On Mon, Jan 10, 2011 at 5:44 PM, Jeff Cohlberg <[email protected]> wrote:
> An easy way to get a Biological Assembly PDB file with separate letters for > each chain designation is from the MakeMultimer.py server ( > http://watcut.uwaterloo.ca/makemultimer/). > > Submitting 3IXP returns a PDB file with new chains A and B from the > original A chain and new chains C and D from the original B chain. Coloring > by chain gives you four separate colors. > > I learned about this from the excellent Protopedia page on Biological Unit > (http://www.proteopedia.org/wiki/index.php/Biological_Unit) > > Jeff > > > Message: 4 > Date: Mon, 10 Jan 2011 18:24:48 -0500 > From: Eric Martz <[email protected]> > Subject: [Jmol-users] Chains in biomolecules > To: [email protected] > Message-ID: <[email protected]> > Content-Type: text/plain; charset="us-ascii"; format=flowed > > I would like to be able to fully use biomolecules constructed by > Jmol. I need to be able to identify chains and color by chain. > > Consider 3ixp which has: > - chains: 2 (A, D) > - polymers: 4 (there is a gap in the middle of each chain, residues > lacking coordinates) > > The biomolecule 1 has 2 copies of the asymmetric unit, so > - chains: 4 (A, A, D, D) > - polymers: 8 > > "color chain" makes everything two colors (A, D). > "color polymer" colors each fragment of a chain a different color (8 > colors). > "color property symop" yields two colors, one for the asymmetric unit > and one for the copy of it. > > Questions: > > 1. How can I color the biomolecule by chain, that is, to get 4 colors > for the biomolecule of 3ixp? Will I need to use a script like this? (It > works.) > > select symop=1 and chain=a > color lightblue > select symop=1 and chain=d > color lightgreen > select symop=2 and chain=a > color pink > select symop=2 and chain=d > color yellow > > Sure, but of course that's rather specialized. You want something that is more straightforward. I'm not comfortable assigning arbitrary chain IDs to chains like MakeMultimer does. That's rather presumtous, I think. But how to do it.... > 2. How do I get Jmol to report a list of the existing chain IDs to > javascript? > > show chain But that just gives the letters. A simple way to get the full list, in order, would be: print {*.ca}.chain That would give you a list: A A A A A... B B B B.... A A A A... B B B ..... like that, which you could utilize along with symop. > 3. How do I get Jmol to report the number of symops in a biomolecule > to javascript? Is there something easier than parsing the REMARK 350 > BIOMT ... records out of the header (using "show pdbheader")? > > print {*}[0].symop gives the symmetry operator for the last atom. That's the count. > 4. How can I identify (hover, pickcallback) which of the "4 chains" > an atom belongs to? As stated in the docs, %[symop] does not work -- > should that be implemented? > Maybe. Var x = {selected}.symop does work, but you are right that you can't insert that into a label. The problem is that in some cases atoms have multiple symmetry operators. Bob > > Thanks, -Eric > > > > -- > Jeffrey A. Cohlberg, Professor and Chair > Department of Chemistry and Biochemistry > California State University, Long Beach > Long Beach, CA 90840 > 562-985-4944 fax 775-248-1263 > [email protected] > > > > ------------------------------------------------------------------------------ > Gaining the trust of online customers is vital for the success of any > company > that requires sensitive data to be transmitted over the Web. Learn how to > best implement a security strategy that keeps consumers' information secure > and instills the confidence they need to proceed with transactions. > http://p.sf.net/sfu/oracle-sfdevnl > _______________________________________________ > Jmol-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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