yago52

> What information do you have about domains? You basically need to put it into a list or array and provide it as an argument either to the main plotting...

thank you. I will test that right away.

I saw a problem with the showDomainBar(). The function is based on the index of resnum and not in the residues of the atomgroup. So the protein spike goes from...

sorry but could you explain it another way. I couldn't understand the atom=ag.

I will show what I'm trying to do, because that's not working. ```python spike_close = parsePDB('6vxx', chain = 'A', subset = 'ca') dom = spike_close dom.setData('domain','NTD') dom.select('all').setData('domain','') dom.select('resindex 13 to...

```python resnum = spike_close.getResnums() #PC1 sf1_pc = calcSqFlucts(pca_all_close[0]) M = 972 * 12 rmsf1_pc = sqrt((1 /M) * sf1_pc) ``` pca_all_close is calculated based on an ensemble with all structures...

I think the solution would be to create a atomgroup with 1273 atoms and then do the selections for the showDomainBar. The only thing that comes to my mind right...

```python test = ensemble_all_close.getAtoms() test.setData('domain','NTD') test.select('all').setData('domain','') test.select('resnum 13 to 303').setData('domain','NTD') test.select('resnum 319 to 541').setData('domain','RBD') test.select('resnum 685 to 1273').setData('domain','S2') fig = plt.figure(num=None, figsize=(12,5), dpi=200, facecolor='w', edgecolor='k') g_pca = GridSpec(ncols=1, nrows=1,width_ratios=[4.5],height_ratios=[4],wspace=0.3,hspace=0.3) #plt.style.use('default')...

The solution for now that I made ```python dom = AtomGroup('Spike') coords= array(np.tile([0,0,1],(1273,1)),dtype=float) dom.setCoords(coords) res = np.repeat(['CA'],1273) dom.setResnames(res) resn = list(range(1,1274)) dom.setResnums(resn) #this would be the standard dom.setData('domain','NTD') dom.select('all').setData('domain','') dom.select('resnum...

Another problem now. If I use text_loc='below' text goes inside the bar. ```python fig = plt.figure(num=None, figsize=(12,5), dpi=200, facecolor='w', edgecolor='k') g_pca = GridSpec(ncols=1, nrows=1,width_ratios=[4.5],height_ratios=[4],wspace=0.3,hspace=0.3) #plt.style.use('default') plt.tick_params(direction='out', length=3, width=1, colors='k', grid_color='k',...