Hi Bernhard,
That sounds fine. I have used the term 'RoseTTAfold/AlphaFold2 model' in
that field for a few SSGCID depositions.
Many times, this field does not really provide an accurate description of
the model that was used: You might trim a model, use separate domains, use
MoRDa that might select
What do people think about depositing the Robetta model to somewhere like
Zenodo (or maybe PDB-Dev) and getting an id from that?
Best wishes
James
On 7 Feb 2022, at 13:25, Loll, Bernhard wrote:
Dear all,
I have recently solved a structure by molecular replacement with a search model
calcula
Dear all,
I have recently solved a structure by molecular replacement with a
search model calculated by the Robetta server.
I am in the process to deposit the coordinates. Now, I am wondering
which information I should give on the starting model. Routinely, I
would provide the the PDB code,
on behalf of Mohamed Noor
[mohamed.n...@staffmail.ul.ie<mailto:mohamed.n...@staffmail.ul.ie>]
Sent: Tuesday, December 30, 2014 3:26 PM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: [ccp4bb] PDB deposition - sequence file
Dear all
The protein that was crystallized is only
ence too.
Phil Jeffrey
Princeton
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Mohamed Noor
[mohamed.n...@staffmail.ul.ie]
Sent: Tuesday, December 30, 2014 3:26 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] PDB deposition - sequence file
Dear all
The protein that was crystallized is only the first 105 residues of a
230-residue protein. In the structure, I can see density for residues 6-72. For
deposition, should the whole native/biological sequence be deposited?
Thanks.
Mohamed
972-8-647-2992 or 972-8-646-1710
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Stephen Cusack
[cus...@embl.fr]
Sent: Friday, May 25, 2012 6:42 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] PDB deposition of internally truncated prote
Dear Stephen,
On Fri, 2012-05-25 at 17:42 +0200, Stephen Cusack wrote:
> Dear All,
> I need to deposit in the PDB the co-ordinates of a protein with an
> internal truncation.
> If I do this in the normal way with consecutive numbering according to
> the actual polypeptide sequence
> in the
Dear All,
I need to deposit in the PDB the co-ordinates of a protein with an
internal truncation.
If I do this in the normal way with consecutive numbering according to
the actual polypeptide sequence
in the crystal, the residue numbers after the truncation will not
correspond to the equiva
Dear Dirk,
Not a remedy, but how about iyour colleague trying a different browser or
deposition site (e.g. www.pdbe.org)?
Cheers, Tim
On Tue, Feb 15, 2011 at 05:00:00PM +0100, Dirk Kostrewa wrote:
> Dear CCP4ers,
>
> a colleague of mine is just going through the PDB deposition process
> using t
Thanks a lot for your suggestions! Meanwhile, my colleague entered the
desired sequence information into the first website without frames, and
after that, the usual frame layout re-appeared! I don't know whether
this is a bug or intended ...
Best regards,
Dirk.
Am 15.02.11 17:00, schrieb Dir
Dear CCP4ers,
a colleague of mine is just going through the PDB deposition process
using the usual ADIT website. In contrast to my experience and to the
ADIT turorial, she has only one frame in the browser. The left frame
with the overview is missing. So, there is no way to jump between the
d
Dear all,
I have just received response from the PDBj Annotator through CCP4BB
My PDBs will be processed within two weeks
As some of you mentioned, the reasons of delaying processing time is due to
holiday season and the extremely large amount of depositions recently
Again, thank you
Dear all,
Thank to your replies, I am so released now!
Thank you a lot for all responses.
Best regards.
Dear all,
Last year, when I deposited PDBs using ADIT, immediately I got an automatic
confirmation email. And after 1 day, I got the responses from the PDBj
Annotator. And within 3 days, all the edition and validation of my structures
were finished with the help of member from the wwPDB. I g
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