mismatch of molecule sizes

[using marvinsketch 5.2.6 on OSX 10.5.8]

When I read in a .mol file sketch scales it to fit in the window. If I then want to modify the structure by adding a drawing of a solvent molecule the scale of the bond distances between the initial molecule and the ring template don't match. I see no way to scale the portions of the molecule nor any setting that'll force the bonds to be of the same distance. This seems like a pretty basic functionality that is missing. At the very least if a scale factor was applied to an incoming molecule the same scale factor should be the default for new bonds or groups.

Am I not finding how to do this?

I saw a post in the archives from early in 2009 that indicated a general arbitrary scaling ability is not considered a high priority. Is this still the case?

Rich

Hello,

I wasn't able to reproduce the problem.
Could you give us more details on how you added the extra drawing after import?

Best Regards,
Erika

After reading in the .mol file I clicked on the benzene ring icon on the bottom of the screen and then clicked in the drawing area to add it to the drawing. As you can see in the attached graphic the newly added ring is much larger than the ones in the imported figure.

 

Rich

The imported mol file probably contains non-zero z coordinates.
Try 2D or 3D clean (Ctrl 2 or Ctrl 3) before starting to add new structures to the imported molecule.

Best Regards,
Erika.

I checked the .mol file and it did have a C atom with -0.5 as a z coordinate. Oddly enough if I edit the file to set this to 0.0 the result is still the same when I open the Recent Files and read it back in. Is the original file cached someplace so that my changes aren't being read?

 

The clean2D works but it changes the appearance/layout drastically and that is something that is not always acceptable.

 

Rich

We are investigating the issue related to Recent Files, and we will respond soon.

We have the bond-length adjustment on our feature request list, but haven't implemented yet.

Regards,
Erika.

We tried to reproduce the problem related to Recent Files - without success.
Could you send us the original mol file please?

Regards,
Erika

Sure. File is attached.

Thank you for the mol file. We checked it and detected that the second line contains information about the dimension in the last two characters: Marvin 01211017083D

Replacing 3D with 2D will result in bond length change.

Regards,

Erika.

Thanks Erika. That file was written (perhaps this is obvious) by MarvinSketch after reading in the original file. The same problem with scaling happens with a .mol file from another source. The header of that file is:

L_000899055_000K
  MACCS-II09195910442D 1   0.00000     0.00000     0
  ISISHOST11120209152D 0   0.00000     0.00000     0
 36 38  0  0  0  0    

 

Rich                 

I assume, this mol file also contains non-zero z coordinates as the previous mol file.
So both changes are necessary for the workaround until we solve this problem.

Regards,
Erika.