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<p>Dear Francesca,</p>
<p><br>
</p>
<p>pdb files are text files.</p>
<p>You can open it with a text editor (not word) and remove the
lines corresponding to the water molecules. Then save and open in
Chimera.</p>
<p><br>
</p>
<p>Best</p>
<p>Marco</p>
<p><br>
</p>
<div class="moz-cite-prefix">Il 10/06/2021 16:47, Francesca
Magarotto - francesca.magarotto2--- via Chimera-users ha scritto:<br>
</div>
<blockquote type="cite"
cite="mid:VI1PR0102MB32454E907F149699669E53E680359@VI1PR0102MB3245.eurprd01.prod.exchangelabs.com">
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<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
Hi,</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
I have a problem using Chimera: I need to delete specific water
molecules with a specific residue number, but this number is in
common with residues that are useful (such as ligands or
co-factors).
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
For example, I type "del :546-893" in the command line in order
to delete these water molecules, but I delete also the ligand
and FAD and I don't want to.</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
I've read the guide about atom specification, but still I don't
know how to do it.</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
Hope someone can help me,</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
thank you.</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
Francesca<br>
</div>
<br>
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</blockquote>
<pre class="moz-signature" cols="72">--
Dr.Marco Sette, Ph.D.
Department of Chemical Sciences and Technology
University of Rome, "Tor Vergata"
via della Ricerca Scientifica, 00133, Rome, Italy
e-mail: <a class="moz-txt-link-abbreviated" href="mailto:sette@uniroma2.it">sette@uniroma2.it</a>
e-mail: <a class="moz-txt-link-abbreviated" href="mailto:m77it@yahoo.it">m77it@yahoo.it</a>
Tel.: +39-0672594424
Fax: +39-0672594328
<a class="moz-txt-link-freetext" href="http://stc.uniroma2.it/?page_id=622&cn-entry-slug=marco-sette">http://stc.uniroma2.it/?page_id=622&cn-entry-slug=marco-sette</a>
Ai sensi del Regolamento (UE) 2016/679 e dei principi contenuti nelle linee guida del Garante per posta elettronica e interne (artt. 2 e 15 Cost.; Corte cost. 17 luglio 1998, n. 281 e 11 marzo 1993, n. 81; art. 49 Codice dell’amministrazione digitale) si precisa che le informazioni contenute in questo messaggio -come pure i dati esteriori delle comunicazioni e i file allegati- sono riservate e ad uso esclusivo del destinatario. Divulgazione, copia, stampa o qualunque altro uso da parte di altri non č autorizzato. Qualora il messaggio in parola Le fosse pervenuto per errore, La preghiamo di eliminarlo senza copiarlo e di non inoltrarlo a terzi, dandocene gentilmente comunicazione al seguente indirizzo e-mail <a class="moz-txt-link-abbreviated" href="mailto:privacy@uniroma2.it">privacy@uniroma2.it</a>.
On the basis of “(UE) Rules 2016/679 and the codes in general guidelines of Garante for electronic and internal mail (artt. 2 e 15 Cost.; Corte cost. 17 luglio 1998, n. 281 e 11 marzo 1993, n. 81; art. 49 Codice dell’amministrazione digitale) information here contained and any attachments is confidential and intended for the recipient(s) only. Dissemination, copying, printing or use by anybody else is unauthorized. If you are not the intended recipient, please delete this message and any attachments and advise the sender by return e-mail to <a class="moz-txt-link-abbreviated" href="mailto:privacy@uniroma2.it">privacy@uniroma2.it</a>.</pre>
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