Re: [PyMOL] select clipped atoms

Hi Johannes, > I can use the function and commands. print clipped("clipsed") - but not > print clipped("3lzt") - shows the indices of the atoms between the clipping > planes print clipped("3lzt") should print the indices of atoms that are clipped off by the clipping planes. That works for me, but

Re: [PyMOL] select clipped atoms

Hello Tsjerk, I can use the function and commands. print clipped("clipsed") - but not print clipped("3lzt") - shows the indices of the atoms between the clipping planes Tsjerk Wassenaar wrote: Hi Johannes, Coincidentally, I found myself in need of the same functionality the other day. I cam

Re: [PyMOL] pisa

ya,i get it... Thanks... On Thu, Mar 3, 2011 at 5:58 PM, Tsjerk Wassenaar wrote: > Hi Kanika, > > > REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC > > It says 'author determined'. It doesn't say how, though. But look at > the following: > > # Get the molecule > fetch 1b8e,async=0 > > # C

Re: [PyMOL] pisa

Why do you expect PISA to agree with author assigned biological units? Read the paper and see if there's a reason the authors made the assignment. If you really don't understand why things might be different, read the intro to the ProtCID paper. -David On Mar 3, 2011, at 6:37 AM, kanika sharma

Re: [PyMOL] pisa

Hi Kanika, > REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC It says 'author determined'. It doesn't say how, though. But look at the following: # Get the molecule fetch 1b8e,async=0 # Create a copy create 1b8e_copy,1b8e # Color it color hotpink, 1b8e_copy # Transform the copy according

[PyMOL] pisa

protein 1b8e says its a dimer by its pdb file info as: BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.00 0.00 0.000.0 REMARK 350 BIOMT2 1 0.00 1.00 0.00