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<div style="font-family: Tahoma; ">Hi Elaine,</div><div><span class="hps" title="Fai clic per visualizzare le traduzioni alternative" style="font-family: arial, sans-serif; ">Thank you very much</span><span title="Fai clic per visualizzare le traduzioni alternative" style="font-family: arial, sans-serif; ">,</span><font class="Apple-style-span" face="arial, sans-serif"> </font><span class="hps" title="Fai clic per visualizzare le traduzioni alternative" style="font-family: arial, sans-serif; ">I will try</span><font class="Apple-style-span" face="arial, sans-serif"> </font><span class="hps" title="Fai clic per visualizzare le traduzioni alternative" style="font-family: arial, sans-serif; ">the methods</span><font class="Apple-style-span" face="arial, sans-serif"> </font><span class="hps" title="Fai clic per visualizzare le traduzioni alternative" style="font-family: arial, sans-serif; ">you</span><font class="Apple-style-span" face="arial, sans-serif"> </font><span class="hps" title="Fai clic per visualizzare le traduzioni alternative" style="font-family: arial, sans-serif; ">have</span><font class="Apple-style-span" face="arial, sans-serif"> </font><span class="hps" title="Fai clic per visualizzare le traduzioni alternative" style="font-family: arial, sans-serif; ">described</span><font class="Apple-style-span" face="arial, sans-serif"> </font><span class="hps" title="Fai clic per visualizzare le traduzioni alternative" style="font-family: arial, sans-serif; ">me</span><span title="Fai clic per visualizzare le traduzioni alternative" style="font-family: arial, sans-serif; ">.</span><font class="Apple-style-span" face="arial, sans-serif"> </font><span class="hps" title="Fai clic per visualizzare le traduzioni alternative" style="font-family: arial, sans-serif; ">Indeed</span><font class="Apple-style-span" face="arial, sans-serif"> </font><span class="hps" title="Fai clic per visualizzare le traduzioni alternative" style="font-family: arial, sans-serif; ">there is</span><font class="Apple-style-span" face="arial, sans-serif"> </font><span class="hps" title="Fai clic per visualizzare le traduzioni alternative" style="font-family: arial, sans-serif; ">a closely related </span><span class="hps" title="Fai clic per visualizzare le traduzioni alternative"><font class="Apple-style-span" face="arial, sans-serif">dimer, so i'll tr</font><font class="Apple-style-span" face="Tahoma">y to match it with my protein,</font><font class="Apple-style-span" face="arial, sans-serif"> using MatchMaker. </font></span></div><div><span class="hps" title="Fai clic per visualizzare le traduzioni alternative"><font class="Apple-style-span" face="arial, sans-serif">With command "sym", Chimera returns me an error, probably it depends on the PDB files.</font></span></div><div><span class="Apple-style-span" style="font-family: arial, sans-serif; "><span class="hps" title="Fai clic per visualizzare le traduzioni alternative">Anyway</span></span><span class="Apple-style-span" style="font-family: arial, sans-serif; "> </span><span class="Apple-style-span" style="font-family: arial, sans-serif; "><span class="hps" title="Fai clic per visualizzare le traduzioni alternative">I'll try</span></span><span class="Apple-style-span" style="font-family: arial, sans-serif; "> </span><span class="Apple-style-span" style="font-family: arial, sans-serif; "><span class="hps" title="Fai clic per visualizzare le traduzioni alternative">other methods. Thanks again for the precious help,</span></span></div><div><span class="Apple-style-span" style="font-family: arial, sans-serif; "><span class="hps" title="Fai clic per visualizzare le traduzioni alternative">F. Biagi</span></span></div><br><br><div id="SkyDrivePlaceholder" style="font-size: 10pt; font-family: Tahoma; "></div><font class="Apple-style-span" size="2" style="font-family: Tahoma; ">> Subject: Re: [Chimera-users] how to make simmetric dimer</font><br><font class="Apple-style-span" size="2" style="font-family: Tahoma; ">> From: meng@cgl.ucsf.edu</font><br><font class="Apple-style-span" size="2" style="font-family: Tahoma; ">> Date: Mon, 25 Apr 2011 13:55:44 -0700</font><br><font class="Apple-style-span" size="2" style="font-family: Tahoma; ">> CC: chimera-users@cgl.ucsf.edu</font><br><font class="Apple-style-span" size="2" style="font-family: Tahoma; ">> To: francescobiagi@live.it</font><br><font class="Apple-style-span" size="2" style="font-family: Tahoma; ">> </font><br><font class="Apple-style-span" size="2" style="font-family: Tahoma; ">> Hi Francesco,</font><br><font class="Apple-style-span" size="2" style="font-family: Tahoma; ">> It depends on the information in the PDB file: it may include matrices describing operations to generate the biological multimer (BIOMT), or copies related by crystallographic symmetry (SMTRY or CRYST1), or copies related by noncrystallographic symmetry (MTRIX).</font><br><font class="Apple-style-span" size="2" style="font-family: Tahoma; ">> </font><br><font class="Apple-style-span" size="2" style="font-family: Tahoma; ">> If this information is already present in the PDB file you can just use the command "sym" (or depending on the type of information, the Unit Cell or Multiscale Models tool) to make the corresponding multimers. </font><br><font class="Apple-style-span" size="2" style="font-family: Tahoma; ">> </font><br><font class="Apple-style-span" size="2" style="font-family: Tahoma; ">> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html> </font><br><font class="Apple-style-span" size="2" style="font-family: Tahoma; ">> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemulti.html></font><br><font class="Apple-style-span" size="2" style="font-family: Tahoma; ">> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/unitcell/unitcell.html></font><br><font class="Apple-style-span" size="2" style="font-family: Tahoma; ">> </font><br><font class="Apple-style-span" size="2" style="font-family: Tahoma; ">> If the PDB file does not contain such information, then possible approaches are:</font><br><font class="Apple-style-span" size="2" style="font-family: Tahoma; ">> </font><br><font class="Apple-style-span" size="2" style="font-family: Tahoma; ">> - use File... Fetch by ID to get the PQS-predicted multimer for this structure (however, not all structures are available from this site)</font><br><font class="Apple-style-span" size="2" style="font-family: Tahoma; ">> </font><br><font class="Apple-style-span" size="2" style="font-family: Tahoma; ">> - specify the dimer axis and center yourself manually in the "sym" command (but it may be hard to figure those out)</font><br><font class="Apple-style-span" size="2" style="font-family: Tahoma; ">> </font><br><font class="Apple-style-span" size="2" style="font-family: Tahoma; ">> - if there is a closely related protein with dimer of known structure, and you expect your protein to dimerize the same way, you can open the other protein, open two copies of your protein, and match them to the monomers of the other protein (for example, with MatchMaker)</font><br><font class="Apple-style-span" size="2" style="font-family: Tahoma; ">> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html></font><br><font class="Apple-style-span" size="2" style="font-family: Tahoma; ">> </font><br><font class="Apple-style-span" size="2" style="font-family: Tahoma; ">> I hope this helps,</font><br><font class="Apple-style-span" size="2" style="font-family: Tahoma; ">> Elaine</font><br><font class="Apple-style-span" size="2" style="font-family: Tahoma; ">> ----------</font><br><font class="Apple-style-span" size="2" style="font-family: Tahoma; ">> Elaine C. Meng, Ph.D. </font><br><font class="Apple-style-span" size="2" style="font-family: Tahoma; ">> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab</font><br><font class="Apple-style-span" size="2" style="font-family: Tahoma; ">> Department of Pharmaceutical Chemistry</font><br><font class="Apple-style-span" size="2" style="font-family: Tahoma; ">> University of California, San Francisco</font><br><font class="Apple-style-span" size="2" style="font-family: Tahoma; ">> </font><br><font class="Apple-style-span" size="2" style="font-family: Tahoma; ">> On Apr 25, 2011, at 10:59 AM, Francesco Biagi wrote:</font><br><font class="Apple-style-span" size="2" style="font-family: Tahoma; ">> </font><br><font class="Apple-style-span" size="2" style="font-family: Tahoma; ">> > Hello everyone. I have a question about Chimera: I want to put two monomers (of a dimer) in simmetry. I tried to do this with mouse, with poor results.</font><br><font class="Apple-style-span" size="2" style="font-family: Tahoma; ">> > I would like to know if there is a method or a script that can help me. </font><br><font class="Apple-style-span" size="2" style="font-family: Tahoma; ">> > Thanks to all.</font><br><font class="Apple-style-span" size="2" style="font-family: Tahoma; ">> > Francesco </font><br><font class="Apple-style-span" size="2" style="font-family: Tahoma; ">> </font><br> </body>
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