3/03-3/11/2017: Week 4
– Studying the Full Capabilities of Multiple Molecular Modelling Softwares
This past
week has been very useful in terms of gaining knowledge on the workings of the PyMol
and Avogadro programs. Unfortunately, I would only be able to share this
information with you through an absurd amount of function definitions and
pictures, which I shall not bore you with.
However,
there are two features which I am particularly excited about. One is the
molecular geometry optimization function of Avogadro. In manually building or
even editing uploaded molecules via the UI, it’s possible to utilize the
Optimize feature so that the molecular geometry is corrected to reflect the
laws of chemistry. This feature touches every aspect of the molecule short of
its atomic pairings.
The second
feature which I found is PyMol’s “movie” feature. This part of the program
allows for an addendum to the load command which gives the option for multiple
files to be loaded in reference to one another as different frames of a single “movie”
or animation. By the syntax of load [file directory-specific name], [selection
name], [state or “frame”].
Additionally,
this week I found that both Avogadro and PyMol are both capable of loading .pdb
files. This revelation makes a batch script I’d developed specifically for the purpose
of automating the transferring Avogadro-created files to the PyMol environment
totally useless. On the bright side, I got to study batch some amount and that
was a rather entertaining adventure in itself.
This
current week, I am beginning to work on my own archetype for the Foldit module
by describing the functionalities I envision would be included in it as well as
illustrating the sorts of coding methods I see being implemented to expand the
platform’ uses.
See you next week!
What's a .pdb file?
ReplyDeletePDB stands for program database and it is a file format developed by Microsoft. These files store the addresses and locations of all the symbols declared in a given file (which may be the PDB file itself). This functionality allows the PDB files to be also used to hold information about 3D models by representing the various shapes and elements as symbols in the PDB file.
DeleteWhat plans do you have for your archetype my good man?
ReplyDeleteWell, old sport, the archetype can be used by researchers as a road map by which they modify the code of Foldit should its source code ever be released. Thus, macros may be developed and new, comprehensive features may be designed which better suit the purposes of the users. Also, with some of the features described in my latest post, the Foldit modelling software may be implemented in education to help biology students better visualize protein construction.
Delete