<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On May 15, 2010, at 5:54 AM, Bala subramanian wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Friends,<br><br>I have just begun to explore the chimera-python linkage. I loaded a pdb file using chimera.openModels function. Then i tried to loop through the residues and display atom information based on a condition.<br> <br>>>>for r in mymodel.residues: <b>#this works for me</b><br> if r.type=='ARG': print r.atoms<br><br>>>>for r in mymodel.residues: <b>#this dose not work. I know there is a ARG residue with id 151.</b><br> if <a href="http://r.id">r.id</a>=='151': print r.atoms<br></blockquote><div><br></div>Hi Bala,</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>A residue's 'id' attribute encodes the chain ID, number, and insertion code. In the above code you would want "if r.id.position == 151". This assumes that no other residues in other chains (or waters, etc.) have the same number.</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>In IDLE, the help() function can get you information about an object's or class's methods and attributes. So:</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>help(chimera.Residue.id)</div><div><br></div><div>would have shown that 'id' is of class MolResId. Then:</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>help(chimera.MolResId)</div><div><br></div><div>would have shown that MolResIds have 'chainId', 'insertionCode', and 'position' attributes and the the first two are strings and the latter is an integer.</div><div><br><blockquote type="cite">I dnt understand how atom attributes are packaged within a residue. Kindly write me few examples of accessing atom information from a residue.</blockquote><div><br></div><span class="Apple-tab-span" style="white-space:pre"> </span>From your code it looks like you know that r.atoms is a list of atoms, though putting it directly in a print statement like that won't be very informative since the 'repr' of each atom gets printed, which is something like:</div><div><br></div><div><_chimera.Atom object at 0x...></div><div><br></div><div>You would want to force the 'str' of the atom to get printed, e.g.:</div><div><br></div><div>print [str(a) for a in r.atoms]</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>The only other atom attribute in a residue I can think of is r.atomsMap, which is a dictionary keyed on atom name whose values are lists of atoms with those names. It's a list since sometimes atoms are not given unique names in a residue (most frequently with small molecules).</div><div><br></div><div>--Eric</div><br><div apple-content-edited="true"> <span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>Eric Pettersen</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>UCSF Computer Graphics Lab</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> </span><a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></p><br class="Apple-interchange-newline"></div></span> </div><br></body></html>