Error when displaying structure

Hi,

I have a spcific structure that reports an error when I am trying to display it using the marvin applet.

I am not sure how to figure out what the problem is, and hope for assistance.

The error message is:

What data will be needed to investigate this..?

The application is running on Marvin Applet: 5.4.0.1 and JChem version is: 5.4.0.1015.

Application is running on windows server 2008R2, MSSQL 2008R2.

Dann

Hi Dann,

I move your question to the forum of Marvin topics.

Best regards,

Krisztina

Hi Dann,

it seems the error message is missing from your post, can you re-attach it to the topic please?

Regards,
Istvan 

.. sure should be attached to this message

It seems from the message that you are trying to load a molecule in smiles format, but that #ffffffff is disturbing me at the end.

Can you please send me the code snippet where the applet is embedded, and the file you are trying to open? 

Hi István

Sorry for the late reply!

I have the data in sql database, a small insert script of the datarow:

 

SET IDENTITY_INSERT [dbo].[ci_structures] ON

INSERT [dbo].[ci_structures] ([cd_id], [cd_structure], [cd_smiles], [cd_formula], [cd_sortable_formula], [cd_molweight], [cd_hash], [cd_flags], [cd_timestamp], [cd_fp1], [cd_fp2], [cd_fp3], [cd_fp4], [cd_fp5], [cd_fp6], [cd_fp7], [cd_fp8], [cd_fp9], [cd_fp10], [cd_fp11], [cd_fp12], [cd_fp13], [cd_fp14], [cd_fp15], [cd_fp16], [cd_pre_calculated]) VALUES (354, 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x0000A17B014DD188 AS DateTime), 151061056, 543166465, 806650114, 805307937, 143654913, 1073745056, 847249536, -1609841664, 5898240, -2139094976, 369164297, 69206080, 16779522, 134234129, 3489936, 268436616, 0)

SET IDENTITY_INSERT [dbo].[ci_structures] OFF

Will you be able to work with this..?

Hi Dann,

sorry for the late reaction, I have missed your answer and just got notified on it.

From the SQL as I see the cd_smiles field content is: "N'[K+].CC(C)(C)OC(=O)N1CCN(C(F)(F)F)CC1" and this is invalid because of the apostrophe character after the starting N. Or the starting N' is being cropped before it is given to the applet where the error occurs?

Regards,
Istvan 

Hi, Thanks for this, I will try to investigate..

 

Dann

Hi

The actual content of the cd_smiles is not N'[K+].CC(C)(C)OC(=O)N1CCN(C(F)(F)F)CC1'

the sql server puts N'' around the string, which makes the correct content of the col:

[K+].CC(C)(C)OC(=O)N1CCN(C(F)(F)F)CC1

Dann

This smiles can be imported by Marvin easily. So I assume the problem is how the structure is specified for the applet. Can you send me the html code example where you add the molecule as a parameter for the applet, that may help a bit more to find out the problem.

If you feel that code is confidential, or just do not want to paste it into a public forum, feel free to contact me in e-mail.

Thanks,
Istvan 

Hi,

This is the setup of the marvin applet:

 

<div id="AppletDiv" style="width: 380px; height: 380px; padding-top: 5px; display: block;
text-align: center">
<!-- Structure area. -->
<script language="JavaScript1.1" type="text/javascript">
mview_name = "MView";
mview_begin("../Tools/marvin", 380, 380);
mview_param("molbg", "#f9f9fb");
mview_param("mol", "[K ].CC(C)(C)OC(=O)N1CCN(C(F)(F)F)CC1");
mview_end();
</script>
</div>

.. wil this do..?

Yes it have helped.

I have copied this into a web page and tested with Marvin, it turned out, in your html code, the structure string has a space character instead of the plus sign after the K atom symbol. If this is true in your environment, and somehow the plus sign is changed to a space character, then that will be the problem since in this case the string is not a valid smiles string.

Can you please confirm this?

Hi,

 

It turned out I was url escaping the string.. I can't remember why, but this was causing the problem:

Server.UrlDecode(compound.CompoundStructure.Molfile)

removing this solved the problem.

Thanks for the help!

Hi,

I am glad to hear it. If you have any further issues, please do not hesitate to contact us.

Regards,
Istvan