different results with same option

Hi,





I have used the Cleaning and Optimize options for the same molcules by both Marvin Sketch and Marvin view and saved the results. But both the results have difference. can it happen??can you Please help me..





Regards,


jiji

You talk about 2D or 3D clean? Can you show an example?

Hi,





i have tried the 3D clean and Optimize options in marvin sketch and Marvin view.then saved the results in MOL format.But it shows much difference.


I am attaching the input file, mview result and Msketch result please check that.





Rergards,


Jiji

Hi Jiji,





Could you let me know (step-by-step) how the "test_msketch" result was produced? I was trying to reproduce it, with no success. Please, also give the version of your Marvin.





Best wishes,





Ödön

jijibio wrote:

Hi, i have tried the 3D clean and Optimize options in marvin sketch and Marvin view.then saved the results in MOL format.But it shows much difference. I am attaching the input file, mview result and Msketch result please check that. Rergards, Jiji

Hi,





ok..now i'm clear that, the version which i was used was different.I have compared the results of mview(version 4.0.5) and msketch(version 4.1.5) of different versions.





The mview and msketch in the same version gives the same result ..no confusion..


Thank You...





one more thing, what makes the difference between the Msketch in different versions(version 4.0.5 and 4.1.5)


(Particularly the Clean 3D and optimize options, how they differ in different versions??)


Once again thanking you for your Quick response..





Regards,


Jiji

Hi Jiji,





- A new version of Clean3D was introduced in Marvin 4.1.


- The development is still in progress and may result in different structures due to changes in defult settings, the culculator plugin (e.g. conformers or leconformer) makes changing the defaults possible.


- The Clean/3D menu have different options:


- Fast uses the old algorithm.


- Fine + hydrogenize should give the same results with Hydrogens than


- Fine with the temporarilz added Hzdrogens removed.


- Build or optimize will build 3D structure for non-3D molecules and just optimize the 3D molecules


- Optimize will just optimize with the Dreiding forcefield


Since simple optimization uses the starting geometry it may give different results the the 3D builder which always build the structure from scratch.





Ödön

jijibio wrote:

Hi, ok..now i'm clear that, the version which i was used was different.I have compared the results of mview(version 4.0.5) and msketch(version 4.1.5) of different versions. The mview and msketch in the same version gives the same result ..no confusion.. Thank You... one more thing, what makes the difference between the Msketch in different versions(version 4.0.5 and 4.1.5) (Particularly the Clean 3D and optimize options, how they differ in different versions??) Once again thanking you for your Quick response.. Regards, Jiji