Dear Eric, I tried the following code but no luck. I dnt see get any error but i dnt see the connection lines between the atoms.

import chimera from numpy import loadtxt,matrix,arange from chimera.colorTable import getColorByName from chimera.misc import getPseudoBondGroup

model=chimera.openModels.open('mypdb.pdb') res=model[0].residues grp = getPseudoBondGroup("mybonds", associateWith=[model]) MAT=loadtxt('mymatrix',dtype=float)

for x in range(len(res)): for y in range(len(res)): if x <> y : value=MAT[x,y] if value > 0.75: b=grp.newPseudoBond(res[x].atomsMap['CA'][0], res[y].atomsMap['CA'][0]) b.lineType = chimera.Dash b.drawmode=1 b.color = getColorByName("lime green")

else: pass

else: continue

Is there something i am missing, Bala

On Tue, Jun 5, 2012 at 8:27 PM, Eric Pettersen pett@cgl.ucsf.edu wrote:

On Jun 4, 2012, at 11:54 PM, Bala subramanian wrote:

Friends,

...

I have written a script to draw lines between atoms (using distance monitor). I dnt want the distance label to be displayed with the pseudo bond. Kindly write me the way to remove the label. My script is below.

model=chimera.openModels.open('myavg.pdb') res=model[0].residues MAT=loadtxt('mymatrix',dtype=float) chimera.runCommand('focus') for x in range(len(res)): for y in range(len(res)): if x <> y : value=MAT[x,y]

    if  0.5 < value > 0.75:

b=distanceMonitor.newPseudoBond(res[x].atomsMap['CA'][0],res[y].atomsMap['CA'][0]) b.drawMode=1 b.radius=0.05 #b.label=None I tried keeping this value as None and empty string but it doesnt help. b.color=getColorByName('red')

    else: pass

  else: continue

Hi Bala, distanceMonitor pseudobonds are designed to do exactly what you find them to be doing: showing an updated distance as the model is moved. What you need to do is make a normal pseudobond group for your own use that doesn't have all the special processing that distanceMonitor provides. Here is some example code:

from chimera.misc import getPseudoBondGroup grp = getPseudoBondGroup("matrix bonds", associateWith=[model])

...then later...

b = grp.newPseudoBond(res[x].atomsMap['CA'][0], res[y].atomsMap['CA'][0])

You will probably want to set some attributes of your group, like color and line type (dashed vs. solid). Here's some code for that:

import chimera from chimera.colorTable import getColorByName grp.color = getColorByName("lime green") grp.lineType = chimera.Dash

--Eric

P.S. BTW, this question is probably better for chimera-dev than chimera-users...