e.g. data_ _atom_sites.entry_