Hello George I am forwarding your message to the Jmol users list, which is the right place to pose these questions.
Following are my comments making a small lesson :-) I hope it leads you along the right track (as I say below, this is not straighforward). I must write this down as I might need it myself at some time ;-D On 1 Feb 2011 at 13:21, GDombi wrote: > I have taken the Jmol image of human serum albumin HSA and touched it up > to show only the His and Lys residues. Not essential now, but what do you mean by "touch it up"? Have you hidden the other residues, or deleted them from file? Your attachment is a state script file, but that does not include the model file. You should use "write jmol xx.pdb" for sending whole info, unless the model comes straight from the internet (like PDB ste). > Background: about 25 sugars will bind to HSA at Lys residues. > About 15 Zn atoms will non-specifically bind to HSA. > There is a specific Zn site at His 67, Asn 99 His 247 and Asp 249. > > How do I show that? I want to put a Zn(II) atom in this coordination > site. I have tried to use the following script: > AS 67, 99, 247, 249,Zn but was not successful. Adding atoms is not the most straightforward thing to do in Jmol. Jmol is basically a viewer for whatever model you feed into it. It's true that now you can edit the model, like adding an atom. Let's see what can be done. Another choice is to add the atoms manually to the file, but the question is how to find out the coordinates. Adding atoms in Jmol is done via the "data" command --which I have little practice with-- See http://www.stolaf.edu/academics/chemapps/jmol/docs/#data For a test, we could instead use a drawn small sphere (which can be moved by hand if desired), then get its coordinates and use them to introduce the atom. http://www.stolaf.edu/academics/chemapps/jmol/docs/#draw For example: load =1ao6; // gets it from PDB display *:A and (His67, Asn99, His247, Asp 249); // hides the remainder zoomto {displayed} 0; // focus now, identify the candidate coordination atoms; say they are e.g. define coordA [HIS]247:A.ND1, [HIS]67:A.NE2, [ASP]249:A.OD1, [ASN]99:A.ND2; // 'coordA' is whatever name you want select coordA; halos on; select all; // just to help seeing them; optional draw posA diameter 0.3 {coordA}; // 'posA' is whatever name you want show draw; // in the console, gives you the coordinates of the drawn dot If you don´t like the position, you can move it by hand, then repeat show set picking draw; // an orange halo shows you have activated the mode // then use Alt+drag to move the dot around; when done, set picking ident; show draw; halos off; Write down the coordinates and now we add the atom there: set appendNew false; data "append myZinc"|1|candidate ligated zinc|Zn 41.74 48.10 25.75|end "append myZinc"; display *:A and (His67, Asn99, His247, Asp 249), _Zn; zoomto {displayed} 0; define coordA [HIS]247:A.ND1, [HIS]67:A.NE2, [ASP]249:A.OD1, [ASN]99:A.ND2; connect (_Zn)(coordA) partial; > Also I hypothesis that Zn will non-specifically bind to single, surface > His residues and if a His residue is next to a Lys residue, then the > extent of sugar binding is reduce. Our experiments with sugar, zinc and > HSA show that zince will shut down sugar binding by about 50% so we are > trying to see how many His residues are close to Lys residues so that Zn > binding to a neighboring His will block sugar binding to Lys. > > Is there a way in Jmol to show a sphere of possible influence of a Zn > bound to a His molecule? You should use "within" command with distance e.g. select His and within(3.0, _Zn); // select atoms of histidines closer than 3 angstroms from a Zn atom > Any information will be appreciated. > I am including a file to show you my HSA molecule. > I tried to add the active site information in this file but I don't > understand what I'm doing and it was ignored. > > Bye for now, > > George > > George W. Dombi, PhD > Chemistry Department > University of Rhode Island > Kingston, RI, 02832 > > gdo...@chm.uri.edu > ------------------------------------------------------------------------------ Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! Finally, a world-class log management solution at an even better price-free! Download using promo code Free_Logger_4_Dev2Dev. Offer expires February 28th, so secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsight-sfd2d _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
