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<div class="elementToProof"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">Hi Elaine,</span></div>
<div class="elementToProof"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);"><br>
</span></div>
<div class="elementToProof"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">Thanks so much for your help, I actually figured out I needed coordset about 2 minutes
before you sent your email!</span></div>
<div class="elementToProof"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);"><br>
</span></div>
<div class="elementToProof"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">And thank you for the other suggestions as well.</span></div>
<div class="elementToProof"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);"><br>
</span></div>
<div class="elementToProof"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">Best,</span></div>
<div class="elementToProof"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">Ben</span></div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Elaine Meng <meng@cgl.ucsf.edu><br>
<b>Sent:</b> Friday, December 9, 2022 2:43 PM<br>
<b>To:</b> Simonson, Benjamin Thomas <bts5242@psu.edu><br>
<b>Cc:</b> chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [chimerax-users] Perframe and distance</font>
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Hi Ben,<br>
You also need a "coordset" command to actually play the trajectory. The perframe frames are graphics frames, not trajectory frames:<br>
<<a href="https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fperframe.html&data=05%7C01%7Cbts5242%40psu.edu%7C0279a5cc1513488de84508dada1daebf%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C638062118279090465%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=iLEFLB2tf79o6ZgR9ZGgHRrXDRXkiBXTAiA00xAF%2B68%3D&reserved=0">https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fperframe.html&data=05%7C01%7Cbts5242%40psu.edu%7C0279a5cc1513488de84508dada1daebf%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C638062118279090465%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=iLEFLB2tf79o6ZgR9ZGgHRrXDRXkiBXTAiA00xAF%2B68%3D&reserved=0</a>><br>
<br>
Here is an example using an NMR structure opened as a trajectory:<br>
<br>
open 1plx coord true<br>
perframe "distance /A:1@N:4@CG; distance save dist$1.txt; ~distance" range 10,80,10; coordset #1; wait 80; ~perframe<br>
<br>
Note that it isn't necessary to name the atoms in the ~distance command. Simply giving ~distance will remove all current distance monitors. The example above will give files dist10.txt, dist20.txt ... dist 80.txt. Or alternatively, to name files dist1.txt,
dist2.txt ... dist8.txt:<br>
<br>
perframe "distance /A:1@N:4@CG; distance save dist$1.txt; ~distance" ; coordset #1 10,80,10; wait 8; ~perframe<br>
<br>
In that second example, one tricky thing is that you need a space between the end quote and the semicolon that follows it.<br>
I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D.<br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
> On Dec 9, 2022, at 8:18 AM, Simonson, Benjamin Thomas via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:<br>
><br>
> Hello! I am trying to measure the distance between two atoms in my trajectory in every 10th frame. My approach was to use the perframe command paired with the distance command. Below was my attempt:<br>
><br>
> perframe "distance /D:15@NH1 /B:42@OD1;distance save dist$1.txt;~distance /D:15@NH1 /B:42@OD1" interval 10<br>
><br>
> However, it instead simply outputs the distance of the currently displayed frame over and over again. Any help would be appreciated!<br>
><br>
> Ben<br>
<br>
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