Ioannis,
I suggest using the CIF file from EBI instead:
http://www.ebi.ac.uk/pdbe/static/entry/download/1hho-assembly-1.cif.gz
It looks good to me -- just one model.
For reference, the RCSB site is using Jmol and is simply loading 1HHO
itself and constructing the assembly *in situ *using the
This approach does not seem to work.
On Monday 22 of February 2016 05:53:14 Thomas Holder wrote:
> Hi all,
>
> The bug seems to be that the "pdb_insure_orthogonal" setting is only applied
> to the first model. Turning the setting off shows the correct assembly:
>
> set pdb_insure_orthogonal,
Hi all,
The bug seems to be that the "pdb_insure_orthogonal" setting is only applied to
the first model. Turning the setting off shows the correct assembly:
set pdb_insure_orthogonal, off
load 1hho.pdb1
If "pdb_insure_orthogonal" is on, PyMOL will apply the SCALE transformation,
which might
Dear all,
Thank you for your informative answers.
For various reasons, I am not yet willing to move to cif.
Indeed remark 285 of the 1hho header:
http://www.rcsb.org/pdb/files/1HHO.pdb?headerOnly=YES
reads:
REMARK 285
1hho does have a non-standard crystal frame. (see remark 285)
If you load the assembly PDB file in rasmol - it displays properly. Pymol
is having the issue.
However, if you fetch the cif file in pymol, and ask it to display the
assembly - it does the right thing.
set assembly, 1
fetch 1hho
This looks like a bug in the PDB's file, and you should definitely let them
know about it. It's a particularly weird case since the second model
doesn't correspond to any of the valid crystallographic operators. Probably
it is a problem with the very non-standard crystal frame specified by the
Hi Mohsen,
if you want to superimpose structures, have a look at the align command:
http://pymolwiki.org/index.php/Align
Cheers,
Julian
On Thu, Feb 18, 2016 at 10:47 PM, Mohsen Chitsaz <
mohsen.chit...@flinders.edu.au> wrote:
> Hi
>
>
>
> In order to superimpose two protein sequences, I am
Dear Ioannis,
I was wondering about that, too. Given the prominence of hemoglobin
structure and oxygen binding in Biochemistry education, the 1 HHO structure
seems to be a bad biological structure to calculate incorrectly. I guess an
email to the PDB might be in order (if it is
