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--></style></head><body lang=EN-GB link=blue vlink="#954F72" style='word-wrap:break-word'><div class=WordSection1><p class=MsoNormal><span lang=DE>Hi Elaine, <o:p></o:p></span></p><p class=MsoNormal><span lang=DE>thanks a lot for the help, I was able to visualize the labeling Information in the pdb. If I have a homooligomer, how should I do it If I have always the same residues? Should I introduce a chain specifier in my .defattr file?<o:p></o:p></span></p><p class=MsoNormal><span lang=DE>Thanks a lot for the help<o:p></o:p></span></p><p class=MsoNormal><span lang=DE><o:p> </o:p></span></p><p class=MsoNormal><span lang=DE>Best wishes</span></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif;color:black'>Alessio Di Ianni <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif;color:black'>PhD Student<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif;color:black'>Department of Pharmaceutical Chemistry and Bioanalytics<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif;color:black'>Center for Structural Mass Spectrometry<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif;color:black'>Institute of Pharmacy<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif;color:black'>Martin Luther University Halle-Wittenberg<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif;color:black'>Kurt-Mothes-Str. 3, Entance C<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif;color:black'>D-06120 Halle/Saale<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif;color:black'>Tel: +49 (0)345 55 25224<o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p><div style='mso-element:para-border-div;border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal style='border:none;padding:0cm'><b>From: </b><a href="mailto:meng@cgl.ucsf.edu">Elaine Meng</a><br><b>Sent: </b>17 January 2022 20:32<br><b>To: </b><a href="mailto:alessio.di-ianni@pharmazie.uni-halle.de">Alessio Di Ianni</a><br><b>Cc: </b><a href="mailto:chimerax-users@cgl.ucsf.edu">ChimeraX Users Help</a><br><b>Subject: </b>Re: [chimerax-users] Assessment of labeling data using ChimeraX</p></div><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Hi Alessio,</p><p class=MsoNormal>Then they are "attribute assignment files" as described here:</p><p class=MsoNormal><https://rbvi.ucsf.edu/chimerax/docs/user/formats/defattr.html></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Those can be read by both Chimera and ChimeraX. Since you're using ChimeraX, the rest of this message refers to ChimeraX.</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>As mentioned in the link above, you just use the "open" command to open such a file (with the corresponding 3D structure(s) already open) and that will automatically assign the attribute. You can either name those files something.defattr so that the format will be known automatically, or if you keep the .txt at the end of the name, use the "format defattr" option in the "open" command.</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal> Then after the attribute is assigned, you can refer to it by name in the command line, e.g. command "color byattribute" or "select" using an attribute value range, see these links:</p><p class=MsoNormal><https://rbvi.ucsf.edu/chimerax/docs/user/attributes.html></p><p class=MsoNormal><https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute></p><p class=MsoNormal>...specifying attribute value ranges in the command line:</p><p class=MsoNormal><https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#attributes></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>For example, to select atoms with bfactor attribute values over 40:</p><p class=MsoNormal>select @@bfactor>40</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>The attribute name in the files is really long (look at the file contents with a text editor to see) and you may want to text-edit the file to change it to something more convenient before you assign the attribute. Again, the format of the file is described in the first link in this message.</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>I hope this helps,</p><p class=MsoNormal>Elaine</p><p class=MsoNormal>-----</p><p class=MsoNormal>Elaine C. Meng, Ph.D. </p><p class=MsoNormal>UCSF Chimera(X) team</p><p class=MsoNormal>Department of Pharmaceutical Chemistry</p><p class=MsoNormal>University of California, San Francisco</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>> On Jan 17, 2022, at 12:30 AM, Alessio Di Ianni via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:</p><p class=MsoNormal>> </p><p class=MsoNormal>> Dear Elaine Meng, </p><p class=MsoNormal>> thanks for the quick answer. This program allows you to analyze different kind of structural MS data and gives you a txt file in which are reported in my case labeling yield for each residue both in absolute way or as protection factor when comparing two different Protein states (e.g. with and without a Ligand for example). They say this file can be easily used by ChimeraX using the define by Attribute command since These are numerical values for a given residue in your Protein of interest. But I am not able to make it readable by the software.</p><p class=MsoNormal>> Hope you can help me out with this</p><p class=MsoNormal>> Best wishes</p><p class=MsoNormal>> </p><p class=MsoNormal>> Alessio Di Ianni </p><p class=MsoNormal>> PhD Student</p><p class=MsoNormal>> Department of Pharmaceutical Chemistry and Bioanalytics</p><p class=MsoNormal>> Center for Structural Mass Spectrometry</p><p class=MsoNormal>> Institute of Pharmacy</p><p class=MsoNormal>> Martin Luther University Halle-Wittenberg</p><p class=MsoNormal>> Kurt-Mothes-Str. 3, Entance C</p><p class=MsoNormal>> D-06120 Halle/Saale</p><p class=MsoNormal>> Tel: +49 (0)345 55 25224</p><p class=MsoNormal>> </p><p class=MsoNormal>> From: Elaine Meng</p><p class=MsoNormal>> Sent: 14 January 2022 18:19</p><p class=MsoNormal>> To: Alessio Di Ianni</p><p class=MsoNormal>> Cc: chimerax-users@cgl.ucsf.edu</p><p class=MsoNormal>> Subject: Re: [chimerax-users] Assessment of labeling data using ChimeraX</p><p class=MsoNormal>> </p><p class=MsoNormal>> Hi Alessio,</p><p class=MsoNormal>> I have no idea what the Mass Spec Studio labeling data looks like, so I can't say anything specific.</p><p class=MsoNormal>> </p><p class=MsoNormal>> However, in general, you would have to look at that data and manually convert to ChimeraX specficiations (e.g. residue numbers) to make commands that change residue or atom display or coloring, or write a script to do it. If it is a list of crosslinks, in ChimeraX you can draw lines (pseudobonds) between pairs of atoms either using the "distance" command or by creating a "pseudobond" input file which is basically a text file that lists ChimeraX specifications of pairs of atoms.</p><p class=MsoNormal>> </p><p class=MsoNormal>> distance command</p><p class=MsoNormal>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/distance.html></p><p class=MsoNormal>> </p><p class=MsoNormal>> pseudobond input file</p><p class=MsoNormal>> <https://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html#pbfiles></p><p class=MsoNormal>> </p><p class=MsoNormal>> crosslink command (can be used to analyze pseudobonds after they are created by one of the two methods above)</p><p class=MsoNormal>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/crosslinks.html></p><p class=MsoNormal>> </p><p class=MsoNormal>> I hope this helps,</p><p class=MsoNormal>> Elaine</p><p class=MsoNormal>> -----</p><p class=MsoNormal>> Elaine C. Meng, Ph.D. </p><p class=MsoNormal>> UCSF Chimera(X) team</p><p class=MsoNormal>> Department of Pharmaceutical Chemistry</p><p class=MsoNormal>> University of California, San Francisco</p><p class=MsoNormal>> </p><p class=MsoNormal>> > On Jan 14, 2022, at 6:53 AM, Alessio Di Ianni via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:</p><p class=MsoNormal>> > </p><p class=MsoNormal>> > Respectable ChimeraX developers, </p><p class=MsoNormal>> > how can I visualize labeling data obtained by Mass Spec Studio into a pdb structure using ChimeraX?</p><p class=MsoNormal>> > A help will be definitely appreciated.</p><p class=MsoNormal>> > Best regards</p><p class=MsoNormal>> > </p><p class=MsoNormal>> > Alessio Di Ianni </p><p class=MsoNormal>> > PhD Student</p><p class=MsoNormal>> > Department of Pharmaceutical Chemistry and Bioanalytics</p><p class=MsoNormal>> > Center for Structural Mass Spectrometry</p><p class=MsoNormal>> > Institute of Pharmacy</p><p class=MsoNormal>> > Martin Luther University Halle-Wittenberg</p><p class=MsoNormal>> > Kurt-Mothes-Str. 3, Entance C</p><p class=MsoNormal>> > D-06120 Halle/Saale</p><p class=MsoNormal>> > Tel: +49 (0)345 55 25224</p><p class=MsoNormal>> </p><p class=MsoNormal>> </p><p class=MsoNormal>> <p53_labeling_absolute.txt><p53_labeling_p_factor.txt>_______________________________________________</p><p class=MsoNormal>> ChimeraX-users mailing list</p><p class=MsoNormal>> ChimeraX-users@cgl.ucsf.edu</p><p class=MsoNormal>> Manage subscription:</p><p class=MsoNormal>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p></div></body></html>