error when displaying MDL V3000 mol file in Marvin

In some cases when we register a compound MDL is returning a V3000 version of the compound which creates an error when we try to display in an applet. Does Marvin support V3000? What version?





The V3000 format looks like:





ISISHOST06170410272D 0 0.00000 0.00000 0





0 0 0 0 0 999 V3000


M V30 BEGIN CTAB


M V30 COUNTS 32 37 0 0 1


M V30 BEGIN ATOM


M V30 1 N -2.1681 -4.6875 0 0


M V30 2 C -2.1693 -5.5148 0 0


.....


....


....


....


M V30 35 1 31 26


M V30 36 1 14 11


M V30 37 1 23 32 CFG=3


M V30 END BOND


M V30 BEGIN COLLECTION


M V30 MDLV30/STERAC1 ATOMS=(1 23)


M V30 END COLLECTION


M V30 END CTAB


M END

bvetter wrote:

In some cases when we register a compound MDL is returning a V3000 version of the compound which creates an error when we try to display in an applet. Does Marvin support V3000?

Yes, at least from version 3.3.3. Marvin calls it the MDL Extended MOLfile format. Here's cyclopentane in that format (drawn in MarvinSketch):








Marvin 06170412462D





0 0 0 0 0 999 V3000


M V30 BEGIN CTAB


M V30 COUNTS 5 5 0 0 0


M V30 BEGIN ATOM


M V30 1 C -5.95 2.885 0 0


M V30 2 C -7.1959 1.9798 0 0


M V30 3 C -6.72 0.5152 0 0


M V30 4 C -5.18 0.5152 0 0


M V30 5 C -4.7041 1.9798 0 0


M V30 END ATOM


M V30 BEGIN BOND


M V30 1 1 1 2


M V30 2 1 1 5


M V30 3 1 2 3


M V30 4 1 3 4


M V30 5 1 4 5


M V30 END BOND


M V30 END CTAB


M END





I don't know why Marvin is throwing an error. Perhaps you don't have automatic recognition of the format turned on. Or perhaps, as you allude, MDL is using a version of the format that Marvin doesn't recognize.

The error I am getting when a V3000 mol file is loading is:





Molfile cannot be loaded because an error occured:


java.io.IOException: V30 CTAB does not end with V30 END CTAB





#0





I am using 3.3.3.

We will check it out. Could you attach a whole V3000 file that doesn't work?

If you include some code like a molfile in the text please use the Code tag. Otherwise whitespaces may be lost.


Thanks,


Ferenc

I took the mol file for cyclopentane given in the post below and tried to open it in your demo web site





(http://www.chemaxon.com/demos/try_marvin.html)





and I also got an invalid format error. I need to get authorization to send the actual file.

Your right the mol file sent below is missing spaces. Ralph will continue this thread. Can you explain how to use "Code tag" in this thread?

Because it was not sent with the Code tag. (See my previous comment) Check this (empty line at the beginning is important):

Code:

Marvin  06170421312D   0  0  0     0  0            999 V3000 M  V30 BEGIN CTAB M  V30 COUNTS 5 5 0 0 0 M  V30 BEGIN ATOM M  V30 1 C -1.6917 1.6847 0 0 M  V30 2 C -3.0253 2.4547 0 0 M  V30 3 C -3.0253 3.9947 0 0 M  V30 4 C -0.358 3.9947 0 0 M  V30 5 C -0.358 2.4547 0 0 M  V30 END ATOM M  V30 BEGIN BOND M  V30 1 1 1 2 M  V30 2 1 1 5 M  V30 3 1 2 3 M  V30 4 1 3 4 M  V30 5 1 4 5 M  V30 END BOND M  V30 END CTAB M  END

I also attched it as a file.


I tested it with the link. It works.


Ferenc

bvetter wrote:

Your right the mol file sent below is missing spaces. Ralph will continue this thread. Can you explain how to use "Code tag" in this thread?

When you edit a message you see Text formatting buttons between the Subject and the Body. See http://www.chemaxon.hu/forum/faq.php?mode=bbcode for details.


Ferenc

I have attached a file that des not work on our server using 3.3.3 Marvin








CODE:








ISISHOST06210413192D 0 0.00000 0.00000 0





0 0 0 0 0 999 V3000


M V30 BEGIN CTAB


M V30 COUNTS 43 51 0 0 1


M V30 BEGIN ATOM


M V30 1 N 0.0027 0.8833 0 0


M V30 2 C 0.0016 -0.1565 0 0


M V30 3 N 0.8372 -0.686 0 0


M V30 4 C 0.8354 1.417 0 0


M V30 5 N 2.6199 -0.4828 0 0 CFG=3


M V30 6 C 1.6883 0.8995 0 0


M V30 7 C 1.6886 -0.1557 0 0


M V30 8 N 0.8374 2.4751 0 0


M V30 9 C 2.9406 -1.615 0 0 CFG=1


M V30 10 C 2.6194 1.2314 0 0


M V30 11 C 3.2064 0.3718 0 0


M V30 12 C 4.2421 0.4553 0 0


M V30 13 C 3.0621 2.1677 0 0


M V30 14 C 4.0966 2.2495 0 0


M V30 15 C 4.6843 1.391 0 0


M V30 16 C 5.572 3.2688 0 0


M V30 17 C 4.5381 3.1817 0 0


M V30 18 C 6.1634 2.4142 0 0


M V30 19 C 5.7149 1.4768 0 0


M V30 20 C 7.7797 1.6456 0 0


M V30 21 C 7.1913 2.4955 0 0


M V30 22 C 7.337 0.7049 0 0


M V30 23 C 6.3032 0.6249 0 0


M V30 24 C 5.8614 -0.3062 0 0


M V30 25 C 6.4483 -1.1575 0 0


M V30 26 C 2.186 -2.3461 0 0


M V30 27 C 2.4391 -3.3569 0 0


M V30 28 C 3.4467 -3.6456 0 0 CFG=1


M V30 29 C 4.2013 -2.9188 0 0


M V30 30 C 3.9483 -1.899 0 0


M V30 31 C 3.6917 -4.6541 0 0


M V30 32 N 4.5208 -5.175 0 0


M V30 33 O 3.0083 -5.3834 0 0


M V30 34 C 7.9232 -0.1391 0 0


M V30 35 C 7.4781 -1.0684 0 0


M V30 36 C 8.0633 -1.9115 0 0


M V30 37 C 9.0894 -1.8302 0 0


M V30 38 C 8.9419 -0.0526 0 0


M V30 39 C 9.5199 -0.8912 0 0


M V30 40 C 10.5327 -0.8089 0 0


M V30 41 C 10.9689 0.1111 0 0


M V30 42 C 10.3846 0.9501 0 0


M V30 43 C 9.3738 0.8637 0 0


M V30 END ATOM


M V30 BEGIN BOND


M V30 1 2 4 1


M V30 2 2 22 20


M V30 3 2 6 7


M V30 4 1 20 21


M V30 5 2 21 18


M V30 6 1 5 11


M V30 7 1 22 23


M V30 8 2 10 11


M V30 9 1 23 24


M V30 10 1 10 6


M V30 11 2 24 25


M V30 12 1 25 35


M V30 13 1 34 22


M V30 14 1 9 26


M V30 15 1 11 12


M V30 16 2 12 15


M V30 17 1 7 5


M V30 18 2 14 13


M V30 19 1 13 10


M V30 20 1 9 30


M V30 21 1 26 27


M V30 22 1 27 28


M V30 23 1 28 29


M V30 24 1 29 30


M V30 25 1 4 8


M V30 26 1 1 2


M V30 27 1 14 15


M V30 28 1 28 31 CFG=1


M V30 29 1 31 32


M V30 30 2 31 33


M V30 31 1 15 19


M V30 32 2 2 3


M V30 33 1 34 35


M V30 34 1 18 16


M V30 35 2 35 36


M V30 36 1 3 7


M V30 37 1 36 37


M V30 38 2 37 39


M V30 39 2 38 34


M V30 40 2 16 17


M V30 41 1 17 14


M V30 42 1 38 39


M V30 43 1 9 5 CFG=3


M V30 44 1 39 40


M V30 45 1 6 4


M V30 46 2 40 41


M V30 47 1 18 19


M V30 48 1 41 42


M V30 49 2 19 23


M V30 50 2 42 43


M V30 51 1 43 38


M V30 END BOND


M V30 BEGIN COLLECTION


M V30 MDLV30/STERAC1 ATOMS=(2 9 28)


M V30 END COLLECTION


M V30 END CTAB


M END

Bob Vetter wrote:

I have attached a file that des not work on our server using 3.3.3 Marvin

I was able to load your file and display the structure using Marvin 3.3.3 at


http://www.chemaxon.com/marvin/doc/dev/example-sketch1.1.html


Please use the File >> Open menu option to test that.


I think this is a scripting error in your application.





If you need our help to fix the bug, please send the HTML page (that is probably generated by your server-side script). Save the HTML file using the File >> Save As menu option of the browser send it as an attachment.





Best regards,


Ferenc

It looks like we were using Marvin3.2 and when I tried to force the Silverstream app server to use Marvin 3.3.3 it did not work. I extracted the jmarvin.jar from Marvin-all-3.3.3.zip and it works.





The only problem is that I am getting a security applet window. Is there a way to default to accepting the loading of the Marvin applet.





Thanks for your help.

Bob Vetter wrote:

It looks like we were using Marvin3.2 and when I tried to force the Silverstream app server to use Marvin 3.3.3 it did not work. I extracted the jmarvin.jar from Marvin-all-3.3.3.zip and it works.

Beside jmarvin.jar, there are several other jars and files in the package that are required!!!! Please see http://www.chemaxon.com/marvin/doc/dev/faq.html#question1 width="90%" cellspacing="0" cellpadding="3" border="0" align="center"> Bob Vetter wrote: The only problem is that I am getting a security applet window. Is there a way to default to accepting the loading of the Marvin applet. If you still get the security window after proper installation, please let us know about that.


If you mean the signed applet warning, just select "Always"


Ferenc