<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Zunera,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>As far as I know your script should work. I have attached a similar script that opens 1gcn, swaps residue 2 to VAL, and then saves a pdb file in your home folder named "val.pdb". Try running it and see if it creates the file and if the file has residue 2 switched to VAL.</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>If the script I sent works then I have two possibilities for what's going wrong with your script. One is that your structure does not have a residue 2 in chain A. The other is that the script is literally saving a file named C\Users\folderval.pdb. That doesn't seem like it's what you want. Maybe you are looking at an old version of the file in some other location that makes you think the script isn't doing the right thing.</div><div class=""><br class=""></div><div class=""><div class="">--Eric</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Eric Pettersen</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>UCSF Computer Graphics Lab</div></div><div class=""><br class=""></div><div class=""></div></body></html>