[Chimera-users] missing ribbon loop

klumpler at sci.muni.cz klumpler at sci.muni.cz
Thu Dec 3 00:30:28 PST 2009

Hallo Elaine,
Im sorry to waste your time with such a thing, in chimera 1.4 it is really
allright. I worked with .py sessions made in 1.3 release and these session
even in chimera 1.4 showed gap - missing ser183 in ribbon repr.
Thank you very much for your kind answers,

> Hi Tomas,
> I don't see any missing ribbon loop when I look at the structure.  I
> see one continuous protein ribbon for residues 56-195 of chain A.
> There is also a short peptide, residues 10-14 of chain Q.   However,
> chains A and Q are separate molecules so they should not be connected,
> if that is what you meant.
> The only weird things I can see in the display are
> - Glu 89 in chain A is broken into two parts because it does not have
> a CG atom
> - Asn 185 in chain A is broken into two parts because it does not have
> a CB atom
> However, neither of these things affects the ribbon because all of the
> backbone atoms are there.  Maybe you are seeing the sidechain pieces
> of these two residues?
> I looked at the structure in both the current 1.4 release candidate
> and the current 1.5 daily builds of Chimera.
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> On Dec 2, 2009, at 3:38 AM, klumpler at sci.muni.cz wrote:
>> Dear Elaine,
>> I think PDB is alright, I send it as a attachment. Could you help me
>> with
>> the editing?
>> Thank you very much
>> Tomas

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