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As I told to Elaine, <br>
i know the problem about pdb file, for me is not a problem
reordering it. Nevertheless, the problem remains: using amber
topology I don't see a continue ribbon.<br>
I'll wait for the fixing of this bug.<br>
<br>
Thanks for your help<br>
<br>
<br>
Il 23/09/2010 21:47, Eric Pettersen ha scritto:
<blockquote
cite="mid:FE5827F7-62A7-4C93-894D-725BBF3A642F@cgl.ucsf.edu"
type="cite">
<div>
<div>Hi Francesco,</div>
<div><span class="Apple-tab-span" style="white-space: pre;"> </span>As
Elaine mentions, as per the PDB standard the chain
connectivity of standard residues (i.e. residues in ATOM
records) is implied by their order in the file, barring TER
records between the residues. This is why Chimera is
producing those longs bonds. For example, your file has
residues 300 and 301 one after the other in the PDB file
without a TER card, so Chimera connects them despite them
being >50A apart. What you really need to do is reorder
the file so that it is in connectivity order.</div>
<div><span class="Apple-tab-span" style="white-space: pre;"> </span>Also,
the file was seemingly made by trjconv, which AFAIK is a
program for converting Gromacs trajectories to PDB format. I
thought you were using an Amber trajectory. Why aren't you
using ambpdb, which directly converts Amber trajectories to
PDB files?</div>
<div><span class="Apple-tab-span" style="white-space: pre;"> </span>Lastly,
trjconv is doing a bad job with justification of hydrogen
names in the 4 columns alloted to the atom name. It does well
with some names, like "1H2*" and " H3*" (so Chimera can deduce
the element type from the first two columns) but then outputs
some stinkers like " 1H7" and " 2H7". Sigh.</div>
<div><br>
</div>
<div>--Eric</div>
<div><br>
</div>
<div>
<div style="margin: 0px; font-size: 16px;"><font style="font:
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Eric Pettersen</font></div>
<div style="margin: 0px; font-size: 16px;"><font style="font:
16px Helvetica;" size="5" face="Helvetica">
UCSF Computer Graphics Lab</font></div>
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<a moz-do-not-send="true"
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<div>On Sep 23, 2010, at 11:31 AM, Elaine Meng wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div>Hi Francesco,<br>
Wow, this is a very pretty structure! However, the PDB
looks somewhat messed up. Perhaps using the AMBER files
solves most of these problems.<br>
<br>
In PDB format, I believe the biopolymer (nucleic acid or
protein) residues are connected by their order in the file,
unless a break is enforced with TER. However, the order in
this PDB file seems to be quite different than what it
should be, for the correct connectivity. Residue 75 is very
far from 76, 150 is very far from 151, etc. every 75
positions. I tried just putting TER after every 75
residues, which does eliminate the very long bonds.
However, it seems like there may be other bonds that are
supposed to be there that are not, and it would be necessary
to do a lot of reorganization and renumbering of residues in
this file to get the correct connectivity. For example, it
looks like maybe 76 is really supposed to be connected to
150, 75 is really supposed to be connected to 1, etc.<br>
<br>
If there were correct ordering in the PDB file (and maybe
this is already true for when you use the AMBER files as
input), the Chimera limitation would give you just one break
in each circular strand. If this DNA is all one big
circular strand, there should be only one break in the
ribbon. <br>
Best,<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>
<br>
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