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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>Dear Elaine Meng, <o:p></o:p></span></p><p class=MsoNormal><span lang=DE>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.<o:p></o:p></span></p><p class=MsoNormal><span lang=DE>Hope you can help me out with this<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>14 January 2022 18:19<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@cgl.ucsf.edu</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>I have no idea what the Mass Spec Studio labeling data looks like, so I can't say anything specific.</p><p class=MsoNormal><o:p> </o:p></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><o:p> </o:p></p><p class=MsoNormal>distance command</p><p class=MsoNormal><https://rbvi.ucsf.edu/chimerax/docs/user/commands/distance.html></p><p class=MsoNormal><o:p> </o:p></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><o:p> </o:p></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><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>> 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><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p></div></body></html>