Diamond shaped fibril

[Thiago Gomes]

 

Dear Rasha Alqus,

we are glad to help.

To build such a fibril you would have to build a larger crystallite (containing more chains) with a command line like this:

./cellulose-builder integer integer 20

(the last argument must be 20 since you want 20 cellobiose units, which equals to 40 glucose units),

and then remove the unwanted cellulose chains (e.g. yanking the corresponding lines in a text editor) using VMD to help you see want are the chains you want and those you don't. In other words, you'll have to carve the crystallite you wish from a larger crystallite.

Unfortunately there is no totally automatic way to produce that shape with cellulose-builder yet, but I intend to implement it in the next releases.

If you are acquainted to VMD, use the 'lines' graphical representation to represent all the system and then create a new representation using the 'CPK' drawing method with the selection ' fragment 0' , so you will know which chain is fragment 0. Then change this selection to 'fragment 1' and so on and take notes of which chains you want and which you do not. (Use Display -> Orthographic for doing this, it is much easier to visualise)

Once you know which chains you want to keep, an easier way to produce the new crystallite from the bigger one (instead of deleting the unwanted lines from a text editor) would be using VMD' s tcl console like this:

set sel [atomselect top fragment 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40]

$sel writepdb new_crystal.pdb

supposing those are the 36 chains you want to keep (which ARE NOT from 4 to 40, since the selection will necessarily be discontinuous, e.g., 4 7 8 11 12 13 17 etc...), those two commands will write a new PDB file containing just the chains you selected.

That would be the general method for building crystallites of arbitrary shape. I know it is not very elegant, nevertheless it enables

for any type of crystallite to be obtained.

I hope that helps. Please feel free to ask any other questions you might have.

Best Regards,

Thiago C. F. Gomes