[Chimera-users] Lost hydrogens when saving mol2 file

Varela, Lawrence Rocco Rocco.Varela at ucsf.edu
Wed Jun 23 15:07:24 PDT 2010

Yes you're right, it's a display setting, I noticed that after opening the same file in DS Visualizer after I sent that email.  Thanks for the quick follow-up.  Kind of a follow-up concern though is that Chimera is consistently crashing when I try to draw a cumulative surface around these molecules.  I can rewrite the question and scenario to the group email if you like, but here are the molecules I'm trying to draw the surface around if you would like to take a quick look.  The file with the word "combined" is obviously the one generated after saving and combining, the other is the original.  The reason why  I'm going through the process of first saving the molecules into a file with a single MOLECULE tag is because I want to draw a surface around the whole group, which I'm using to analyze some other results I have.  Am I doing this all wrong?

From: Elaine Meng [meng at cgl.ucsf.edu]
Sent: Wednesday, June 23, 2010 2:42 PM
To: Varela, Lawrence Rocco
Cc: chimera-users at cgl.ucsf.edu BB
Subject: Re: [Chimera-users] Lost hydrogens when saving mol2 file

Hi Rocco,
Doublecheck that the hydrogens are not merely undisplayed (for example, use the command "display" to display all atoms).  It might be that the smart initial display hides hydrogens.  I think it decides based on how many atoms are in the molecule, and when the molecules are combined rather than separate, it may go over that threshold.

If they really aren't there, please use "Help... Report a Bug" in the Chimera menu to report a bug,  providing enough information for us to reproduce the problem.
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jun 23, 2010, at 2:36 PM, Varela, Lawrence Rocco wrote:

> I'm encountering a problem where I'm loosing hydrogens from my small molecules after saving them in Chimera.  Here is the situation: the original mol2 file I open has a number of small molecules listed under separate MOLECULE tag identifiers.  Using the GUI menu I select "save Mol2", select all the models to save, and select the Save multiple models in "a single file [combined @MOLECULE section] option.  When I open the newly saved Mol2 file with the combined MOLECULE section it's obvious that the hydrogens have been removed.  How do a save multiple models in a combinedMOLECULE section without loosing any hydrogen atoms?
> Thanks :-)
> Rocco
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