[phenixbb] Incorrect secondary structure assignment in a .pdb
mjj5qk at virginia.edu
Fri Jun 29 08:05:58 PDT 2018
I was using the 'pdb extract' online tool provided by the PDB website. This
creates a .cif file but removes SS info.
Your way of doing things creates .cif files with SS info in them (at least
in my hands phenix works better here). The fact that Chimera does not read
SS info from cif files is another story, but cif support is limited.
I think this is as good as it gets. Most importantly, my pdbs are in order,
so I should now be in the clear - regardless what individual viewers
display. Thank you for the explanation!
On Thu, Jun 28, 2018 at 4:37 PM, Oleg Sobolev <osobolev at lbl.gov> wrote:
> Hi Maciej,
> The main problem in my original question is that when I (or the pdb
>> extract tool that converts a .pdb file to a .cif file for submission to
> Can you describe more specifically what exactly the tool you are using?
> One way around it would be to convert your pdb to mmcif using
> tool which will preserve SS information.
>> How can you have SS elements displayed if it description is missing from
>> the header?
> As pointed by Ricardo, visualization programs usually can display SS
> without any header. On top of that, whether they will use the header if it
> is present - also depend on particular program.
> Best regards,
> Oleg Sobolev.
>> On Thu, Jun 28, 2018 at 12:38 PM, Pavel Afonine <pafonine at lbl.gov> wrote:
>>> Hi Maciej,
>>> please have a look at item #10 and Notes section here:
>>> One sentence summary is: Make sure you use secondary structure (SS)
>>> restraints in refinement, also making sure you provide SS annotations as
>>> HELIX/SHEET records in input PDB that are as accurate as possible; this is
>>> critical for successful refinement.
>>> If you have more questions please get back to us!
>>> Good luck!
>>> On 6/28/18 09:23, Maciej Jagielnicki wrote:
>>> Hi All,
>>> I used a combination of phenix real space refine and Coot to build a
>>> model into a cryoEM density map. I used an existing .pdb file as a starting
>>> point for my building. During the build, some helical elements became
>>> strands and vice versa (it was very clear to my eyes). Unfortunately,
>>> neither Phenix nor Coot would automatically update the header information
>>> for secondary structure elements, and I had to manually edit the header so
>>> that helices would show up in correct places when the .pdb file was viewed
>>> in Chimera or similar software. Not an ideal way of doing this which is
>>> likely related to what happened next.
>>> When the header information is removed, however, as it happens when the
>>> pdb.extract tool prepares a .pdb file for submission by turning it into a
>>> .cif file, the secondary structure elements are still displayed when a .cif
>>> file is visualized (bizzare in itself) but also the secondary structure is
>>> taken straight from the starting .pdb file (the one I used as a base for my
>>> model to which there is no connection whatsoever). The question is this -
>>> where does the incorrect secondary information come from in the absence of
>>> the header? How to fix this? I cannot deposit a file that shows
>>> helices/sheets wherever it wants...
>>> Maciej J.
>>> Maciej Jagielnicki, MS.
>>> Graduate Student
>>> University of Virginia
>>> Molecular Physiology and Biological Physics
>>> 480 Ray C Hunt Drive Rm 320
>>> Charlottesville, VA
>>> Lab Phone: 434-243-2520
>> Maciej Jagielnicki, MS.
>> Graduate Student
>> University of Virginia
>> Molecular Physiology and Biological Physics
>> 480 Ray C Hunt Drive Rm 320
>> Charlottesville, VA
>> Lab Phone: 434-243-2520
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> Unsubscribe: phenixbb-leave at phenix-online.org
Maciej Jagielnicki, MS.
University of Virginia
Molecular Physiology and Biological Physics
480 Ray C Hunt Drive Rm 320
Lab Phone: 434-243-2520
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