Jekyll2026-04-19T09:50:36+00:00https://chem-bla-ics.linkedchemistry.info/feed/by_tag/pdb.xmlchem-bla-icsChemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.Egon WillighagenCDK Bug Squash Party - Day 3 and 42006-09-22T00:00:00+00:002006-09-22T00:00:00+00:00https://chem-bla-ics.linkedchemistry.info/2006/09/22/cdk-bug-squash-party-day-3-and-4Because I was struggling hard with default values for cdk.interfaces fields, I did not have time to write up the Bug Squash Party report for day 3 (see also day 1 and day 2 ). But here it is.

Day 3

Kai worked hard on getting the cdk.interfaces API cleaned up, as agreed upon earlier. Christian added a test for the RMSD calculator (see getAllAtomRMSD()), and cleaned up his code a bit. Stefan continued his bug-squashing on JChemPaint and fixed another one or two bugs.

Rajarshi uploaded a patch to set undefined atomic properties, like partial and formal charges and the implicit hydrogen count, to UNSET by default. However, this broke the CDK at many places, as apparently many class methods assume the default to be zero. After discussing the issue at the CUBIC, it turned out that this was sort of the intended, though undocumented, behavior: use the default Java values.

And I added missing clone() methods, closing one bug on SourceForge, added files for Eclipse to know how to build the CDK with Ant (thanx to Nico for similar files for Jmol), and got CDK compiled again against Classpath.

Day 4

Miguel uploaded his first patched for support saving PDBPolymer data structures into and restoring them again from CML, addressing an almost two-year-old bug. He created new cdk.interfaces for them, to address module dependencies, but a large set of JUnit tests are yet missing.

Kai continued his cdk.interfaces refactoring, working on the more involved changes. Stefan, Tobias, and me worked on a poster and three three-fold flyers for our CDK booth at CompLife2006, so have not been very productive in bug squashing. But we are happy with the result. Below is a screenshot on one side of the main CDK folder:

With 77 failing JUnit test, and still a too large number of open bugs on SourceForge, there is plenty of things to do today.

]]>Egon WillighagenComplex PDB documents using the Bioclipse ChildResourceCreator2006-09-14T00:00:00+00:002006-09-14T00:00:00+00:00https://chem-bla-ics.linkedchemistry.info/2006/09/14/complex-pdb-documents-using-bioclipseSome time ago I blogged about the ChildResourceCreator extension point in Bioclipse and hinted as using that for PDB files. which contain 3D molecular models, sequences and bibliographic information. Using the new extension point, Bioclipse now treats PDB files as complex documents, creating child resources for the 3D molecular model (using the CDK plugin), and a sequence resource (using the BioJava plugin).

]]>Egon WillighagenUncertainty in NMR based 3D protein models2006-04-02T00:00:00+00:002006-04-02T00:00:00+00:00https://chem-bla-ics.linkedchemistry.info/2006/04/02/uncertainty-in-nmr-based-3d-proteinWhile I was working on implementing proper author-given chain IDs in PDB structures for Jmol’s mmCIF reader today, I thought it was interesting to mention the recent article Traditional Biomolecular Structure Determination by NMR Spectroscopy Allows for Major Errors by Nabuurs (DOI:10.1371/journal.pcbi.0020009, open access), working at the CMBI, two floors away from my former working location at the Radboud University Nijmegen.

Nabuurs discusses in this article the uncertainties that come with NMR derived 3D molecular structures of proteins. These studies do not give factual data on atomic coordinates, but generally give facts about interatomic distances. Solving the 3D geometry is then an optimization problem where the task is to find the 3D geometry that best reproduces the factual interatomic distances.

Now, this optimization has many closeby, i.e. in terms of matching the experimental data, minima, corresponding, possibly, to quite different structures.

This is nicely demonstrated in the article, by comparing the folds of 1Y4O and 1TGQ, as shown in the figure below (CCAL license):

Figure 1 from the article: Sequence and Structure Ensembles of Two DLC2A Structures.

It is interesting to note that 1TGQ got replaced by 2B95 about the same time the article by Nabuurs was published, which shows a 3D model that is homologous with that of 1Y4O, and different from that in the Nabuurs article.

]]>Egon WillighagenUncertainty in NMR based 3D protein models2006-04-02T00:00:00+00:002006-04-02T00:00:00+00:00https://chem-bla-ics.linkedchemistry.info/2006/04/02/uncertainty-in-nmr-based-3d-proteinWhile I was working on implementing proper author-given chain IDs in PDB structures for Jmol’s mmCIF reader today, I thought it was interesting to mention the recent article Traditional Biomolecular Structure Determination by NMR Spectroscopy Allows for Major Errors by Nabuurs (DOI:10.1371/journal.pcbi.0020009, open access), working at the CMBI, two floors away from my former working location at the Radboud University Nijmegen.

Nabuurs discusses in this article the uncertainties that come with NMR derived 3D molecular structures of proteins. These studies do not give factual data on atomic coordinates, but generally give facts about interatomic distances. Solving the 3D geometry is then an optimization problem where the task is to find the 3D geometry that best reproduces the factual interatomic distances.

Now, this optimization has many closeby, i.e. in terms of matching the experimental data, minima, corresponding, possibly, to quite different structures.

This is nicely demonstrated in the article, by comparing the folds of 1Y4O and 1TGQ, as shown in the figure below (CCAL license):

Figure 1 from the article: Sequence and Structure Ensembles of Two DLC2A Structures.

It is interesting to note that 1TGQ got replaced by 2B95 about the same time the article by Nabuurs was published, which shows a 3D model that is homologous with that of 1Y4O, and different from that in the Nabuurs article.

]]>Egon Willighagen