[chimera-dev] [Chimera-users] undisplay label in distance monitor

[Bala subramanian]

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 at 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...
>
>
>


-- 
C. Balasubramanian
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