[Jmol-users] Jmol-14.6.1_2016.08.09
https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.6/Version%2014.6.1/Jmol-14.6.1_2016.08.09-binary.zip/download
This release upgrades the MMTF and PyMOL PSE file reading capabilities of
Jmol.
What's cool about this release is that it includes a new way to access PDB
data. We have the tabular PDB format with its obvious limitations, the
structured mmCIF format providing flexibility, and now a flexible binary
MMTF format that is specifically designed to focus on a minimum of critical
information, reduce transfer speed on the Web, and load structures
considerably faster than other formats.
My congratulations to Peter Rose and the team at RCSB for this contribution.
I'm pleased to say that Jmol and JSmol read this format natively in Java
and JavaScript. If you wish to try it, simply download this version and
add ".mmtf" to your = load syntax:
load =1u19.mmtf
Bob
Jmol.___JmolVersion="14.7.1_2016.08.09"
sycnronized with Jmol 14.6.1
bug fix: upgrade of RCSB mmtf format reading to version 0.2 specs
load =2tbv.mmtf {1 1 1} filter "biomolecule 1;*.ca"
new feature: Jmol reads PyMOL 1.8 PSE files with "set dump_binary, 1"
bug fix: COMPARE command can fail if an atom has no bonds
bug fix: write x.pdb for multimodel file does not work.
--
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
--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. http://sdm.link/zohodev2dev___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
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Re: [Jmol-users] Hirshfeld Surfaces
I know that CrystalExplorer (http://hirshfeldsurface.net/) will generate Hirshfeld surfaces, but I haven’t used it much. It relies on some kind of wavefunction calculation (Tonto or Gaussian in the case of CrystalExplorer), so I imagine that Jmol will similarly require more than just coordinates. Dean On August 10, 2016 at 7:13:50 PM, Robert Hanson (hans...@stolaf.edu) wrote: OK, well, do let me know if you find something. What I read is that it is "relatively simple to implement". Bob On Tue, Aug 9, 2016 at 12:36 PM, S Westrip wrote: > Thanks > > No - I don't have an algorithm - literally just started to look into > this... > > I was just using Jmol as my first "port of call" - Jmol often has the > answers and saves we the work :-) > > Cheers > > Simon > > On Aug 09, 2016, at 05:49 pm, Robert Hanson wrote: > > No, it cannot. Have an algorithm? > > On Tue, Aug 9, 2016 at 11:40 AM, S Westrip > wrote: > >> Hello >> >> Does anyone know if Jmol can render Hirshfeld surfaces? >> >> Cheer >> >> Simon >> >> >> -- >> What NetFlow Analyzer can do for you? Monitors network bandwidth and >> traffic >> patterns at an interface-level. Reveals which users, apps, and protocols >> are >> consuming the most bandwidth. Provides multi-vendor support for NetFlow, >> J-Flow, sFlow and other flows. Make informed decisions using capacity >> planning reports. http://sdm.link/zohodev2dev >> ___ >> Jmol-users mailing list >> Jmol-users@lists.sourceforge.net >> 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 > > > 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 > > > -- > What NetFlow Analyzer can do for you? Monitors network bandwidth and > traffic > patterns at an interface-level. Reveals which users, apps, and protocols > are > consuming the most bandwidth. Provides multi-vendor support for NetFlow, > J-Flow, sFlow and other flows. Make informed decisions using capacity > planning reports. http://sdm.link/zohodev2dev > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > -- > What NetFlow Analyzer can do for you? Monitors network bandwidth and > traffic > patterns at an interface-level. Reveals which users, apps, and protocols > are > consuming the most bandwidth. Provides multi-vendor support for NetFlow, > J-Flow, sFlow and other flows. Make informed decisions using capacity > planning reports. http://sdm.link/zohodev2dev > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > 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 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 -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports. http://sdm.link/zohodev2dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports. http://sdm.link/zohodev2dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Hirshfeld Surfaces
OK, well, do let me know if you find something. What I read is that it is "relatively simple to implement". Bob On Tue, Aug 9, 2016 at 12:36 PM, S Westrip wrote: > Thanks > > No - I don't have an algorithm - literally just started to look into > this... > > I was just using Jmol as my first "port of call" - Jmol often has the > answers and saves we the work :-) > > Cheers > > Simon > > On Aug 09, 2016, at 05:49 pm, Robert Hanson wrote: > > No, it cannot. Have an algorithm? > > On Tue, Aug 9, 2016 at 11:40 AM, S Westrip > wrote: > >> Hello >> >> Does anyone know if Jmol can render Hirshfeld surfaces? >> >> Cheer >> >> Simon >> >> >> -- >> What NetFlow Analyzer can do for you? Monitors network bandwidth and >> traffic >> patterns at an interface-level. Reveals which users, apps, and protocols >> are >> consuming the most bandwidth. Provides multi-vendor support for NetFlow, >> J-Flow, sFlow and other flows. Make informed decisions using capacity >> planning reports. http://sdm.link/zohodev2dev >> ___ >> Jmol-users mailing list >> Jmol-users@lists.sourceforge.net >> 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 > > > 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 > > > -- > What NetFlow Analyzer can do for you? Monitors network bandwidth and > traffic > patterns at an interface-level. Reveals which users, apps, and protocols > are > consuming the most bandwidth. Provides multi-vendor support for NetFlow, > J-Flow, sFlow and other flows. Make informed decisions using capacity > planning reports. http://sdm.link/zohodev2dev > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > -- > What NetFlow Analyzer can do for you? Monitors network bandwidth and > traffic > patterns at an interface-level. Reveals which users, apps, and protocols > are > consuming the most bandwidth. Provides multi-vendor support for NetFlow, > J-Flow, sFlow and other flows. Make informed decisions using capacity > planning reports. http://sdm.link/zohodev2dev > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > 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 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 -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports. http://sdm.link/zohodev2dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol on Maven Central
Thanks, Spencer. I am in the process of releasing an important update for
BioJava, as a matter of fact -- PyMOL 1.8 dump_binary PSE files and the new
MMTF format from RCSB (which is FANTASTIC by the way...)
Bob
On Wed, Aug 10, 2016 at 9:25 AM, Spencer Bliven
wrote:
> Hey,
>
> I also took a crack at getting the dist-release command to complete, since
> it would be extremely nice to get BioJava using a more recent version of
> Jmol. Using the latest trunk I got all steps to complete by modifying
> tools/jmol-sonatype.xml as you suggest to refer to "${Jmol.properties.Jmol
> .___JmolVersion}" in line 30. This creates the build/dist-maven directory
> as desired.
>
> Right now only Tomas (plusik) and Nico (nicov) appear to be authorized to
> upload to maven central. It would be great if some additional people (e.g.
> Mark, Bob, perhaps even myself if desired) could get added to this.
> Authorization
> is granted by adding a user to your OSS project ticket (
> https://issues.sonatype.org/browse/OSSRH-3633).
>
> Any work towards a maven release is much appreciated. Let me know if I can
> do anything to help with this.
>
> -Spencer
>
>
>
> On Sat, Jul 30, 2016 at 4:39 AM, Robert Hanson wrote:
>
>> I'm not sure how ${Jmol.properties.___JmolVersion} would be the version
>> number. In Build.xml it is:
>>
>> > />
>> > override = "true"
>> input="${version}"
>> regexp='"'
>> replace=""
>> global="true"
>> />
>>
>>
>>
>> So you are missing that regex process.
>>
>>
>>
>> On Mon, Jul 25, 2016 at 9:18 AM, Mark Williamson wrote:
>>
>>> On 17/05/16 23:15, Robert Hanson wrote:
>>> > Will be checking in Jmol 14.6 release as soon as I can. But it's not a
>>> Maven release. Someone else has to do that.
>>>
>>> Sorry for the delay in replying. I have been attempting to use the ant
>>> build script, tools/jmol-sonatype.xml, to build some artifacts for
>>> deployment to Maven central. Here is my protocol (apologies, I am not
>>> that familiar with ant and may have made some basic errors):
>>>
>>>
>>> Preamble
>>> -
>>> 0) Start with a 64 bit install of Ubuntu 14.04.4
>>>
>>> 1) Install the following packages
>>>sudo apt-get install mvn libsaxon-java openjdk-7-jdk ant
>>>
>>> 2) Create ~/.jmol.build.properties file with contents
>>>
>>>
>>>
>>> Main
>>>
>>> 1) Obtain the source code and extract
>>>wget
>>> http://heanet.dl.sourceforge.net/project/jmol/Jmol/Version%2
>>> 014.6/Version%2014.6.1/Jmol-14.6.1_2016.07.11-full.tar.gz
>>>
>>>tar xfvz Jmol-14.6.1_2016.07.11-full.tar.gz
>>>cd jmol-14.6.1_2016.07.11
>>>
>>> 2) Add a required jar to enable docs to be built
>>>cp /usr/share/java/saxon.jar ./jars/
>>>
>>> 3) Build jar target
>>>ant jar
>>>
>>>
>>> 4) Build dist target
>>>ant dist
>>>
>>>
>>> This fails with an error stating that “srcjsv does not exist” and this
>>> is because I do not have the source to JSpecView in the tree. However,
>>> if I should omit the line 1216 in build.xml, for the sake of reaching
>>> the next step:
>>>
>>>
>>>
>>> And proceed to this:
>>>
>>>ant -f ./tools/jmol-sonatype.xml dist-release
>>>
>>> Then, the following error is seen:
>>> BUILD FAILED
>>> /home/mw529/code/jmol/dev/jmol-14.6.1_2016.07.11/tools/jmol-
>>> sonatype.xml:91:
>>> Warning: Could not find file
>>> /home/mw529/code/jmol/dev/jmol-14.6.1_2016.07.11/build/dist/
>>> jmol-${Jmol.properties.___JmolVersion}-javadoc.jar
>>> to copy.
>>>
>>>
>>> I am guessing that this seems to be some form of mis-parsing of the
>>> Jmol.properties.___JmolVersion in the build/dist directory?
>>>
>>> Do you have any suggestions on how to resolve this?
>>>
>>> Thanks,
>>>
>>> Mark
>>>
>>>
>>>
>>>
>>> --
>>> What NetFlow Analyzer can do for you? Monitors network bandwidth and
>>> traffic
>>> patterns at an interface-level. Reveals which users, apps, and protocols
>>> are
>>> consuming the most bandwidth. Provides multi-vendor support for NetFlow,
>>> J-Flow, sFlow and other flows. Make informed decisions using capacity
>>> planning
>>> reports.http://sdm.link/zohodev2dev
>>> ___
>>> Jmol-users mailing list
>>> Jmol-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>
>>
>>
>> --
>> Robert M. Hanson
>> Larson-Anderson Professor of Chemistry
>> St. Olaf College
>> Northfield, MN
>> http://www.stolaf.edu/people/hansonr
>>
>>
>> If nature does not answer first what we want,
>> it is better to take what answer we get.
>>
>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>
>>
>>
>> --
>>
>> ___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-use
Re: [Jmol-users] Jmol on Maven Central
Hey,
I also took a crack at getting the dist-release command to complete, since
it would be extremely nice to get BioJava using a more recent version of
Jmol. Using the latest trunk I got all steps to complete by modifying tools/
jmol-sonatype.xml as you suggest to refer to
"${Jmol.properties.Jmol.___JmolVersion}"
in line 30. This creates the build/dist-maven directory as desired.
Right now only Tomas (plusik) and Nico (nicov) appear to be authorized to
upload to maven central. It would be great if some additional people (e.g.
Mark, Bob, perhaps even myself if desired) could get added to this.
Authorization
is granted by adding a user to your OSS project ticket (
https://issues.sonatype.org/browse/OSSRH-3633).
Any work towards a maven release is much appreciated. Let me know if I can
do anything to help with this.
-Spencer
On Sat, Jul 30, 2016 at 4:39 AM, Robert Hanson wrote:
> I'm not sure how ${Jmol.properties.___JmolVersion} would be the version
> number. In Build.xml it is:
>
>/>
>override = "true"
> input="${version}"
> regexp='"'
> replace=""
> global="true"
> />
>
>
>
> So you are missing that regex process.
>
>
>
> On Mon, Jul 25, 2016 at 9:18 AM, Mark Williamson wrote:
>
>> On 17/05/16 23:15, Robert Hanson wrote:
>> > Will be checking in Jmol 14.6 release as soon as I can. But it's not a
>> Maven release. Someone else has to do that.
>>
>> Sorry for the delay in replying. I have been attempting to use the ant
>> build script, tools/jmol-sonatype.xml, to build some artifacts for
>> deployment to Maven central. Here is my protocol (apologies, I am not
>> that familiar with ant and may have made some basic errors):
>>
>>
>> Preamble
>> -
>> 0) Start with a 64 bit install of Ubuntu 14.04.4
>>
>> 1) Install the following packages
>>sudo apt-get install mvn libsaxon-java openjdk-7-jdk ant
>>
>> 2) Create ~/.jmol.build.properties file with contents
>>
>>
>>
>> Main
>>
>> 1) Obtain the source code and extract
>>wget
>> http://heanet.dl.sourceforge.net/project/jmol/Jmol/Version%2
>> 014.6/Version%2014.6.1/Jmol-14.6.1_2016.07.11-full.tar.gz
>>
>>tar xfvz Jmol-14.6.1_2016.07.11-full.tar.gz
>>cd jmol-14.6.1_2016.07.11
>>
>> 2) Add a required jar to enable docs to be built
>>cp /usr/share/java/saxon.jar ./jars/
>>
>> 3) Build jar target
>>ant jar
>>
>>
>> 4) Build dist target
>>ant dist
>>
>>
>> This fails with an error stating that “srcjsv does not exist” and this
>> is because I do not have the source to JSpecView in the tree. However,
>> if I should omit the line 1216 in build.xml, for the sake of reaching
>> the next step:
>>
>>
>>
>> And proceed to this:
>>
>>ant -f ./tools/jmol-sonatype.xml dist-release
>>
>> Then, the following error is seen:
>> BUILD FAILED
>> /home/mw529/code/jmol/dev/jmol-14.6.1_2016.07.11/tools/jmol-
>> sonatype.xml:91:
>> Warning: Could not find file
>> /home/mw529/code/jmol/dev/jmol-14.6.1_2016.07.11/build/dist/
>> jmol-${Jmol.properties.___JmolVersion}-javadoc.jar
>> to copy.
>>
>>
>> I am guessing that this seems to be some form of mis-parsing of the
>> Jmol.properties.___JmolVersion in the build/dist directory?
>>
>> Do you have any suggestions on how to resolve this?
>>
>> Thanks,
>>
>> Mark
>>
>>
>>
>>
>> --
>> What NetFlow Analyzer can do for you? Monitors network bandwidth and
>> traffic
>> patterns at an interface-level. Reveals which users, apps, and protocols
>> are
>> consuming the most bandwidth. Provides multi-vendor support for NetFlow,
>> J-Flow, sFlow and other flows. Make informed decisions using capacity
>> planning
>> reports.http://sdm.link/zohodev2dev
>> ___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> 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
>
>
> 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
>
>
>
> --
>
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. http://sdm.link/zohodev2dev
