<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Nikolay,<div><span class="Apple-tab-span" style="white-space:pre"> </span>The short answer is: keep looking! You will find all the hydrogens after the heavy atoms. Chimera outputs atoms in Mol2 files in the same order that they were encountered in the input. Atoms added afterward are therefore placed after the original input atoms. Perhaps it would be better if it kept all residue atoms together, at least as an option, but right now it doesn't.</div><div><br></div><div>--Eric</div><div><br></div><div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; font-size: 16px; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> Eric Pettersen</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> UCSF Computer Graphics Lab</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> <a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></div><br class="Apple-interchange-newline"></div><div><div>On Apr 24, 2012, at 5:05 PM, Nikolay Igorovich Rodionov wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div><font face="Calibri" size="2"><span style="font-size: 11pt; "><div>Thank you, I will try that. Also, I was just comparing the charge data of a subunit between one set generated using Chimera with AMBER and the other using pdb2pqr with PARSE. I noticed that the chimera generated file did not have records for hydrogen atoms even though they were explicitly added using addh. Is this due to an error on my part, or has it something to do with the 2mol formatting?</div><div> </div><div>To give you an idea of what I am talking about here is the data for the first amino acid:</div><div> </div><div> --- > .2mol</div><div> 68<span class="Apple-converted-space"> </span><b>N</b> 26.7840 15.9620 -1.4880 N.4 4 SER1 0.1849</div><div> 69<span class="Apple-converted-space"> </span><b>CA<span class="Apple-converted-space"> </span></b> 25.7660 16.9460 -1.9070 C.3 4 SER1 0.0567</div><div> 70<span class="Apple-converted-space"> </span><b>C<span class="Apple-converted-space"> </span></b> 25.2870 16.6990 -3.3350 C.2 4 SER1 0.6163</div><div> 71<span class="Apple-converted-space"> </span><b>O<span class="Apple-converted-space"> </span></b> 26.1060 16.6940 -4.2710 O.2 4 SER1 -0.5722</div><div> 72<span class="Apple-converted-space"> </span><b>CB <span class="Apple-converted-space"> </span></b> 26.3460 18.3420 -1.7240 C.3 4 SER1 0.2596</div><div> 73<span class="Apple-converted-space"> </span><b>OG</b> 26.8010 18.5430 -0.4010 O.3 4 SER1 -0.6714</div><div> </div><div> --- > .pqr</div><div><font face="Courier New" size="2"><span style="font-size: 10pt; ">ATOM 1 <span class="Apple-converted-space"> </span><b>N</b> SER P 1 78.482 33.268 37.386 -0.7800 1.5000</span></font></div><div><font face="Courier New" size="2"><span style="font-size: 10pt; ">ATOM 2 <span class="Apple-converted-space"> </span><b>CA</b> SER P 1 77.464 34.252 36.967 -0.0000 2.0000</span></font></div><div><font face="Courier New" size="2"><span style="font-size: 10pt; ">ATOM 3 <span class="Apple-converted-space"> </span><b>C</b> SER P 1 76.985 34.005 35.539 0.5500 1.7000</span></font></div><div><font face="Courier New" size="2"><span style="font-size: 10pt; ">ATOM 4 <span class="Apple-converted-space"> </span><b>O</b> SER P 1 77.804 34.000 34.603 -0.5500 1.4000</span></font></div><div><font face="Courier New" size="2"><span style="font-size: 10pt; ">ATOM 5 <span class="Apple-converted-space"> </span><b>CB</b> SER P 1 78.044 35.648 37.150 0.0000 2.0000</span></font></div><div><font face="Courier New" size="2"><span style="font-size: 10pt; ">ATOM 6 <span class="Apple-converted-space"> </span><b>OG</b> SER P 1 78.499 35.849 38.473 -0.4900 1.4000</span></font></div><div><font face="Courier New" size="2"><span style="font-size: 10pt; ">ATOM 7 <span class="Apple-converted-space"> </span><span style="background-color: yellow; ">H2</span> SER P 1 78.147 32.756 38.163 0.3900 1.0000</span></font></div><div><font face="Courier New" size="2"><span style="font-size: 10pt; ">ATOM 8 <span class="Apple-converted-space"> </span><span style="background-color: yellow; ">H</span> SER P 1 78.673 32.645 36.625 0.3900 1.0000</span></font></div><div><font face="Courier New" size="2"><span style="font-size: 10pt; ">ATOM 9 <span class="Apple-converted-space"> </span><span style="background-color: yellow; ">HA</span> SER P 1 76.672 34.153 37.584 0.0000 0.0000</span></font></div><div><font face="Courier New" size="2"><span style="font-size: 10pt; ">ATOM 10 <span class="Apple-converted-space"> </span><span style="background-color: yellow; ">HB3</span> SER P 1 77.336 36.321 36.945 0.0000 0.0000</span></font></div><div><font face="Courier New" size="2"><span style="font-size: 10pt; ">ATOM 11 <span class="Apple-converted-space"> </span><span style="background-color: yellow; ">HB2</span> SER P 1 78.811 35.764 36.522 0.0000 0.0000</span></font></div><div><font face="Courier New" size="2"><span style="font-size: 10pt; ">ATOM 12 <span class="Apple-converted-space"> </span><span style="background-color: yellow; ">HG</span> SER P 1 78.357 35.015 39.006 0.4900 1.0000</span></font></div><div> </div><div>I wrote a new PDB file for the altered molecule using the "write pdb" option and the hydrogen atoms were present in that file, so I know they are on my model.</div><div> </div><div>Nikolay Rodionov</div><div> </div><div>-----Original Message-----<br>From: Elaine Meng [<a href="mailto:meng@cgl.ucsf.edu">mailto:meng@cgl.ucsf.edu</a>]<span class="Apple-converted-space"> </span><br>Sent: Tuesday, April 24, 2012 4:36 PM<br>To: Nikolay Igorovich Rodionov<br>Cc: Chimera BB<br>Subject: Re: [Chimera-users] Charge data</div><div> </div><div>Hi Nikolay,</div><div>You're welcome, I'm glad Chimera does some of what you want!</div><div> </div><div>Hmmm, that's a good question. I think it could be done by opening the structure, using only commands to carefully translate (and rotate, if needed) by some exact amount, then saving the transformed coordinates.</div><div> </div><div>You would have to determine the needed amounts of motion. I guess pure translation would be relatively simple if you know the current coordinates of the helix center you want to make the origin: if (a,b,c) you could use commands:</div><div> </div><div>move x -a</div><div>move y -b</div><div>move z -c </div><div> </div><div><<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/move.html">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/move.html</a>></div><div> </div><div>As for finding out helix center and axis if you don't already know them, commands "measure center" "measure inertia" and/or ("define axis" "define centroid" + Save button on axis/centroid table) may be useful:</div><div><<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html</a>></div><div><<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/define.html">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/define.html</a>></div><div> </div><div>I hope this helps,</div><div>Elaine</div><div>----------</div><div>Elaine C. Meng, Ph.D.</div><div>UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco</div><div> </div><div> </div><div>On Apr 24, 2012, at 3:14 PM, Nikolay Igorovich Rodionov wrote:</div><div> </div><div>> Thank you so much, you've helped me a lot within the last week. I have one more question, is it possible to set a new origin for the axis? I have a helical molecule which was built from HETAM transformations so the origin is at the located in the center of the original molecule. I would like the move the origin to the center of the helix.</div><div>> Nikolay Rodionov</div><div>></div><div> </div><div> </div><div> </div></span></font>_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br><a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br></div></span></blockquote></div><br></div><br><br></body></html>