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<p class="MsoNormal">Have downloaded ChimeraX as I would like to include a ribosome structure or part of it in my work.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">ChimeraX is, I am aware, largely a command based operational process.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I feel like a real dummy because I do not understand how to achieve the imagery that I would like<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I have been able to open PDB 4WPO can rotate it and similar things, and there seem to be two molecules in the unit cell. I stumbled on a list of all the proteins, rRNAs and some other components in the structure such as EFG, an elongation
factor.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Can’t figure out how to delete one of the model units from the image, as I was able to do with Chimera. I find it virtually impossible to understand the logic of the commands. Of course the command structure is similar to that in Chimera,
but I only used that infrequently. I used the menu driven tools etc almost exclusively. I could achieve what I wanted with them and the learning curve was quite tolerable. Then when I got stuck I received excellent advice from Chimera staff on how to use
the commands when needed.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">For example <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span style="font-size:13.5pt;font-family:"Times New Roman",serif;color:black">color <a href="atomspec.html"><i><span style="color:blue">spec</span></i></a> <a href="#colorname"><i><span style="color:blue">colorname</span></i></a>
<a href="#general-options"><i><span style="color:blue">general-options</span></i></a></span></b><span style="font-size:13.5pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal">What is the designation or meaning of <b><i><u><span style="color:#0070C0">spec
</span></u></i></b><span style="color:#0070C0">? </span>How would I select the EGF protein from the ribosome to color it.
<b><span style="font-size:13.5pt;font-family:"Times New Roman",serif;color:red">4wpo #1, chain DZ: 50S ribosomal protein L9,Elongation factor G</span></b><span style="font-size:10.0pt">.
</span>4WPO is the pdb number, #1, I believe to one of the two units in the model. Chain DZ refers to the protein. I tried several permutations of this information and only received error messages.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><b><span style="color:red"><a href="help:user/commands/color.html"><span style="color:red;font-weight:normal">color</span></a> 4wpo #1, chain BZ: 50S ribosomal protein L9,Elongation factor G<o:p></o:p></span></b></p>
<p class="MsoNormal"><b><span style="color:red">Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bypolymer', 'fromatoms', or 'random' or a keyword</span></b><span style="color:red"> <o:p></o:p></span></p>
<p class="MsoNormal"><b><span style="color:red"><a href="help:user/commands/color.html"><span style="color:red;font-weight:normal">color</span></a> red 4wpo #1, chain BZ: 50S ribosomal protein L9,Elongation factor G<o:p></o:p></span></b></p>
<p class="MsoNormal"><b><span style="color:red">Expected one of 'atoms', 'bonds', 'cartoons', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword</span></b><span style="color:red"> <o:p></o:p></span></p>
<p class="MsoNormal"><b><span style="color:red"><a href="help:user/commands/color.html"><span style="color:red;font-weight:normal">color</span></a> ribbons red 4wpo #1, chain BZ: 50S ribosomal protein L9,Elongation factor G<o:p></o:p></span></b></p>
<p class="MsoNormal"><b><span style="color:red">Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bypolymer', 'fromatoms', or 'random' or a keyword</span></b><span style="color:red"> <o:p></o:p></span></p>
<p class="MsoNormal"><b><span style="color:red"><a href="help:user/commands/color.html"><span style="color:red;font-weight:normal">color</span></a> ribbons red 4wpo #1, chain BZ<o:p></o:p></span></b></p>
<p class="MsoNormal"><b><span style="color:red">Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bypolymer', 'fromatoms', or 'random' or a keyword</span></b><span style="color:red"> <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:red"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span style="color:red"><o:p> </o:p></span></b></p>
<p class="MsoNormal"><b><i><u><span style="color:#0070C0">Colorname</span></u></i></b> I think I understand, and I think that I have found a log of the different colors.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Have no idea of what <b><i><u><span style="color:#0070C0">general-options</span></u></i></b> might refer to.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Here is more of my log.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="background:#DDDDDD"><b><span style="font-size:13.5pt;font-family:"Times New Roman",serif;color:black"><a href="help:user/commands/show.html"><span style="color:blue">show</span></a> selAtoms ribbons<o:p></o:p></span></b></p>
<p class="MsoNormal" style="background:#DDDDDD"><b><span style="font-size:13.5pt;font-family:"Times New Roman",serif;color:black"><a href="help:user/commands/help.html"><span style="color:blue">help</span></a> help:user<o:p></o:p></span></b></p>
<p class="MsoNormal" style="background:#DDDDDD"><b><span style="font-size:13.5pt;font-family:"Times New Roman",serif;color:black"><a href="help:user/commands/select.html"><span style="color:blue">select</span></a> </span></b><b><span style="font-size:13.5pt;font-family:"Times New Roman",serif;color:white;background:crimson">4wpo
#1, chain BZ</span></b><b><span style="font-size:13.5pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></b></p>
<p class="MsoNormal"><b><span style="font-size:13.5pt;font-family:"Times New Roman",serif;color:crimson">Expected an objects specifier or a keyword</span></b><span style="font-size:13.5pt;font-family:"Times New Roman",serif;color:black"> </span><o:p></o:p></p>
<p class="MsoNormal" style="background:#DDDDDD"><b><span style="font-size:13.5pt;font-family:"Times New Roman",serif;color:black"><a href="help:user/commands/help.html"><span style="color:blue">help</span></a> help:contact.html<o:p></o:p></span></b></p>
<p class="MsoNormal" style="background:#DDDDDD"><b><span style="font-size:13.5pt;font-family:"Times New Roman",serif;color:black"><a href="help:user/commands/help.html"><span style="color:blue">help</span></a> help:contact.html<o:p></o:p></span></b></p>
<p class="MsoNormal" style="background:#DDDDDD"><b><span style="font-size:13.5pt;font-family:"Times New Roman",serif;color:black"><a href="help:user/commands/color.html"><span style="color:blue">color</span></a> #1 </span></b><b><span style="font-size:13.5pt;font-family:"Times New Roman",serif;color:white;background:crimson">BZ
red</span></b><b><span style="font-size:13.5pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></b></p>
<p class="MsoNormal"><b><span style="font-size:13.5pt;font-family:"Times New Roman",serif;color:crimson">Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bypolymer', 'fromatoms', or 'random' or a keyword</span></b><span style="font-size:13.5pt;font-family:"Times New Roman",serif;color:black"> </span><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Similarly I can’t understand what the terms in <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span style="font-size:13.5pt;font-family:"Times New Roman",serif;color:black">select <a href="atomspec.html"><i><span style="color:blue">spec</span></i></a> [ polymer <a href="atomspec.html"><i><span style="color:blue">chain-spec</span></i></a> ]<o:p></o:p></span></b></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">might mean.<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">The learning curve will be very much steeper than that for Chimera.<o:p></o:p></span></p>
<h3>Please allow me to make a suggestion. It would be useful to have a list with the definition of the terms used in the commands with clear examples. One example is
<b><i><u><span style="color:#0070C0">spec</span></u></i></b><span style="color:#0070C0">
</span>another would be <b><i><u><span style="color:#0070C0">ref-spec </span></u></i></b>or
<b><span style="font-size:13.5pt;font-family:"Times New Roman",serif"> </span></b><b><a href="#general-options"><i><span style="color:blue">general-options</span></i></a></b><b><span style="font-size:13.5pt;font-family:"Times New Roman",serif"> <o:p></o:p></span></b></h3>
<p class="MsoNormal">I couldn’t find one if it was there.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">These are only a few examples. Such terms are not defined anywhere. The persons most familiar with them are the persons who have written the programs, and those who have used the programs extensively.<o:p></o:p></p>
<h3>Some things like ( <b>cartoon | ribbon ) <a href="atomspec.html"><i><span style="color:blue">atom-spec</span></i></a> [ smooth <i>factor</i> | default ] [ suppressBackboneDisplay true | false ]</b>
<span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext">
appear to be well explained but again atom-spec is not defined nor an example given at least none that I c</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext">ould find.<o:p></o:p></span></h3>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="font-size:12.0pt;color:#00B050">Kindly consider my comments as questions and friendly suggestions.
<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I downloaded Pymol the other day, and couldn’t get to first base. Would have to take a course on how to use it. I removed it from my computer. I don’t have the time to learn even the basics about Pymol, and there are no clear explanations
anywhere. I assume students learn from their colleagues who have spent considerable time learning the nuances of the program.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I have a similar view of Photoshop – huge learning curve.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Maybe an interactive course on YouTube video might be useful for ChimeraX<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Regards<o:p></o:p></p>
<p class="MsoNormal">And thanks.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">AGS<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><o:p> </o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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