<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Mar 23, 2011, at 2:32 AM, Amit Kumar wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><b><br clear="all">Dear Pettersen,<br>first of all I like to thanks you as i am getting always nice graphics from chimera software and hope you still involve in improving it to compete all over good structure visualizers....<br> I am a frequent user of this visualizer and already cited in all my papers internationally published. I am struggling in getting ...<br></b></blockquote><div><br></div>I'm happy you've gotten good results with Chimera, and thanks for the citations -- they help us get our funding renewed!</div><div><br><blockquote type="cite"><b>1) user guide of UCSF Chimera in pdf version as whole<br></b></blockquote><div><br></div>If you go to the Chimera home page and click on the "Documentation" link, there will be a list of links to various documentation. One of those links will be for a PDF of the 1.5 version of the User's Guide. It's about 12.5 MB (828 pages).</div><div><br></div><div>The Chimera documentation was always designed to be hyperlinked web pages, so the PDF version is not as well organized or concise as it would be if the documentation was PDF-based. I hope you know that the HTML User Guide is bundled with each Chimera download and therefore all the Help buttons in dialogs, the "help" command, and the various functions in the Help menu just access your local copy and don't go over the web.</div><div><br><blockquote type="cite"><b>2) if i build structure - add atom in structure ----whether we can plced the atom at my desired place or coordination...if yes how...and whether i can dragg that atom specifically to some unique place....how?<br></b></blockquote><div><br></div>The atom gets placed in the center of the view, so if you can get the center of the view to be your desired location then you're set. Otherwise, you can use the "Movement Mouse Mode" tool (in the Movement tools category) to move the atom wherever you want it positioned.</div><div><br><blockquote type="cite"><b>3)whether we can allign the specific atom/residue and accordingly whole molecule....how? Although i use match maker that allign whole molecules but my specific residue miss out<br></b></blockquote><div><br></div>Use the "match" command to match specific atoms/residues. Open the command line (Favorites->Command Line) and type "help match" for details. As an example if you wanted to match residue 14 in model 0 with residue 20 in model 1 (and they were the same residue type with the same atom names) then "match #0:14 #1:20" will move model 0 so that its residue 14 will be superimposed on model 1's residue 20.</div><div><br><blockquote type="cite"><b>4)how i can allign heteroatom like in my case i am trying to allign heme from different hemoglobin molecule with maximum efficiency...as heme are chemically same for both molecule it should allign perfectly and accordingly their globin (apoprotein) part...<br></b></blockquote><div><br></div>Similarly, if the hemes have the same number of atoms and the same atom names then something like "match #0:HEM #1:HEM" would work (also assuming only one heme per model). If the hemes have differing numbers of atoms or different atom names then you would have to use a more detailed match command where you actually specify the atom names so Chimera knows which atoms to pair up in the match.</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>