[Chimera-users] Reading Frame Problem

Eric Pettersen pett at cgl.ucsf.edu
Sat Jun 10 12:44:37 PDT 2006

To supplement Elaine's reply a little, if the problem is that the 
receptors' coordinates differ, you can use the "match" command to 
superimpose them.  So for example if the receptor is composed of 
residues 1-200 and the two copies are open in models 0 and 1, then 
"match #0:1-200 #1:1-200" should superimpose them.


On Jun 10, 2006, at 11:26 AM, Elaine Meng wrote:

> Dear Mark,
> The structures should automatically be in the same coordinate system
> (i.e. all the transformations applied by rotating and scaling
> interactively will apply to all open models, or if you haven't
> manipulated anything, they will both be in shown in their untransformed
> coordinates).
> The only thing I can think of is that during preparation for GOLD
> docking, some transformation was applied to the system, resulting in
> its differing from the original coordinates of the system. You could
> try comparing the original receptor coordinates with the receptor in
> its prepared state to check for that.
> If you don't think anything like that happened, it would be great if
> you could supply two example files and tell us why/how you can tell
> that they are not in a consistent coordinate system when displayed in
> Chimera.  You could send the info just to me (and I'd share it only
> with the Chimera development team) if you'd like.
> When/if the structures are in the same frame of reference, you would
> then use the command "rmsd" to calculate the RMSD without performing
> fitting.
> Manual page for rmsd:
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html
> Best,
> Elaine
> On Jun 9, 2006, at 4:26 PM, markcunningham wrote:
>> Could someone please help with this. .
>>   Using Chimera, I am trying to calculate rmsd between an observed
>> ligand versus GOLD docked ligand, however the problem is the ligands
>> load into different reading frames. The format for both ligands is
>> .mol2. How can I correct this problem, in other words load both
>> ligands into the same reading frame so that I can then calculate their
>> rmsd.
>> Thanks.
>> Mark
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> -----
> Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
> UCSF Computer Graphics Lab and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>                       http://www.cgl.ucsf.edu/home/meng/index.html
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