[Chimera-users] Double coordinates for same residue

Hurt, Darrell (NIH/NIAID) [E] darrellh at niaid.nih.gov
Thu Sep 15 10:11:44 PDT 2011

Hi Francesco,

I'm sure the Python script will work for you. However, it should be easy
enough to select the B alternative positions with "@.b" and then use
"Actions > Atom/Bonds > delete" to wipe them out. Then save the new PDB
file. This will do exactly the same thing as the script you identified and
may be easier for you.

If you want to consider occupancy values, you may have to manually inspect
the PDB file yourself. But maybe Elaine can come up with a clever way to
do that in Chimera...

Best of luck!

Darrell Hurt, Ph.D.
Section Head, Computational Biology
Bioinformatics and Computational Biosciences Branch (BCBB)
31 Center Drive, Room 3B62G, MSC 2135
Bethesda, MD 20892-2135
Office  301-402-0095
Mobile 301-758-3559
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On 9/15/11 12:54 PM, "Francesco Pietra" <chiendarret at gmail.com> wrote:

>At any event I am at Debian GNU-Linux. In the meantime I came across a
>possible solution that should work on both Linux and Darwin, although
>it does not take account of the occupancy values. Probably, however,
>in the case I am interested in, the occupancy values are not too
>dissimilar (have to check), otherwise the authors would have not
>published so many alternate locations.
>On Thu, Sep 15, 2011 at 6:35 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> Hmm, that's very puzzling to me -- I'm using a Mac now and I tested
>>exactly that before replying!
>> Elaine
>> for example:
>> open 2fma
>> disp
>> focus :170
>> ~disp @.b
>> (or, ~disp :170 at .b)
>> On Sep 15, 2011, at 9:28 AM, Hurt, Darrell (NIH/NIAID) [E] wrote:
>>> Hi everyone,
>>> It is my experience with Chimera on a Macintosh computer that the
>>> alternate designation must be case-sensitive. In other words:
>>> ~disp :42 at .b
>>> - will NOT undisplay alternate location B atoms in residue 42
>>> ~disp :42 at .B
>>> - will undisplay alternate location B atoms in residue 42
>>> YMMV,
>>> Darrell
>Chimera-users mailing list
>Chimera-users at cgl.ucsf.edu

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