Re: [Jmol-users] incomplete cartoons in Calpha-only files

Terrific! Thank you. On Fri, Jul 8, 2016 at 10:43 AM, Sameer Velankar wrote: > Hi All, > I am assuming this request on Jmil-user list came from Jaime and so > copying him as well. This is now updated and the error is fixed so the new > file has "_struct_sheet_range.sheet_id". > Kind regards, >

Re: [Jmol-users] incomplete cartoons in Calpha-only files

Bob Suggest you send these msgs to PDBe Joel Sent from my iPhone > On Jul 8, 2016, at 17:59, Robert Hanson wrote: > > Jmol is expecting at the very least _struct_sheet_range... > > final private static String[] structSheetRangeFields = { > "*_sheet_id", > "*_beg_auth_asym_id",

Re: [Jmol-users] incomplete cartoons in Calpha-only files

On Fri, Jul 8, 2016 at 9:09 AM, Herráez Sánchez Ángel wrote: > Thank you, Bob > > > > I recommend that Proteopedia not remove the helix/sheet records. > > > Of course. That is feasible with the pdb files that were formerly used, > and we had thought of it (me and Jaime). > > > The problem now is

Re: [Jmol-users] incomplete cartoons in Calpha-only files

Jmol is expecting at the very least _struct_sheet_range... final private static String[] structSheetRangeFields = { "*_sheet_id", "*_beg_auth_asym_id", "*_beg_auth_seq_id", "*_pdbx_beg_pdb_ins_code", "*_end_auth_asym_id", "*_end_auth_seq_id", "*_pdbx_e

Re: [Jmol-users] incomplete cartoons in Calpha-only files

[forwarding this to EBI] I'm going to *suggest* that EBI is producing invalid files: http://mmcif.wwpdb.org/dictionaries/mmcif_std.dic/Items/_struct_sheet_range.sheet_id.html Item name_struct_sheet_range.sheet_idCategory namestruct_sheet_range

Re: [Jmol-users] incomplete cartoons in Calpha-only files

Yes, but the file is supposed to be an (mm)CIF file! They are changing the rules Doesn't surprise me -- there is no assembly-file reader in Jmol. And note the file loads fine in Jmol when it is complete, it's the Calpha-only filter that brings the failure. Am

Re: [Jmol-users] incomplete cartoons in Calpha-only files

Doesn't surprise me -- there is no assembly-file reader in Jmol. ​ -- Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San Francisco, CA to explore cutting-edge tech and listen to tech luminaries present

Re: [Jmol-users] incomplete cartoons in Calpha-only files

Jmol is unable to extract and render Sheet information from the new PDBe generated cif files, with chain IDs in sheet records are specified as A-2, A-3 , see http://www.ebi.ac.uk/pdbe/coordinates/1stp/assembly?id=1 On 8 Jul 2016, at 5:09 PM, Herráez Sánchez Ángel mailto:angel.herr...@uah.es>>

Re: [Jmol-users] incomplete cartoons in Calpha-only files

Thank you, Bob > I recommend that Proteopedia not remove the helix/sheet records. Of course. That is feasible with the pdb files that were formerly used, and we had thought of it (me and Jaime). The problem now is that Protepedia is now swiatching to using a copy of the "assembly" mmCIF fil

Re: [Jmol-users] incomplete cartoons in Calpha-only files

It's a design feature, not a bug. The calculation uses: // // alpha-carbon-only secondary structure determination // // Levitt and Greer // Automatic Identification of Secondary Structure in Globular Proteins // J.Mol.B

Re: [Jmol-users] incomplete cartoons in Calpha-only files

Same problem in both. Now I am testing with 2016.06.30 and Proteopedia is using 2016.06.22 (both 14.6.0) I am starting to suspect the file contents (mmCIF, assembly mmCIF) more than Jmol version itself -- Attend Shape

Re: [Jmol-users] incomplete cartoons in Calpha-only files

ries) > > > De: Herráez Sánchez Ángel mailto:angel.herr...@uah.es>> > Enviado: jueves, 30 de junio de 2016 17:07 > Para: jmol-users list > Asunto: [Jmol-users] incomplete cartoons in Calpha-only files > > We are seeing a problem in Proteopedia that apparently was n

Re: [Jmol-users] incomplete cartoons in Calpha-only files

other issues -strands broken into triangles- so I have mixed memories) De: Herráez Sánchez Ángel Enviado: jueves, 30 de junio de 2016 17:07 Para: jmol-users list Asunto: [Jmol-users] incomplete cartoons in Calpha-only files We are seeing a problem in Proteopedia

[Jmol-users] incomplete cartoons in Calpha-only files

We are seeing a problem in Proteopedia that apparently was not present before (it is unlikely that it had went unnoticed). I wonder if it is the result of upgrade to recent Jmol versions. (14.4 at least, 14.6 for sure) I am still seeing it with today's release 14.6.0_2016.06.30 It affects both