Answers.Body: <p>Ok, this is not an answer, but to better visualize the problem I recreated the question/answer on <code>Chimera</code> that has a different syntax for the <code>transparency</code>  command see : <a href="https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/transparency.html" rel="nofollow noreferrer">https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/transparency.html</a> and <a href="https://www.cgl.ucsf.edu/chimerax/docs/user/commands/transparency.html" rel="nofollow noreferrer">https://www.cgl.ucsf.edu/chimerax/docs/user/commands/transparency.html</a> .</p>
  <p>Input file is <code>marker.cmm</code> , to be opened in <code>FILE MENU</code> of <code>VOLUME TRACER</code> from <code>VOLUME MENU</code> :</p>
  <pre><code>&lt;marker_set name=&quot;marker set 1&quot;&gt;
  &lt;marker id=&quot;14&quot; x=&quot;0.018&quot; y=&quot;-0.180&quot; z=&quot;0.215&quot; r=&quot;1.000000&quot; g=&quot;0.254900&quot; b=&quot;0.050980&quot; a=&quot;0&quot; radius=&quot;0.018754&quot; /&gt;
  &lt;marker id=&quot;15&quot; x=&quot;-0.032&quot; y=&quot;-0.191&quot; z=&quot;0.241&quot; r=&quot;1.000000&quot; g=&quot;0.254900&quot; b=&quot;0.050980&quot; a=&quot;0&quot; radius=&quot;0.018754&quot; /&gt;
  &lt;marker id=&quot;16&quot; x=&quot;-0.033&quot; y=&quot;-0.117&quot; z=&quot;0.246&quot; r=&quot;1.000000&quot; g=&quot;0.254900&quot; b=&quot;0.050980&quot; a=&quot;0&quot; radius=&quot;0.018754&quot; /&gt;
  &lt;marker id=&quot;17&quot; x=&quot;0.020&quot; y=&quot;-0.138&quot; z=&quot;0.244&quot; r=&quot;1.000000&quot; g=&quot;0.254900&quot; b=&quot;0.050980&quot; a=&quot;0&quot; radius=&quot;0.018754&quot; /&gt;
  &lt;marker id=&quot;18&quot; x=&quot;0.047&quot; y=&quot;-0.083&quot; z=&quot;0.280&quot; r=&quot;1.000000&quot; g=&quot;0.254900&quot; b=&quot;0.050980&quot; a=&quot;0&quot; radius=&quot;0.018754&quot; /&gt;
  &lt;marker id=&quot;19&quot; x=&quot;0.073&quot; y=&quot;-0.061&quot; z=&quot;0.240&quot; r=&quot;1.000000&quot; g=&quot;0.254900&quot; b=&quot;0.050980&quot; a=&quot;0&quot; radius=&quot;0.018754&quot; /&gt;
  &lt;marker id=&quot;20&quot; x=&quot;0.010&quot; y=&quot;-0.068&quot; z=&quot;0.271&quot; r=&quot;1.000000&quot; g=&quot;0.254900&quot; b=&quot;0.050980&quot; a=&quot;0&quot; radius=&quot;0.018754&quot; /&gt;
  &lt;link id1=&quot;14&quot; id2=&quot;15&quot; r=&quot;0.800000&quot; g=&quot;0.800000&quot; b=&quot;0.000000&quot; a=&quot;0&quot; radius=&quot;0.006251&quot;/&gt;
  &lt;link id1=&quot;15&quot; id2=&quot;16&quot; r=&quot;0.800000&quot; g=&quot;0.800000&quot; b=&quot;0.000000&quot; a=&quot;0&quot; radius=&quot;0.006251&quot;/&gt;
  &lt;link id1=&quot;17&quot; id2=&quot;18&quot; r=&quot;0.800000&quot; g=&quot;0.800000&quot; b=&quot;0.000000&quot; a=&quot;0&quot; radius=&quot;0.006251&quot;/&gt;
  &lt;link id1=&quot;18&quot; id2=&quot;19&quot; r=&quot;0.800000&quot; g=&quot;0.800000&quot; b=&quot;0.000000&quot; a=&quot;0&quot; radius=&quot;0.006251&quot;/&gt;
  &lt;link id1=&quot;19&quot; id2=&quot;20&quot; r=&quot;0.800000&quot; g=&quot;0.800000&quot; b=&quot;0.000000&quot; a=&quot;0&quot; radius=&quot;0.006251&quot;/&gt;
  &lt;/marker_set&gt;
  </code></pre>
  <p>Image before command :</p>
  <p><a href="https://i.sstatic.net/Kb0kq.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/Kb0kq.png" alt="enter image description here" /></a></p>
  <p>Image after <code>transparency  50,a,b #0:16-end</code></p>
  <p>(#0 being 0 model as the only loaded model on my <code>Chimera</code> instance) :</p>
  <p><a href="https://i.sstatic.net/v3Ny2.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/v3Ny2.png" alt="enter image description here" /></a></p>
  <p>Better transparency visualizations :</p>
  <p><a href="https://i.sstatic.net/yaYRC.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/yaYRC.png" alt="enter image description here" /></a></p>
  <p><a href="https://i.sstatic.net/V7AXk.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/V7AXk.png" alt="enter image description here" /></a></p>
  <p>Dont get why a='50' or a='0.5' in <code>marker</code>,<code>link</code> definition dont work with <code>chimera</code> too</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-09-21T09:40:02.423Z
Answers.Text: Together with my edited question I think this all suffice as "good enough" for now at least. I am satisfied for the moment just using something like `transparency #1:2492-end 90 'All'`, but I guess when I get more complicated regions it would be good to be able to load the marker spec, i.e. e.g. #1:2492-2500, 3000-3500, ... from a file if that is possible. But I guess one can run command-files right? and I suppose there's no limit on the length on the spec, so perhaps I could just create one very long command in a file. (Many thanks for your efforts!!! unfortunately I need more rep to upvote)
Answers.UserDisplayName: ciru_4011
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-09-21T07:41:40.300Z
Answers.LastActivityDate: 2023-09-21T08:17:42.907Z
Answers.LastEditDate: 2023-09-21T08:17:42.907Z
Answers.UserDisplayName: pippo1980
Body: <p>I am using the software <a href="https://www.rbvi.ucsf.edu/chimerax/" rel="nofollow noreferrer">Chimera X</a> to visualize the 3d composition of molecules. I am very new to Chimera and only use it for visualization. The files I'm using are cmm files (xml-formatted) basically looking like below:</p>
  <pre class="lang-xml prettyprint-override"><code>...
  &lt;marker id=&quot;14&quot; x=&quot;0.018&quot; y=&quot;-0.180&quot; z=&quot;0.215&quot; r=&quot;1.000000&quot; g=&quot;0.254900&quot; b=&quot;0.050980&quot; a=&quot;0&quot; radius=&quot;0.018754&quot; /&gt;
  &lt;marker id=&quot;15&quot; x=&quot;-0.032&quot; y=&quot;-0.191&quot; z=&quot;0.241&quot; r=&quot;1.000000&quot; g=&quot;0.254900&quot; b=&quot;0.050980&quot; a=&quot;0&quot; radius=&quot;0.018754&quot; /&gt;
  &lt;marker id=&quot;16&quot; x=&quot;-0.033&quot; y=&quot;-0.117&quot; z=&quot;0.246&quot; r=&quot;1.000000&quot; g=&quot;0.254900&quot; b=&quot;0.050980&quot; a=&quot;0&quot; radius=&quot;0.018754&quot; /&gt;
  &lt;marker id=&quot;17&quot; x=&quot;0.020&quot; y=&quot;-0.138&quot; z=&quot;0.244&quot; r=&quot;1.000000&quot; g=&quot;0.254900&quot; b=&quot;0.050980&quot; a=&quot;0&quot; radius=&quot;0.018754&quot; /&gt;
  &lt;marker id=&quot;18&quot; x=&quot;0.047&quot; y=&quot;-0.083&quot; z=&quot;0.280&quot; r=&quot;1.000000&quot; g=&quot;0.254900&quot; b=&quot;0.050980&quot; a=&quot;0&quot; radius=&quot;0.018754&quot; /&gt;
  &lt;marker id=&quot;19&quot; x=&quot;0.073&quot; y=&quot;-0.061&quot; z=&quot;0.240&quot; r=&quot;1.000000&quot; g=&quot;0.254900&quot; b=&quot;0.050980&quot; a=&quot;0&quot; radius=&quot;0.018754&quot; /&gt;
  &lt;marker id=&quot;20&quot; x=&quot;0.010&quot; y=&quot;-0.068&quot; z=&quot;0.271&quot; r=&quot;1.000000&quot; g=&quot;0.254900&quot; b=&quot;0.050980&quot; a=&quot;0&quot; radius=&quot;0.018754&quot; /&gt;
  ...
  &lt;link id1=&quot;0&quot; id2=&quot;1&quot; r=&quot;0.800000&quot; g=&quot;0.800000&quot; b=&quot;0.000000&quot; a=&quot;0&quot; radius=&quot;0.006251&quot;/&gt;
  &lt;link id1=&quot;1&quot; id2=&quot;2&quot; r=&quot;0.800000&quot; g=&quot;0.800000&quot; b=&quot;0.000000&quot; a=&quot;0&quot; radius=&quot;0.006251&quot;/&gt;
  &lt;link id1=&quot;2&quot; id2=&quot;3&quot; r=&quot;0.800000&quot; g=&quot;0.800000&quot; b=&quot;0.000000&quot; a=&quot;0&quot; radius=&quot;0.006251&quot;/&gt;
  &lt;link id1=&quot;3&quot; id2=&quot;4&quot; r=&quot;0.800000&quot; g=&quot;0.800000&quot; b=&quot;0.000000&quot; a=&quot;0&quot; radius=&quot;0.006251&quot;/&gt;
  &lt;link id1=&quot;4&quot; id2=&quot;5&quot; r=&quot;0.800000&quot; g=&quot;0.800000&quot; b=&quot;0.000000&quot; a=&quot;0&quot; radius=&quot;0.006251&quot;/&gt;
  ...
  </code></pre>
  <p>i.e. just a simple polymer consisting of alot of markers (spheres) and links between them (cylinders), and with colors for each one specified in rgb (see <a href="https://www.cgl.ucsf.edu/chimerax/docs/user/markers.html" rel="nofollow noreferrer">here</a>). This is all well and good, but now I would like to set transparency for a subset of the markers and associated links. Preferably I would set this directly in the attributes in the cmm files, but I cannot find how to do this. The manual does mention that colours in general can be set with rgba where a means alpha level, but when trying to set a like seen in the xml block above, nothing happens (I tried values close to both 0 and 1; no difference)</p>
  <p>The manual documents a function called 'transparency' which I tried to use with for example <code>transparency 50,a #0:10-1200</code>
  to make atoms 10-1200 50% transparent. But I just get the error: &quot;Missing or invalid &quot;percent&quot; argument: Expected a number&quot;. If I only type <code>transparency 50</code> everything does turn transparent, however, I wouldn't really call it transparent since I cannot really see through them to see the other molecules on the other side, they just turn bleak.</p>
  <p>Questions:</p>
  <ol>
  <li><em>(Would someone explain how I could simply change the actual transparency of a large set of markers and links)</em> (preferably by loading some file with specified marker id:s)? Also, is it possible to assign this directly in the cmm files, and if so, how?</li>
  </ol>
  <p>UPDATE: The command <code>transparency #1:2492-end 90 'All'</code> worked to set the transparency of markers e.g. 2492-end. What I would still like to know is if it is possible to set this directly in the cmm-files.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-09-20T13:04:00.503Z
Comments.Text: RGBA color values are an extension of RGB color values with an alpha channel - which specifies the opacity for a color. An RGBA color value is specified with: rgba(red, green, blue, alpha). The alpha parameter is a number between 0.0 (fully transparent) and 1.0 (fully opaque). , what does the  a="0"  do in your xml formatted markers and links ?
Comments.UserDisplayName: pippo1980
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-09-20T15:59:59.090Z
Comments.Text: So, the 'a="0"' was a naive attempt by me to set the alpha-level directly in the xml file, which as I noted above did not work. I have since figured out how to set the transparency and will update my question.
Comments.UserDisplayName: ciru_4011
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-09-20T16:47:34.770Z
Comments.Text: you should try to report the bug a = 0 not working to chimerax developers. To report a problem with ChimeraX:
  
      If possible, please use Help... Report a Bug in the ChimeraX menu. Otherwise (for example, if ChimeraX will not start), send e-mail to chimerax-bugs@cgl.ucsf.edu, making sure to include any information needed to reproduce the problem: program version, specific data, actions/steps taken, etc. The information will be publicly accessible, so do not include data or descriptions that you wish to remain private.
  from https://www.cgl.ucsf.edu/chimerax/docs/contact.html
Comments.UserDisplayName: pippo1980
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-09-21T07:18:54.943Z
Comments.Text: I will look in to that, however I am not certain it is a bug: Even though it seems very reasonable to be able to set it that way, that was a guess on my part. The general support of rgba colors is however otherwise documented in the manual. Regarding your suggested edit: The markers are literally referred to as 'atoms' in Chimera, and it is those which I wish to make transparent. (I am however changing it to 'marker' as a compromise =).)
Comments.UserDisplayName: ciru_4011
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-09-21T07:26:00.887Z
Comments.Text: A marker is a pseudoatom, typically used to mark the position of some feature within volume data; markers are implemented as atoms, so actions that apply to atoms in ChimeraX also apply to markers: they can be specified in commands, selected, etc. https://www.cgl.ucsf.edu/chimerax/docs/user/markers.html
Comments.UserDisplayName: pippo1980
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-09-21T07:47:50.230Z
Comments.Text: dont know why I didnt like ChimeraX at the time , ages ago,  but haved worked only with just plain Chimera, had to dig an old VMwareVM to take these few pics
Comments.UserDisplayName: pippo1980
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-09-21T08:16:33.160Z
Comments.Text: users mailing list is https://mail.cgl.ucsf.edu/mailman/mailman3/lists/chimera-users.cgl.ucsf.edu/ .. dont get why  a='50' or a='0.5' dont work with chimera too
Comments.UserDisplayName: pippo1980
Tags: <visualization><3d-structure><software-usage>
Title: Changing transparency of markers in Chimera X
ThreadText: # Changing transparency of markers in Chimera X
  
  (Asked by: username_0 on 2023-09-19)
  
  I am using the software [Chimera X](https://www.rbvi.ucsf.edu/chimerax/) to visualize the 3d composition of molecules. I am very new to Chimera and only use it for visualization. The files I'm using are cmm files (xml-formatted) basically looking like below:
  
  ```xml
  ...
  <marker id="14" x="0.018" y="-0.180" z="0.215" r="1.000000" g="0.254900" b="0.050980" a="0" radius="0.018754" />
  <marker id="15" x="-0.032" y="-0.191" z="0.241" r="1.000000" g="0.254900" b="0.050980" a="0" radius="0.018754" />
  <marker id="16" x="-0.033" y="-0.117" z="0.246" r="1.000000" g="0.254900" b="0.050980" a="0" radius="0.018754" />
  <marker id="17" x="0.020" y="-0.138" z="0.244" r="1.000000" g="0.254900" b="0.050980" a="0" radius="0.018754" />
  <marker id="18" x="0.047" y="-0.083" z="0.280" r="1.000000" g="0.254900" b="0.050980" a="0" radius="0.018754" />
  <marker id="19" x="0.073" y="-0.061" z="0.240" r="1.000000" g="0.254900" b="0.050980" a="0" radius="0.018754" />
  <marker id="20" x="0.010" y="-0.068" z="0.271" r="1.000000" g="0.254900" b="0.050980" a="0" radius="0.018754" />
  ...
  <link id1="0" id2="1" r="0.800000" g="0.800000" b="0.000000" a="0" radius="0.006251"/>
  <link id1="1" id2="2" r="0.800000" g="0.800000" b="0.000000" a="0" radius="0.006251"/>
  <link id1="2" id2="3" r="0.800000" g="0.800000" b="0.000000" a="0" radius="0.006251"/>
  <link id1="3" id2="4" r="0.800000" g="0.800000" b="0.000000" a="0" radius="0.006251"/>
  <link id1="4" id2="5" r="0.800000" g="0.800000" b="0.000000" a="0" radius="0.006251"/>
  ...
  
  ```
  
  i.e. just a simple polymer consisting of alot of markers (spheres) and links between them (cylinders), and with colors for each one specified in rgb (see [here](https://www.cgl.ucsf.edu/chimerax/docs/user/markers.html)). This is all well and good, but now I would like to set transparency for a subset of the markers and associated links. Preferably I would set this directly in the attributes in the cmm files, but I cannot find how to do this. The manual does mention that colours in general can be set with rgba where a means alpha level, but when trying to set a like seen in the xml block above, nothing happens (I tried values close to both 0 and 1; no difference)
  
  The manual documents a function called 'transparency' which I tried to use with for example `transparency 50,a #0:10-1200`
  to make atoms 10-1200 50% transparent. But I just get the error: "Missing or invalid "percent" argument: Expected a number". If I only type `transparency 50` everything does turn transparent, however, I wouldn't really call it transparent since I cannot really see through them to see the other molecules on the other side, they just turn bleak.
  
  Questions:
  
  1. *(Would someone explain how I could simply change the actual transparency of a large set of markers and links)* (preferably by loading some file with specified marker id:s)? Also, is it possible to assign this directly in the cmm files, and if so, how?
  
  UPDATE: The command `transparency #1:2492-end 90 'All'` worked to set the transparency of markers e.g. 2492-end. What I would still like to know is if it is possible to set this directly in the cmm-files.
  
  **Tags:** visualization, 3d-structure, software-usage
  
  > **Comments:**
  > **username_1**: RGBA color values are an extension of RGB color values with an alpha channel - which specifies the opacity for a color. An RGBA color value is specified with: rgba(red, green, blue, alpha). The alpha parameter is a number between 0.0 (fully transparent) and 1.0 (fully opaque). , what does the  a="0"  do in your xml formatted markers and links ?  
  > **username_0**: So, the 'a="0"' was a naive attempt by me to set the alpha-level directly in the xml file, which as I noted above did not work. I have since figured out how to set the transparency and will update my question.  
  > **username_1**: you should try to report the bug a = 0 not working to chimerax developers. To report a problem with ChimeraX:      If possible, please use Help... Report a Bug in the ChimeraX menu. Otherwise (for example, if ChimeraX will not start), send e-mail to chimerax-bugs@cgl.ucsf.edu, making sure to include any information needed to reproduce the problem: program version, specific data, actions/steps taken, etc. The information will be publicly accessible, so do not include data or descriptions that you wish to remain private. from https://www.cgl.ucsf.edu/chimerax/docs/contact.html  
  > **username_0**: I will look in to that, however I am not certain it is a bug: Even though it seems very reasonable to be able to set it that way, that was a guess on my part. The general support of rgba colors is however otherwise documented in the manual. Regarding your suggested edit: The markers are literally referred to as 'atoms' in Chimera, and it is those which I wish to make transparent. (I am however changing it to 'marker' as a compromise =).)  
  > **username_1**: A marker is a pseudoatom, typically used to mark the position of some feature within volume data; markers are implemented as atoms, so actions that apply to atoms in ChimeraX also apply to markers: they can be specified in commands, selected, etc. https://www.cgl.ucsf.edu/chimerax/docs/user/markers.html  
  > **username_1**: dont know why I didnt like ChimeraX at the time , ages ago,  but haved worked only with just plain Chimera, had to dig an old VMwareVM to take these few pics  
  > **username_1**: users mailing list is https://mail.cgl.ucsf.edu/mailman/mailman3/lists/chimera-users.cgl.ucsf.edu/ .. dont get why  a='50' or a='0.5' dont work with chimera too  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2023-09-21. Score: 0
  
  Ok, this is not an answer, but to better visualize the problem I recreated the question/answer on `Chimera` that has a different syntax for the `transparency` command see : <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/transparency.html> and <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/transparency.html> .
  
  Input file is `marker.cmm` , to be opened in `FILE MENU` of `VOLUME TRACER` from `VOLUME MENU` :
  
  ```
  <marker_set name="marker set 1">
  <marker id="14" x="0.018" y="-0.180" z="0.215" r="1.000000" g="0.254900" b="0.050980" a="0" radius="0.018754" />
  <marker id="15" x="-0.032" y="-0.191" z="0.241" r="1.000000" g="0.254900" b="0.050980" a="0" radius="0.018754" />
  <marker id="16" x="-0.033" y="-0.117" z="0.246" r="1.000000" g="0.254900" b="0.050980" a="0" radius="0.018754" />
  <marker id="17" x="0.020" y="-0.138" z="0.244" r="1.000000" g="0.254900" b="0.050980" a="0" radius="0.018754" />
  <marker id="18" x="0.047" y="-0.083" z="0.280" r="1.000000" g="0.254900" b="0.050980" a="0" radius="0.018754" />
  <marker id="19" x="0.073" y="-0.061" z="0.240" r="1.000000" g="0.254900" b="0.050980" a="0" radius="0.018754" />
  <marker id="20" x="0.010" y="-0.068" z="0.271" r="1.000000" g="0.254900" b="0.050980" a="0" radius="0.018754" />
  <link id1="14" id2="15" r="0.800000" g="0.800000" b="0.000000" a="0" radius="0.006251"/>
  <link id1="15" id2="16" r="0.800000" g="0.800000" b="0.000000" a="0" radius="0.006251"/>
  <link id1="17" id2="18" r="0.800000" g="0.800000" b="0.000000" a="0" radius="0.006251"/>
  <link id1="18" id2="19" r="0.800000" g="0.800000" b="0.000000" a="0" radius="0.006251"/>
  <link id1="19" id2="20" r="0.800000" g="0.800000" b="0.000000" a="0" radius="0.006251"/>
  </marker_set>
  
  ```
  
  Image before command :
  
  [![enter image description here](https://i.sstatic.net/Kb0kq.png)](https://i.sstatic.net/Kb0kq.png)
  
  Image after `transparency 50,a,b #0:16-end`
  
  (#0 being 0 model as the only loaded model on my `Chimera` instance) :
  
  [![enter image description here](https://i.sstatic.net/v3Ny2.png)](https://i.sstatic.net/v3Ny2.png)
  
  Better transparency visualizations :
  
  [![enter image description here](https://i.sstatic.net/yaYRC.png)](https://i.sstatic.net/yaYRC.png)
  
  [![enter image description here](https://i.sstatic.net/V7AXk.png)](https://i.sstatic.net/V7AXk.png)
  
  Dont get why a='50' or a='0.5' in `marker`,`link` definition dont work with `chimera` too
  
  > **Comments:**
  > **username_0**: Together with my edited question I think this all suffice as "good enough" for now at least. I am satisfied for the moment just using something like `transparency #1:2492-end 90 'All'`, but I guess when I get more complicated regions it would be good to be able to load the marker spec, i.e. e.g. #1:2492-2500, 3000-3500, ... from a file if that is possible. But I guess one can run command-files right? and I suppose there's no limit on the length on the spec, so perhaps I could just create one very long command in a file. (Many thanks for your efforts!!! unfortunately I need more rep to upvote)  
  
  ---
  
  