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<p>Hi Ms. Meng,</p>
<p>Thank you again for the help! My research head and I had one more question, we opened the structure and visualized the sequence and we want to delete from 90-124 to match up our sequences of our protein. I attached an image of what we are trying to cut out. </p>
<p>Thank you again!</p>
<p>Rayna DeChance</p>
<p>Western New England University </p>
<p>Student </p>
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<div id="x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Elaine Meng <meng@cgl.ucsf.edu><br>
<b>Sent:</b> Friday, November 6, 2020 2:51:14 PM<br>
<b>To:</b> Rayna L. DeChance<br>
<b>Cc:</b> chimera-users@cgl.ucsf.edu<br>
<b>Subject:</b> Re: [Chimera-users] help</font>
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<div class="PlainText">The External Email below originated from outside the University. Unless you recognize the sender, do not click links, open attachments, or respond.<br>
<br>
<br>
Hi Rayna,<br>
In the Save PDB dialog (menu: File... Save PDB), there are options to "Save only displayed atoms" or "Save only selected atoms."<br>
<br>
First show all the atoms, so you can actually see what is there, e.g. menu: Presets... Interactive 1 (all atoms). Then either select the ones you want or hide the ones you don't want. Then in the Save PDB dialog turn on the appropriate option.<br>
<<a href="https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb">https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb</a>><br>
<br>
You can select with the mouse (Ctrl-click/drag) or with the "select" command. In the command you can specify model number, ranges of residue numbers, etc., for example:<br>
<br>
select #3:45-83,90-98<br>
<br>
<<a href="https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html">https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html</a>><br>
<br>
Alternatively you can just delete all the atoms you don't want before you save the file, e.g. with the "delete" command.<br>
<<a href="https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/delete.html">https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/delete.html</a>><br>
<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 Nov 6, 2020, at 11:58 AM, Rayna L. DeChance <rayna.dechance@wne.edu> wrote:<br>
><br>
> Hi,<br>
> I was wondering if you knew how to cut out (clip) a part of the protein and save the remaining part as a PDB file. I attached the file I was working with that has the two proteins that are aligned together and we want only a certain part of this alignment
to be clip.<br>
> Thank you<br>
> <session 1.py><br>
<br>
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