possible bug in ball-and-stick model

User 5d37306f8a

05-09-2007 20:11:51

Hi,





When I view the attached file using ball-and-stick models,


the bonds between hydrogen atoms and heavy atoms are not shown.


(I clicked "ball-and-stick" and "hydrogen").


Am I doing something wrong?





Thanks,


Wonpil


ChemAxon efa1591b5a

07-09-2007 11:19:02

Hi,





try a workaround that should solve the problem: rename all ATOM record in your PDB file to HETATM. Then you can display your hydrogen atoms.





MSpace is quite strict in following the PDB standard, that allow ATOM blocks to represent amino acid or nucleic acid residues only. The rest should go in HETATM records.





We realized that most 3rd party applications treat the PDB standard losely so well do the same... well, soon, in one of the next releases of MSpace.





HTH


regards


Miklos

User 5d37306f8a

17-09-2007 02:41:06

I changed ATOM into HETATM for some files, and it did work, but not for all.


Please, let me know how I can visualize the attached molecule with hydrogens. (HETATM did not work for this)





Or, if there is any other format that MSpace can better represent, please let me know.





Thanks,


Wonpil

ChemAxon efa1591b5a

17-09-2007 08:31:37

Hi,





beside of changing ATOM to HETATM you also need to rename the residue from ASN to anything else (NNN etc).


MSpace's PDB import recognizes your structure as a modified asparagine residue (base don the ASN residue name). Then it gets confused by the first atom CAY as its name is not a standard atom name in asparagine.





This problem will be fixed in some of the future releases.





Regards,


Miklos

User 5d37306f8a

17-09-2007 14:47:28

Dear Miklos,





Thanks for the suggestions. It almost worked, but I am now facing two problems;


(1) it automatically displays lone pairs and I have to turn off "Lone Pairs" twice to remove them.


(2) When I click "Hydrogens", there are too may hydrogens (even four hydrogens on nitrogen atoms!)





Any suggestions?





Cheers,


Wonpil

ChemAxon efa1591b5a

19-09-2007 10:08:29

Dear Wonpil,





(1) did not manage to reproduce!


(2) BUG! we'll fix it.





Apologies for the inconvenience, we'll let you know when patch is available.





Miklos

User 5d37306f8a

20-09-2007 00:58:15

Dear Miklos,





The lone pairs are removed when I click the "Lone Pairs" option twice.


I think, it should not be there at the first place because there is the "Lone Pairs" option.





I hope that you can fix these bugs soon.





Thanks,


Wonpil

ChemAxon 909aee4527

21-09-2007 08:54:46

Dear Wonpil,





(1) is fixed, it will be available in 4.1.13 which is planned to be released in days.





Kind regards,


Judit

User 5d37306f8a

22-09-2007 00:15:25

Dear Judit,





Thanks for the fix.


Will it be possible to include the bug fix of (2) multiple hydrogens in the release?





Cheers,


Wonpil

ChemAxon 909aee4527

24-09-2007 11:57:39

Dear Wonpil,





4.1.13 was released last Friday (we have monthly patch releases in the middle of each month).


Fix of (1) could go with it in the last minute but fix of (2) is unfortunately not ready yet.


We hope to release 5.0 before the next patch release (4.1.14), and we'll try to give the fix with it.





Kind regards,


Judit