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<p>Hello Conrad,</p>
<p>thank you for your reply. Attached is a test file that is causing
problems in ChimeraX (see below for the log). This testfile is a
cut-down version of the original file (containing informations on
docking scores from GOLD suite) that was created in Chimera by
saving it as mol2 file <i>and manually removing the zeros in line
8</i>, as Chimera was sanitizing this line upon saving. If I add
the two zeros in the original file, ChimeraX was loading the
structures successfully, still complaining about the
metainformations though.<br>
</p>
<p>I'm using <span style="color: rgb(0, 0, 0); font-size: medium;
font-style: normal; font-variant-ligatures: normal;
font-variant-caps: normal; font-weight: normal; letter-spacing:
normal; text-align: start; text-indent: 0px; text-transform:
none; white-space: normal; word-spacing: 0px;
-webkit-text-stroke-width: 0px; display: inline !important;
float: none;">version 0.9 (2019-03-12) of Chimera X on Win10
(1809) and was using Chimera 1.13.1 to generate the testfile.<br>
</span></p>
<p><span style="color: rgb(0, 0, 0); font-size: medium; font-style:
normal; font-variant-ligatures: normal; font-variant-caps:
normal; font-weight: normal; letter-spacing: normal; text-align:
start; text-indent: 0px; text-transform: none; white-space:
normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;
display: inline !important; float: none;">Thank you and best
regards,</span></p>
<p><span style="color: rgb(0, 0, 0); font-size: medium; font-style:
normal; font-variant-ligatures: normal; font-variant-caps:
normal; font-weight: normal; letter-spacing: normal; text-align:
start; text-indent: 0px; text-transform: none; white-space:
normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;
display: inline !important; float: none;">Marco</span></p>
<p><span style="color: rgb(0, 0, 0); font-family: "Times New
Roman"; font-size: medium; font-style: normal;
font-variant-ligatures: normal; font-variant-caps: normal;
font-weight: normal; letter-spacing: normal; orphans: 2;
text-align: start; text-indent: 0px; text-transform: none;
white-space: normal; widows: 2; word-spacing: 0px;
-webkit-text-stroke-width: 0px; display: inline !important;
float: none;"><br>
</span></p>
<div class="cxcmd" style="display: block; font-weight: bold;
margin-top: 0.5em; background-color: rgb(221, 221, 221); color:
rgb(0, 0, 0); font-family: "Times New Roman"; font-size:
medium; font-style: normal; font-variant-ligatures: normal;
font-variant-caps: normal; letter-spacing: normal; orphans: 2;
text-align: start; text-indent: 0px; text-transform: none;
white-space: normal; widows: 2; word-spacing: 0px;
-webkit-text-stroke-width: 0px;">
<div class="cxcmd_as_doc" style="display: inline;"><a
href="help:user/commands/open.html">open</a><span
class="Apple-converted-space"> </span>"C:\\Users\\Marco\\Desktop\\benzotriazol\\chimeratest.mol2"</div>
</div>
<table style="font-family: "Times New Roman";
letter-spacing: normal; orphans: 2; text-indent: 0px;
text-transform: none; widows: 2; word-spacing: 0px;
-webkit-text-stroke-width: 0px;" cellspacing="0" cellpadding="4"
border="1">
<thead><tr>
<th colspan="2">Summary of feedback from opening
C:\Users\Marco\Desktop\benzotriazol\chimeratest.mol2</th>
</tr>
</thead><tbody>
<tr>
<td><i>warnings</i></td>
<td style="background-color: rgb(255, 185, 97);">line 8: bad
molecule data<br>
line 8: ignore unexpected line '57 62 1'<br>
line 9: ignore unexpected line 'SMALL'<br>
line 10: ignore unexpected line 'USER_CHARGES'</td>
</tr>
</tbody>
</table>
<br style="color: rgb(0, 0, 0); font-family: "Times New
Roman"; font-size: medium; font-style: normal;
font-variant-ligatures: normal; font-variant-caps: normal;
font-weight: normal; letter-spacing: normal; orphans: 2;
text-align: start; text-indent: 0px; text-transform: none;
white-space: normal; widows: 2; word-spacing: 0px;
-webkit-text-stroke-width: 0px;">
<p><span style="color: rgb(0, 0, 0); font-family: "Times New
Roman"; font-size: medium; font-style: normal;
font-variant-ligatures: normal; font-variant-caps: normal;
font-weight: normal; letter-spacing: normal; orphans: 2;
text-align: start; text-indent: 0px; text-transform: none;
white-space: normal; widows: 2; word-spacing: 0px;
-webkit-text-stroke-width: 0px; display: inline !important;
float: none;">Opened chimeratest.mol2 containing 0 structures (0
atoms, 0 bonds)</span></p>
<br>
<div class="moz-cite-prefix">Am 14.03.2019 um 00:18 schrieb Conrad
Huang:<br>
</div>
<blockquote type="cite"
cite="mid:03767379-1fc3-6200-c014-8343d96ec294@cgl.ucsf.edu">Hi,
Marco.
<br>
<br>
Can you send me the file that is causing the problem? When I
change a working Mol2 file to remove those two fields, I get a few
error messages but the molecules are opened. I'm concerned that
some other error is preventing import of your file.
<br>
<br>
Conrad
<br>
<br>
On 3/13/2019 2:23 AM, Marco J. Müller wrote:
<br>
<blockquote type="cite">Dear ChimeraX Team,
<br>
<br>
when I try to load structure outputs of docking runs in .mol2
format into ChimeraX, it fails to load them, while the same can
be imported by Chimera successfully. After a bit of playing
around I found that the following section is relevant and fails
in this format:
<br>
<br>
@<TRIPOS>MOLECULE
<br>
MYCOOLMOLECULE
<br>
57 62 1
<br>
SMALL
<br>
USER_CHARGES
<br>
<br>
The problem seems to be that ChimeraX requires explicit
definitions of /#features/ and/#sets/ in the third line (apart
from /#atoms #bonds #substructures/), while they are typically
omitted in most programs. So the following lines could be
imported:
<br>
<br>
@<TRIPOS>MOLECULE
<br>
MYCOOLMOLECULE
<br>
57 62 1 0 0
<br>
SMALL
<br>
USER_CHARGES
<br>
<br>
Can this case be addressed in a future version of ChimeraX?
<br>
<br>
Thank you in advance,
<br>
<br>
Marco
<br>
<br>
-- <br>
Marco J. Müller
<br>
PhD student
<br>
<br>
Technische Universität Braunschweig
<br>
Institute of Medicinal and Pharmaceutical Chemistry
<br>
<a class="moz-txt-link-freetext" href="https://www.tu-bs.de/pharmchem">https://www.tu-bs.de/pharmchem</a>
<br>
Beethovenstr. 55 | 38106 Braunschweig | Germany
<br>
<br>
<br>
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<br>
<br>
</blockquote>
</blockquote>
<pre class="moz-signature" cols="72">--
Marco J. Müller
Technische Universität Braunschweig
Institut für Medizinische und Pharmazeutische Chemie
<a class="moz-txt-link-freetext" href="https://www.tu-bs.de/pharmchem">https://www.tu-bs.de/pharmchem</a>
Beethovenstr. 55 | 38106 Braunschweig | Germany
Tel.: +49 531 391 2768 | <a class="moz-txt-link-abbreviated" href="mailto:marco.mueller@tu-bs.de">marco.mueller@tu-bs.de</a></pre>
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