Re: [Jmol-users] Use of variable in a call to getProperty

How about here? http://wiki.jmol.org/index.php/Scripting/GetProperty On Jul 8, 2016, at 11:46 AM, Angel Herráez > wrote: Sure! The question is... where to locate it? Goes to the to-do list. Suggestions or actual page edition are welcome

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

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

-- Forwarded message -- From: sameer Date: Fri, Jul 8, 2016 at 10:01 AM Subject: Re: [Jmol-users] incomplete cartoons in Calpha-only files To: Robert Hanson Cc: jmol-users@lists.sourceforge.net Thanks Bob for pointing this out. Will get

Re: [Jmol-users] Use of variable in a call to getProperty

Sure! The question is... where to locate it? Goes to the to-do list. Suggestions or actual page edition are welcome On 8 Jul 2016 at 9:59, Robert Hanson wrote: Might be a nice addition to the Wiki. -- Attend Shape:

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", >

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). >

Re: [Jmol-users] Use of variable in a call to getProperty

Might be a nice addition to the Wiki. On Fri, Jul 8, 2016 at 9:16 AM, Latévi Max LAWSON DAKU wrote: > Dear Bob, > > Thanks a lot for your answer. > > Your solution is also the one given by Matt and it works :) > > > I'm attaching a README file, which I wrote to keep track

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",

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] MF function question...

Bob, Thanks, that email is a big help on the @ usage. Otis --Otis rothenbergero...@chemagic.org http://chemagic.org > On Jul 8, 2016, at 9:19 AM, Robert Hanson wrote: > > > Happy to address that. @ is tricky because it has multiple uses: > > > 1. Original use:

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 Tech Expo July 15-16. Meet us at AT 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

Re: [Jmol-users] Use of variable in a call to getProperty

Dear Bob, Thanks a lot for your answer. Your solution is also the one given by Matt and it works :) I'm attaching a README file, which I wrote to keep track of what I did. It's far from being perfect. But I hope it may be helpful to someone. Thanks again, Bob, Matt and Angel! Best, Max

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

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 //

Re: [Jmol-users] MF function question...

Happy to address that. @ is tricky because it has multiple uses: 1. Original use: "define" *$ @molecule1 molecule=1* *$ select molecule1* 2. Shortcut to {atomno=n} *$ @3.color = "red"* *$ draw @1 @3* 3. Math insertion into a Jmol command: *$ draw ID @{"line"+i} * 4. Explicit

Re: [Jmol-users] Export x3d problem.

Send me a PNGJ file that cannot be produced, and I will take a look at it. Do all testing in both X3D and VRML so that we can see if it affects both or just one. ​ -- Attend Shape: An AT Tech Expo July 15-16. Meet us at