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17

This is called a phosphene — the experience of perceiving light in the visual cortex without light actually entering the eye. This commonly happens due to stimulation of the retinal ganglion cells by something else. The most frequent source in normal individuals is pressure to the retina (e.g. rubbing a closed eye.) It is also possible for phosphenes ...


11

The simplest way of course is to add it to the supplementary materials. However, 220 species are not that many, you should be able to fit that into a page. You have not shown us your tree so it is kind of hard to give specific advice but I am guessing that you have a linear rather than circular tree. If you convert it to a circular tree you should be able to ...


7

If you have simple 1:1 connections or can list your data in that manner, you can try Cytoscape (freely available). There are numerous plug-ins to customize what you have in mind in terms of visualization.


4

You are making a few assumptions that are likely not valid for all PDB files. For example: Residue indices are not necessarily sequential, nor do they have to start at 1 Not all possible residues have 1-letter code equivalents, there are thousands of possible exotic residues, not only the standard amino acids PDB files are not only used for proteins, but ...


3

The PDB file format was specified in the dawn of computing to fit on punch cards. So it has some shortcomings that have led to generations of scientists cursing the fixed-width column format. By now, it has been superseded by an XML-like format: PDBML. Of course XML is less space-efficient than a column layout, so you can see that disk space was not the main ...


2

http://www.turbosquid.com/3d-models/max-human-brain/580672 That one is only 30 which really isn't bad for a model. You will have trouble finding an anatomically correct model for free. I am curious, is the male brain that much different from the female brain? And do you want just the brain or a whole head with the skeleton and other anatomical features? ...


2

I haven't tried it, but this StackOverflow answer suggests that you can import a GraphViz network into OmniGraffle (for Mac), which makes it very easy to produce a pretty network (much easier than Photoshop/Illustrator).


2

Also, don't forget that you can deposit your full tree in treebase. So you can show the collapsed tree in the paper, and give a link to the full tree somewhere in the text.


2

It is not always essential to show a big tree. My opinion might be biased but it seems to me that huge figures with illegible labels are just a gimmick to make the reader feel that it is a great analysis (another case is that of networks). First of all it is important to decide what is that you really want to convey from your figure. For example if your ...


1

The basic problem is one of prior knowledge. The information you have about E. coli metabolism is in the form of a simple network, i.e. a list of nodes and the edges (along with their weights) that connect them. From this information alone it's impossible to know, for example, that the reactions in the TCA cycle should be plotted as a perfect circle (that's ...


1

I'm not sure if they will be useful for your application, but you should look into software used to visualize ecological networks (and maybe also software used for drawing electrical charts). The type of data used there is very similar to what you want to plot, with nodes and links along with metadata for links on e.g. rates or connection strenghts. I can ...


1

A very clear description is given in Wikipedia. The starting point is an alignment for the region under investigation. A. Basically, to get the height of the stack of letters for every position one has to calculate the degree of certainty about the residue (= degree of conservation) at this position in the sequences belonging to this class. I'll explain ...


1

Try this out with BioPython: from Bio.PDB.PDBSuperimposer import PDBSuperimposer as superimposer from Bio.PDB.PDBParser import PDBParser parser = PDBParser() sup = superimposer() struct_1 = parser.get_structure("XXXX","first_pdb") struct_2 = parser.get_structure("XXXX","second_pdb") atoms1 = struct_1.get_atoms() atoms2 = struct_2.get_atoms() ...


1

After you load the molecule in VMD, from the menu bar select Graphics->Representations... In the box labeled Selected Atoms, type "hetero" and hit enter. You should now see only your ligand (and whatever other non-protein/DNA atoms that happen to be in your PDB file). Hit the Create Rep button, enter "protein" in the Selected Atoms box and hit enter (you can ...



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