From: James S. <jms...@gm...> - 2012-01-24 16:15:10
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Dear PyMol Users! In the PyMol Wizard I've found very userful option called distance measurements beyween selected atoms. I wounder to know how I could realize such operation via PyMol console in the simplest manner. My current task consist of making different point mutations and subsiquent quick measurement of the new distance between new mutated residue and some other native residue. In addition I'd like to measure potential H-bond distance between above residues (polar contacts between electronegative groups) as well as tight packing forces ( distance between non-polar residues). Is there any simplest method for that purpose ? Thanks, James |
From: Thomas H. <sp...@us...> - 2012-01-24 16:27:58
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Hi James, use the distance command: http://pymolwiki.org/index.php/Distance For the potential h-bonds, use it with mode=2. Cheers, Thomas On 01/24/2012 05:15 PM, James Starlight wrote: > Dear PyMol Users! > > In the PyMol Wizard I've found very userful option called distance > measurements beyween selected atoms. > > I wounder to know how I could realize such operation via PyMol console > in the simplest manner. > > My current task consist of making different point mutations and > subsiquent quick measurement of the new distance between new mutated > residue and some other native residue. > > In addition I'd like to measure potential H-bond distance between above > residues (polar contacts between electronegative groups) as well as > tight packing forces ( distance between non-polar residues). > > Is there any simplest method for that purpose ? > > Thanks, > > James -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen |
From: James S. <jms...@gm...> - 2012-01-25 06:11:44
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Thanks Thomas! I've already tried use this command. I want just ask about Hbond representation between 2 selected regions. E.g I want to represent Hbonds beetween 2 helices Firstly I've added donor Hydrogens H_add donors and than distance 3sn6 and resi 197-220, 3sn6 and resi 275-298, cutoff=4, mode=2 where first selection is the 1st helix and second selection is another helix of my protein. I've noticed that in some cases there are errors in the h-bond network. How I could fix it ? James 2012/1/24 Thomas Holder <sp...@us...> > Hi James, > > use the distance command: > http://pymolwiki.org/index.**php/Distance<http://pymolwiki.org/index.php/Distance> > > For the potential h-bonds, use it with mode=2. > > Cheers, > Thomas > > > On 01/24/2012 05:15 PM, James Starlight wrote: > >> Dear PyMol Users! >> >> In the PyMol Wizard I've found very userful option called distance >> measurements beyween selected atoms. >> >> I wounder to know how I could realize such operation via PyMol console >> in the simplest manner. >> >> My current task consist of making different point mutations and >> subsiquent quick measurement of the new distance between new mutated >> residue and some other native residue. >> >> In addition I'd like to measure potential H-bond distance between above >> residues (polar contacts between electronegative groups) as well as >> tight packing forces ( distance between non-polar residues). >> >> Is there any simplest method for that purpose ? >> >> Thanks, >> >> James >> > > -- > Thomas Holder > MPI for Developmental Biology > Spemannstr. 35 > D-72076 Tübingen > |