<br><br><div class="gmail_quote">On Mon, Mar 7, 2011 at 10:14 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div><div></div><div class="h5"><br>
<br>
ZHAO Lina wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi,<br>
<br>
after added ions, I got a solv_ions.gro.<br>
<br>
I use trjconv<br>
<br>
to produce the solv_ions.pdb<br>
<br>
when I view it in pymol.<br>
<br>
I showed sequence,<br>
it like<br>
<br>
1 2 3 4 6<br>
ODOAOEOROHODOGOOYE<br>
<br>
But the solv_ions.pdb looks pretty regular.<br>
<br>
my problem is that,<br>
<br>
how could I choose the protein parts.<br>
<br>
I tried the select protein, resi 1-48<br>
some waters are inclusive.<br>
<br>
</blockquote>
<br></div></div>
Do you have a very large system? If so, PDB format can only handle a fixed number of digits in the residue and atom numbering fields, so the numbering of your waters restarts from zero. Such is the limitation when dealing with .pdb files.<br>
</blockquote><div><br>Kind of large.<br>I was wrong before, the newly-produced solv_ions.pdb is not regular.<br>Before those chains numbered in sequence.<br>now different chains numbered from 1-48 1-48 again, former is 1-96 in .gro. <br>
<br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
If you just need to make selections in PyMOL, strip the water out of the file first.<br></blockquote><div><br>It's short, the protein part, I did it manually, but the "show cartoon" failed to show all, only show first 1-48.<br>
<br>I guess I gotta modify the .pdb a little.<br><br>Thanks for your answering.<br><br>lina <br> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
-Justin<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Thanks for any suggestion.<br>
<br>
lina<br>
<br>
</blockquote>
<br></div>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br><font color="#888888">
-- <br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</font></blockquote></div><br>