<div dir="ltr"><div><div><div>Dear chimera users,<br></div>I am running into troubles displaying a map of a 650x650x650 volume and I was wondering if there is a box size limit to chimera or what else could be the problem. The way it displays the 3D .mrc file is as a single slice rather than a volume. It will also go straight to solid display rather than surface, did anyone encounter such a problem before? I can open the map in coot and relion (slices), so I do not think that the map is corrupt. Thank you for your time.<br><br></div>Best wishes,<br></div>Linda<br><div><div><div><div><div><div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Jun 6, 2016 at 11:14 PM, <span dir="ltr"><<a href="mailto:chimera-users-request@cgl.ucsf.edu" target="_blank">chimera-users-request@cgl.ucsf.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Send Chimera-users mailing list submissions to<br>
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Today's Topics:<br>
<br>
1. Re: coloring by RMSD (conformational variability) (Elaine Meng)<br>
2. Re: Chimera-win10-install (Greg Couch)<br>
3. Re: coloring by RMSD (conformational variability) (George Tzotzos)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Mon, 6 Jun 2016 12:55:52 -0700<br>
From: Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>><br>
To: George Tzotzos <<a href="mailto:gtzotzos@me.com">gtzotzos@me.com</a>><br>
Cc: "<a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a> BB" <<a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a>><br>
Subject: Re: [Chimera-users] coloring by RMSD (conformational<br>
variability)<br>
Message-ID: <<a href="mailto:5242FA3C-E185-453E-93DD-BEF75F495BBC@cgl.ucsf.edu">5242FA3C-E185-453E-93DD-BEF75F495BBC@cgl.ucsf.edu</a>><br>
Content-Type: text/plain; charset=utf-8<br>
<br>
Hi George,<br>
I?m not really sure how you got those flat ribbons, but I think you can just use the transparency command. It takes a percentage transparency, so for 75% transparent, a command something like:<br>
<br>
transp 75,r :1-10,124-125<br>
<br>
? where the ?,r? part does NOT have any space before it, and ?r? stands for ribbons.<br>
<br>
I hope this helps,<br>
Elaine<br>
----------<br>
Elaine C. Meng, Ph.D.<br>
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
<br>
> On Jun 6, 2016, at 11:36 AM, George Tzotzos <<a href="mailto:gtzotzos@me.com">gtzotzos@me.com</a>> wrote:<br>
><br>
> Following PC analysis, I have obtained pseudo trajectories for each of the first 3 principal components. I used Chimera to colour the regions exhibiting the largest structural variations as per instructions of Elain Meng, which I attach for easy reference.<br>
><br>
> I have placed side by side, say the 1st PC, of two independent pseudo trajectories (see attached image). As the structure is disordered between residues 1-10 and 124-125, I?d like to render these ranges of residues semitransparent. I?ve tried to do this with the transparency command but this applies to ribbons only (I think).<br>
><br>
> I?d appreciate any suggestions as to how this can be done.<br>
><br>
> Thank you in advance<br>
><br>
> George<br>
><br>
> <dimer_deet2015_6MH2016.tif><br>
> From: Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>><br>
> Subject: coloring by RMSD (conformational variability)<br>
> Date: 25 March 2014 at 19:32:47 GMT+1<br>
> To: George Tzotzos <<a href="mailto:gtzotzos@me.com">gtzotzos@me.com</a>><br>
> Cc: chimera List <<a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a>><br>
> Reply-To: "<a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a> BB" <<a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a>><br>
><br>
> Hi George,<br>
> Sure, you can do it by having Chimera calculate the CA-RMSD at each position and then mapping that value to color. The file is a little strange in that it has only CA atoms and all the residues are ALA, but it will still work:<br>
><br>
> (1) show the sequence (menu: Favorites? Sequence). Just choose any one of the 34 -- it doesn't matter which one, since they all have the same sequence.<br>
><br>
> (2) associate all 34 copies of the structure with the one sequence: in the sequence window menu, choose Structure? Associations. In that dialog, change all the "none" to the same sequence, then click OK. This is somewhat tedious, but I just did it, so you can too! Now, all of the structures will be connected to that one sequence.<br>
><br>
> (3) tell Chimera to calculate the RMSD at each position: in the sequence window menu, choose Headers? RMSD. Now the sequence window will have an RMSD histogram above the sequence. It may almost look like a line because most of the bars in the histogram (the RMSD values) are very low.<br>
><br>
> (4) color the structures by the RMSD values with Render by Attribute (in main Chimera menu under Tools? Depiction). In that tool, choose attributes of "residues" and attribute name "mavRMSD" (the "mav" part stands for Multalign Viewer, which is showing the sequence). It will show a histogram of the values with some vertical colored bars. You use those bars to define how the values are mapped to color. The bars can be dragged left and right, and you can delete bars or add more bars with Ctrl-click. You can change the color of each bar by clicking it and then clicking the "Color" square below the histogram and using the Color Editor, or you can just use one of the Palette options below that. You can keep clicking Apply and then adjusting the coloring until it is how you like it. For example, I show coloring by RMSD from blue->red->yellow (and then menu: Presets? Publication 1) in the attached image.<br>
><br>
> I hope this helps,<br>
> Elaine<br>
> _______________________________________________<br>
> Chimera-users mailing list: <a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br>
> Manage subscription: <a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" rel="noreferrer" target="_blank">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br>
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<br>
<br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Mon, 6 Jun 2016 14:01:18 -0700<br>
From: Greg Couch <<a href="mailto:gregc@cgl.ucsf.edu">gregc@cgl.ucsf.edu</a>><br>
To: Mitja Ogrizek <<a href="mailto:ogrizek.mitja@gmail.com">ogrizek.mitja@gmail.com</a>>,<br>
<a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a><br>
Subject: Re: [Chimera-users] Chimera-win10-install<br>
Message-ID: <<a href="mailto:5755E49E.7070006@cgl.ucsf.edu">5755E49E.7070006@cgl.ucsf.edu</a>><br>
Content-Type: text/plain; charset="windows-1252"; Format="flowed"<br>
<br>
Hello Mitja,<br>
<br>
I was able to get the Windows installer to fail in one situation -- I<br>
hope this is the same problem you're having.<br>
<br>
If you download the installer as a non-administrative user and then try<br>
to run it, it fails because it can't install Chimera in the default<br>
location even though you've typed in an administrative password. My<br>
workaround was to use the file browser to locate the installer on the<br>
disk, do a right-mouse click on the installer, and then "Run as<br>
Administrator". I expect that it would also work if you installed<br>
Chimera to a non-system directory.<br>
<br>
HTH,<br>
<br>
Greg<br>
<br>
On 06/04/2016 05:46 AM, Mitja Ogrizek wrote:<br>
> Dear all,<br>
><br>
> I tried to install a new version of chimera on my laptop with win10,<br>
> but it doesn't want to load and start the setup.<br>
> Has anybody else reported or had the same troubles?<br>
><br>
> Kind regards,<br>
> Mitja Ogrizek<br>
><br>
><br>
> _______________________________________________<br>
> Chimera-users mailing list: <a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br>
> Manage subscription: <a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" rel="noreferrer" target="_blank">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br>
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Message: 3<br>
Date: Mon, 06 Jun 2016 22:13:15 +0200<br>
From: George Tzotzos <<a href="mailto:gtzotzos@me.com">gtzotzos@me.com</a>><br>
To: "<a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a> BB" <<a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a>><br>
Subject: Re: [Chimera-users] coloring by RMSD (conformational<br>
variability)<br>
Message-ID: <<a href="mailto:E8E115FF-478E-4C4A-AD42-C1084C536E3F@me.com">E8E115FF-478E-4C4A-AD42-C1084C536E3F@me.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi Elaine,<br>
<br>
Grateful for the prompt and useful response.<br>
<br>
The flat ribbons come for a cluster of pdb files sampled from the first eigenvector of PCA. I?m attaching such a file.<br>
<br>
Once again, many thanks<br>
<br>
George<br>
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> On 6 Jun 2016, at 21:55, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>> wrote:<br>
><br>
> Hi George,<br>
> I?m not really sure how you got those flat ribbons, but I think you can just use the transparency command. It takes a percentage transparency, so for 75% transparent, a command something like:<br>
><br>
> transp 75,r :1-10,124-125<br>
><br>
> ? where the ?,r? part does NOT have any space before it, and ?r? stands for ribbons.<br>
><br>
> I hope this helps,<br>
> Elaine<br>
> ----------<br>
> Elaine C. Meng, Ph.D.<br>
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br>
> Department of Pharmaceutical Chemistry<br>
> University of California, San Francisco<br>
><br>
><br>
>> On Jun 6, 2016, at 11:36 AM, George Tzotzos <<a href="mailto:gtzotzos@me.com">gtzotzos@me.com</a>> wrote:<br>
>><br>
>> Following PC analysis, I have obtained pseudo trajectories for each of the first 3 principal components. I used Chimera to colour the regions exhibiting the largest structural variations as per instructions of Elain Meng, which I attach for easy reference.<br>
>><br>
>> I have placed side by side, say the 1st PC, of two independent pseudo trajectories (see attached image). As the structure is disordered between residues 1-10 and 124-125, I?d like to render these ranges of residues semitransparent. I?ve tried to do this with the transparency command but this applies to ribbons only (I think).<br>
>><br>
>> I?d appreciate any suggestions as to how this can be done.<br>
>><br>
>> Thank you in advance<br>
>><br>
>> George<br>
>><br>
>> <dimer_deet2015_6MH2016.tif><br>
>> From: Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>><br>
>> Subject: coloring by RMSD (conformational variability)<br>
>> Date: 25 March 2014 at 19:32:47 GMT+1<br>
>> To: George Tzotzos <<a href="mailto:gtzotzos@me.com">gtzotzos@me.com</a>><br>
>> Cc: chimera List <<a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a>><br>
>> Reply-To: "<a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a> BB" <<a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a>><br>
>><br>
>> Hi George,<br>
>> Sure, you can do it by having Chimera calculate the CA-RMSD at each position and then mapping that value to color. The file is a little strange in that it has only CA atoms and all the residues are ALA, but it will still work:<br>
>><br>
>> (1) show the sequence (menu: Favorites? Sequence). Just choose any one of the 34 -- it doesn't matter which one, since they all have the same sequence.<br>
>><br>
>> (2) associate all 34 copies of the structure with the one sequence: in the sequence window menu, choose Structure? Associations. In that dialog, change all the "none" to the same sequence, then click OK. This is somewhat tedious, but I just did it, so you can too! Now, all of the structures will be connected to that one sequence.<br>
>><br>
>> (3) tell Chimera to calculate the RMSD at each position: in the sequence window menu, choose Headers? RMSD. Now the sequence window will have an RMSD histogram above the sequence. It may almost look like a line because most of the bars in the histogram (the RMSD values) are very low.<br>
>><br>
>> (4) color the structures by the RMSD values with Render by Attribute (in main Chimera menu under Tools? Depiction). In that tool, choose attributes of "residues" and attribute name "mavRMSD" (the "mav" part stands for Multalign Viewer, which is showing the sequence). It will show a histogram of the values with some vertical colored bars. You use those bars to define how the values are mapped to color. The bars can be dragged left and right, and you can delete bars or add more bars with Ctrl-click. You can change the color of each bar by clicking it and then clicking the "Color" square below the histogram and using the Color Editor, or you can just use one of the Palette options below that. You can keep clicking Apply and then adjusting the coloring until it is how you like it. For example, I show coloring by RMSD from blue->red->yellow (and then menu: Presets? Publication 1) in the attached image.<br>
>><br>
>> I hope this helps,<br>
>> Elaine<br>
>> _______________________________________________<br>
>> Chimera-users mailing list: <a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br>
>> Manage subscription: <a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" rel="noreferrer" target="_blank">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br>
><br>
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</blockquote></div><br></div></div></div></div></div></div></div></div>