Question: Pymol selected residue have dots that are not part of the residue
gravatar for nilaylale88
8 weeks ago by
nilaylale880 wrote:

Hello guys,

I am working on pymol recently and there is one thing i dont understand. When i select a residue on the sequence tab i see on the visualisation window that it picks it as some dots are rounding the residue, however there are some dots that appear beyond my residue. Is there anyone who can explain about this to me as i was not avaliable to find it on my search. Below i am also attaching a screen shot. By the way i deleted the solvents and there are no hydrogen atoms.

As you can see below i picked only one residue which is Threonine on position 185 but selection shows some dots that are beyond my selection and this happens for every residue that i pick.

As you can see i picked only one residue which Threonine on position 185

Thanks in advance.

pymol • 107 views
ADD COMMENTlink modified 8 weeks ago • written 8 weeks ago by nilaylale880

Hi, when you select a residue, it selects the atoms of the residues. If you change the representation for sticks for example, you will have a better view of the residue structure with their atoms.

ADD REPLYlink written 8 weeks ago by lumal2980

Thanks for the reply, yeah I have checked the PDB file and apparently number of dots are same as the atoms that residue. I changed the representation for sticks, and it seems the same. As i understand from the PDB file and comparing with various selections, it seems like those dots that goes beyond represent "C, O and N atoms". Anywho when i change my view to spheres it seems like it covers all the dots. Just one more question eventho i ve checked it, i just wanna make sure. When i am measuring distances between two residues, representation would not effect the measured distance right? Thanks again.

ADD REPLYlink written 8 weeks ago by nilaylale880

Indeed, the representation doesn't affect the distance.

ADD REPLYlink written 8 weeks ago by lumal2980

Problem solved. Upon further investigation, apparently we did not show the main chain, only showed the side chain. Those dots that show up with no line are the main chain. If we show all the main and side chains, then all is good. Thank you all for your comments.

ADD REPLYlink modified 8 weeks ago • written 8 weeks ago by nilaylale880
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