Visualizations

[MonZop]

Apparently the MainChain visualization does not work. Main chain means only the N-CA-C atoms of every aminoacid. Sometimes it is good to see only these atoms, to get an idea of the general folding of the protein.

[MonZop]

Surface does work; however, if, after having calculated the surface, one want to see all atoms, or Main chain atoms only, the result is that Blender shows the surface again.

[zeffii]

when did this stop working?

[MonZop]

I noticed just now, a couple of days ago it was OK

[zeffii]

what about master?

[MonZop]

I can re-check, but it did work

[zeffii]

if master works, I can do a differential.

[MonZop]

Master _main_fixes dos not work

[zeffii]

and Master?

It would really help me if there were several smaller files that I could test, 03,04,05 just take forever to import.

[MonZop]

For this 06 should be sufficient:

Master does not work :(

[zeffii]

current master is literally only three changes, all of which are necessary. When you close Blender and reopen can you take another note of the errors / screenshot please

[MonZop]

[zeffii]

untick those, press save User Settings and then press Ctrl+U to store the change in the startup.blend

[MonZop]

It works with Blender 2.70 and BioBlender_master

[zeffii]

I think I know why this is.. and it relates directly to the fix for the final conformation.. I will return to this later.

[zeffii]

the last lines of 02_4IHVonlyDNA.pdb are

ATOM   1088  C7   DT D  27      22.394  -3.354 124.626  1.00 35.02           C
TER    1088       DT D  27 
END

and 03_3IV5_DNA_proteinComplex

HETATM 2620  O   HOH B 104      15.805   1.185  -2.720  1.00 24.86           O  
HETATM 2621  O   HOH B 105      35.829  17.152 -10.049  1.00 39.75           O  
HETATM 2622  O   HOH C  28      16.856  -0.777  37.497  1.00 44.91           O  
MASTER      412    0    0    9    4    0    0    6 2618    4    0   22          
END                                                                             

this is the nuance in pdb files that depend on the content.. and perhaps the program that writes the pdb.

[zeffii]

[MonZop]

Yes, if the pdb contains only one conformation (of as many chains as you want), there is no need to introduce the MODEL (and the ENDMDL). MODELs refer to several different conformations of the same molecule. Water is ignored by BioBlender (the HETATM in 03 are the water oxygens): they are there because the experiment revealed their location, and are probalby 'stable waters'. We can safely ingore them. We also ingore the line MASTER.

[zeffii]

I had never used the View panel before. So please guide me here.

Click on an atom, and then in View clicking on +mainChain should select other atoms too? (of that chain?) I notice that after the surface is generated using View, that if one hides the surface, then clicks on an atom, then picks any other option that view list, it will unhide the surface (I imagine this is not desirable behaviour)

[MonZop]

The idea is to show the entire protein in one of 4 modes, that's why clicking on a single atom highlight all atoms of the aminoacid (the building block of a protein), but the selection affects the entire molecule. In the rare case that Hydrogens are imported, the default view shows all atoms, including hydrogens. Options Main Chain, and Side Chain simply hyde the unwanted atoms. The option Surface builds the mesh around all atoms, leaving them visible inside , as one can see by moving the surface away or by hyding it. Once the surface is built, selecting any other option, should hyde the surface and reveal the requested atoms (either all or only some of them). The behavior that you observe is not what should happen.