Hi Oliver, Chimera doesn't handle unwrapped trajectories. You will need to use the ptraj "image" command to prevent molecules from being split across box boundaries in your final trajectory. Perhaps the other errors will not occur with the re-imaged trajectory. If not, please let me know. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Aug 19, 2009, at 4:15 AM, Koch, O (Oliver) wrote:

Dear Chimera Team,

I have a problem opening an AMBER trajectory using chimera v1.3 (2000/12/09).

When I look at the frames, they show this "spider web" phenomenon: Connections between atoms that should not be there. Furthermore, I got errors throughout the whole file: "Error: line too long in:"

I have a topology file and a coordinate file created using leap/ ptraj from the Amber Tools 1.2. I could look at the files using vmd with the options "Amber 7 parm" for the topology file and "Amber coordinates with periodic box" for the coordinate file. Therefore, the files should not be corrupt, but, of course, I would prefer to use Chimera for visualizing...

Can you give me any advice how to open the files correctly?

Thanks in advance.

Kind regards, Oliver

Dr. Oliver Koch BioChemInformatics Postdoctoral-Fellow Intervet Innovation GmbH Zur Propstei 55270 Schwabenheim, Germany

E-Mail: oliver.koch@sp.intervet.com Phone: +49 (6130) 948 396 Fax: +49 (6130) 948 517

Home http://www.intervet.com

Sitz der Gesellschaft: Schwabenheim Amtsgericht Mainz, HRB 23 166 Geschäftsführer: Dr. Peter Schmid

-------------------------------------- This message and any attachments are solely for the intended recipient.

If you are not the intended recipient, disclosure, copying, use or distribution of the information included in this message is prohibited

-- please immediately and permanently delete. -------------------------------------- _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users