<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">To supplement what Elaine said, without the column-positioning of the atom name it would be impossible to distinguish a carbon alpha (CA) from a calcium (CA). Though if you provide the element symbol in columns 77-78 then the atom name will be ignored for determining the element.<div><br></div><div>--Eric</div><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><div><div>On Mar 17, 2009, at 8:41 AM, Elaine Meng wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi Christian,<br>Here are the rules for atom names in correct PDB format, as I <br>understand them:<br><br>Atom names start with element symbols right-justified in columns 13-14 <br>as permitted by the length of the name. For example, the symbol FE for <br>iron appears in columns 13-14, whereas the symbol C for carbon appears <br>in column 14. If an atom name has four characters, however, it must <br>start in column 13 even if the element symbol is a single character <br>(for example, some hydrogens).<br><br>So while it is true that columns 13-16 are for atom names, just <br>putting the names anywhere in that area does not mean the format is <br>correct.<br><br>The Chimera User's Guide includes some information on PDB format:<br><<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.html">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.html</a> <br><blockquote type="cite"><br></blockquote><br>I hope this helps,<br>ELaine<br>-----<br>Elaine C. Meng, Ph.D. <a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a><br>UCSF Computer Graphics Lab and Babbitt Lab<br>Department of Pharmaceutical Chemistry<br>University of California, San Francisco<br> <a href="http://www.cgl.ucsf.edu/home/meng/index.html">http://www.cgl.ucsf.edu/home/meng/index.html</a><br><br>On Mar 17, 2009, at 6:57 AM, Christian Schudoma wrote:<br><br><blockquote type="cite">Hello Chimera-Users and -Devs,<br></blockquote><blockquote type="cite">I encountered the following problem when trying to visualise the<br></blockquote><blockquote type="cite">following purine molecule (Actually, I tried to do something more<br></blockquote><blockquote type="cite">complex(*) but the same problem can be reproduced with this more <br></blockquote><blockquote type="cite">simple<br></blockquote><blockquote type="cite">example). For clarification, the first lines contain the column <br></blockquote><blockquote type="cite">numbers.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> 1 2 3 4 5 6 7<br></blockquote><blockquote type="cite">123456789012345678901234567890123456789012345678901234567890123456789012345678<br></blockquote><blockquote type="cite">HETATM 1 N1 CKN A 1 -0.003 1.586 -3.371 0.00<br></blockquote><blockquote type="cite">0.00 N<br></blockquote><blockquote type="cite">HETATM 2 C2 CKN A 1 1.016 1.511 -4.278 0.00<br></blockquote><blockquote type="cite">0.00 C<br></blockquote><blockquote type="cite">HETATM 3 N3 CKN A 1 2.313 1.566 -3.865 0.00<br></blockquote><blockquote type="cite">0.00 N<br></blockquote><blockquote type="cite">HETATM 4 C4 CKN A 1 2.576 1.683 -2.541 0.00<br></blockquote><blockquote type="cite">0.00 C<br></blockquote><blockquote type="cite">HETATM 5 C5 CKN A 1 1.559 1.758 -1.597 0.00<br></blockquote><blockquote type="cite">0.00 C<br></blockquote><blockquote type="cite">HETATM 6 C6 CKN A 1 0.224 1.717 -2.032 0.00<br></blockquote><blockquote type="cite">0.00 C<br></blockquote><blockquote type="cite">HETATM 7 N7 CKN A 1 2.100 1.858 -0.373 0.00<br></blockquote><blockquote type="cite">0.00 N<br></blockquote><blockquote type="cite">HETATM 8 C8 CKN A 1 3.434 1.842 -0.568 0.00<br></blockquote><blockquote type="cite">0.00 C<br></blockquote><blockquote type="cite">HETATM 9 N9 CKN A 1 3.731 1.742 -1.876 0.00<br></blockquote><blockquote type="cite">0.00 N<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">When I load a pdb file containing these coordinates into Chimera, I <br></blockquote><blockquote type="cite">get<br></blockquote><blockquote type="cite">9 non-connected dots (obviously representing the atoms) which can<br></blockquote><blockquote type="cite">neither be coloured by hetero-atom, nor by element. Note that the atom<br></blockquote><blockquote type="cite">names are located in the appropriate columns, i.e. between columns 13<br></blockquote><blockquote type="cite">and 16, more specifically in columns 15 and 16.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I noticed that in other pdb structures 2-character atom names are<br></blockquote><blockquote type="cite">located in columns 14 and 15 and when I put my atom names there, <br></blockquote><blockquote type="cite">Chimera<br></blockquote><blockquote type="cite">displays the purine ring system which then can be coloured by<br></blockquote><blockquote type="cite">hetero-atom/element. Now it is nice that this workaround fixes my<br></blockquote><blockquote type="cite">problem, however, according to the pdb file format specification<br></blockquote><blockquote type="cite">(columns 13-16 are reserved for the atom name), atom names located in<br></blockquote><blockquote type="cite">columns 15 and 16 are valid(*) and as such should be processible by<br></blockquote><blockquote type="cite">visualisation tools etc.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">The behaviour occurs with the latest daily build as well as some older<br></blockquote><blockquote type="cite">versions I found on my hard disk...<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">(*) The purine is part of a larger cytokinin. I stumbled upon the<br></blockquote><blockquote type="cite">described behaviour while using the AddHydrogen function on the whole<br></blockquote><blockquote type="cite">molecule, which lead to the replacement of the purine with a hydrogen.<br></blockquote><blockquote type="cite">(**) Unless there are some additional rules regarding the placement of<br></blockquote><blockquote type="cite">atom names shorter than 4 characters, in which case I apologise for<br></blockquote><blockquote type="cite">bugging you with this.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Any comments on this?<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Best regards,<br></blockquote><blockquote type="cite">Christian Schudoma<br></blockquote><br>_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br>http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users<br></div></blockquote></div><br></div></body></html>