This message and the one before it reappeared due to a malfunction in our mailing-list software.  That problem has been fixed.  Sorry for the spam.  The problem in the mail itself has been fixed also, as per the response I sent to the original messages.

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu

On Jul 16, 2010, at 2:58 AM, Gesa Volkers wrote:

Dear Eric,

thanks for your suggestions. Unfortunately removing the SEQRES record
did not help. I also downloaded and installed the new chimera-version
today. The false numbering in the alignment still occurs. Also when I
remove the SEQRES record and try with the new chimera version the false
numbering appears. Quite annoying... The pdb-file is not in the protein
data bank yet.

Any more suggestions? Could I add "dummy atoms" in the structure?

Thanks,
Gesa



Eric Pettersen schrieb:
On Jul 14, 2010, at 6:53 AM, Gesa Volkers wrote:

Dear All,

I observed an issue with the alignment function of Chimera.
I loaded a crystal structure where in between a loop is not modelled
due to low electron density- so these residues are missing in the
structure and the numbering also has this gap. When I align this
structure with others, the missing residues are not recognized and
chimera just overrides the numbering so after this loop all the
numbers in the alignment do not fit anymore to the residues they
should belong to although the structure and numberings are shown in
the right way in the graphics window. How can I overcome this issue?
Should I change the pdb-file? In which way?

Thanks for all responses!

Hi Gesa,
I had a similar problem reported with 1JFF 12 days ago and haven't yet
worked on fixing it.  It seems to only happen for a small subset of
structures.  1JFF has a missing loop and also exactly one missing
residue at the N terminus.  Is your structure like that?  Is it a
standard PDB entry (if so, what's the ID code)? I'll add you to the
recipient list for the ticket we have open in our bug database for
this (#8585) so you will be notified when it gets fixed.  It'll
probably be fairly soon.
Until then the only workaround that occurs to me is for you to remove
the SEQRES records from the PDB file before you open it.  Then the
Sequence viewer will depict only the residues physically present in
the structure -- no gaps (incorrect or otherwise) will be depicted.

--Eric

                       Eric Pettersen

                       UCSF Computer Graphics Lab

                       http://www.cgl.ucsf.edu





--
Gesa Volkers
Institut für Biochemie, Molekulare Strukturbiologie
Felix-Hausdorff-Straße 4
17489 Greifswald
Germany
+49 (3834)-864392


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