Awesome. BioJava has good mmtf support, so if we can get the new Jmol
release into maven then MMTF might be a good exchange format for passing
structures to Jmol. We're currently stuck with using PDB and are hurting
from the limitations (e.g. on chain identifiers & number of atoms).
-Spencer
On Wed, Aug 10, 2016 at 6:41 PM, Robert Hanson <hans...@stolaf.edu> wrote:
> 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 <spencer.bli...@gmail.com>
> 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 <hans...@stolaf.edu>
>> wrote:
>>
>>> I'm not sure how ${Jmol.properties.___JmolVersion} would be the
>>> version number. In Build.xml it is:
>>>
>>> <property name="version" value="${Jmol.properties.Jmol.___JmolVersion}"
>>> />
>>> <propertyregex property="version"
>>> override = "true"
>>> input="${version}"
>>> regexp='"'
>>> replace=""
>>> global="true"
>>> />
>>> <echo message="version=${version}" />
>>>
>>>
>>> So you are missing that regex process.
>>>
>>>
>>>
>>> On Mon, Jul 25, 2016 at 9:18 AM, Mark Williamson <m...@mjw.name> 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
>>>> <property name="keystore.name" value="selfSignedCertificate" />
>>>>
>>>>
>>>> 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
>>>> <input ~/.jmol.build.properties as the private property file >
>>>>
>>>> 4) Build dist target
>>>> ant dist
>>>> <input ~/.jmol.build.properties as the private property file >
>>>>
>>>> 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:
>>>>
>>>> <!-- <fileset dir="srcjsv" />-->
>>>>
>>>> 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
>> _______________________________________________
>> 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
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