Re: [Jmol-users] The world of Jmol - an update: crystallography

2014-09-05 Thread Robert Hanson
You want the other 23? :) On Fri, Sep 5, 2014 at 10:54 AM, Angel Herráez wrote: > Bob, I added the links for the 2 presentations in the Wiki > > http://wiki.jmol.org/index.php/Events > > Good job! > > > > -- > Slashdot

Re: [Jmol-users] The world of Jmol - an update: crystallography

2014-09-05 Thread Angel Herráez
Bob, I added the links for the 2 presentations in the Wiki http://wiki.jmol.org/index.php/Events Good job! -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/

Re: [Jmol-users] Setting cutoff with some maps causes map to fail to load

2014-09-05 Thread Robert Hanson
That's what the header says MRC header: dmin,dmax,dmean: 0.0,0.4836611,0.037913516 I just opened it in Chimera as well. So Jmol has some sort of bug reading mrc files. On Fri, Sep 5, 2014 at 10:18 AM, wrote: > It opens fine in Chimera and CCP4MG, but we have just noticed that the > data val

Re: [Jmol-users] Setting cutoff with some maps causes map to fail to load

2014-09-05 Thread chris.wood
It opens fine in Chimera and CCP4MG, but we have just noticed that the data values in the map range from 0 to 0.48 – is this likely to cause a problem? Chris From: Robert Hanson [mailto:hans...@stolaf.edu] Sent: 05 September 2014 15:49 To: jmol-users@lists.sourceforge.net Subject: Re: [Jmol-user

Re: [Jmol-users] Using Jmol to convert crystals into 3D Printable files

2014-09-05 Thread Scalfani, Vincent
Yes, I think they are always only triangles?? Though many small triangles can make a nice sphere… There are typically some holes in the surface where the bonds meet the atoms, and we are able to correct this with Netfabb. From: Robert Hanson [mailto:hans...@stolaf.edu] Sent: Friday, September

Re: [Jmol-users] Using Jmol to convert crystals into 3D Printable files

2014-09-05 Thread Robert Hanson
It's not a great format, but we do that for other formats as well. On Fri, Sep 5, 2014 at 9:35 AM, Angel Herráez wrote: > 5 Sep 2014, 9:12, Robert Hanson wrote: > > > On Fri, Sep 5, 2014 at 8:29 AM, Scalfani, Vincent > > wrote: > > > > P.S. An STL writer in Jmol would be AWESOME! > > > > s

Re: [Jmol-users] Using Jmol to convert crystals into 3D Printable files

2014-09-05 Thread Angel Herráez
5 Sep 2014, 9:12, Robert Hanson wrote: > On Fri, Sep 5, 2014 at 8:29 AM, Scalfani, Vincent > wrote: >   > P.S. An STL writer in Jmol would be AWESOME! >   > show me the spec. The info I see for STL in Wikipedia speaks only of triangles. We'd need cylinders and spheres too for a go

Re: [Jmol-users] Setting cutoff with some maps causes map to fail to load

2014-09-05 Thread Robert Hanson
On Fri, Sep 5, 2014 at 8:46 AM, wrote: > Hi Bob, > > > > I should have probably said that this is an EM map, not a crystallography > one! > doesn't matter. It's still messed up. Jmol reads EM maps just fine as far as I know. You sure it's OK? > - Is JMol able to set absolute cutoffs (a

Re: [Jmol-users] Using Jmol to convert crystals into 3D Printable files

2014-09-05 Thread Robert Hanson
On Fri, Sep 5, 2014 at 8:29 AM, Scalfani, Vincent wrote: > > > P.S. An STL writer in Jmol would be AWESOME! > > > > show me the spec. -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/

Re: [Jmol-users] Setting cutoff with some maps causes map to fail to load

2014-09-05 Thread chris.wood
Hi Bob, I should have probably said that this is an EM map, not a crystallography one! - Is JMol able to set absolute cutoffs (as normally required for EM maps), rather than using relative sigma values? - What is the default value of cutoff? The third object does display 1akeA_10A.

Re: [Jmol-users] Using Jmol to convert crystals into 3D Printable files

2014-09-05 Thread Scalfani, Vincent
Thanks Bob, We did include Jmol briefly in Scheme 1 and the supporting info. ☺ Actually now I see a mistake in Scheme 1, it should also have .cif to .wrl with Jmol, not just .pdb to .wrl. That work was actually done a year ago (J. Chem. Ed is very slow….) before we discovered Jmol as a great r