Dear Paul,
A few options may be of interest:
RCSB PDB Sequence Searching:
Paste your sequence into the sequence search box at:
http://www.pdb.org/pdb/search/advSearch.do?st=SequenceQuery
(also available from Advanced Search and from the Sequence Search of
the left hand menu).
Sequence search
Some afterthoughts:
Of course avoid the common MR problems - assigning wrong SG, saturating
low resolution data etc etc..
1) Any sequence search tool might have told you there was only a poor
match available. 23% is very marginal for MR and with that degree of
similarity you are very wise to
This is generally a good idea, but removal of residues is a subjective process,
and a little trial and error. If your sequence searching finds multiple search
models you can superimpose them and systematically remove the poorer fitting
regions based upon RMSD. We have built a server for this a
You've also applied BRAIN 2.0 ?
I mean looked at homologous structures, superimposed them and decided which
parts are to be removed ?
Never trust programs :-) There could be a flexible alpha helix which if you
removed it would have given you in all programs a solution.
it's Monday,
Jürgen
On
Dear Paul,
Thank you for initiating this thread, for so carefully evaluating the
suggestions you received, and for reporting the outcome.
Your astonishment gives renewed motivation to people who believe it is
still worthwhile continuing to push the frontiers of experimental phasing
and
The last molrep job just finished and it found only an odd solution. So I
think I will try to get my phases elsewhere. But I am somewhat astonished
that there are still enough cases you can't solve by MR.
Thanks to all who replied. Here is a list of servers/programs to find a MR
model:
http://www
BS"D
You can also use the OCA browser for FASTA searches of the PDB
oca.weizmann.ac.il
Harry
On May 23, 2010, at 10:23 PM, Paul Lindblom wrote:
Hi everybody,
I just crystallized a new project protein. How can I find a
possible model for using molecular replacement? I have the sequence
Yes, you can try a sequence search of the PDB. But if your sequence
matches only part of an existing entry, be aware there is a bug in the
PDB sequence search so that it reports the wrong residue numbers for the
existing entry. This bug has been reported to RCSB, but they apparently
have not fo
unambiguous space group ?
Jürgen
On May 23, 2010, at 4:52 PM, Paul Lindblom wrote:
> Thank you all for your quick answers. I already tried the phyre server but
> could not find a appropriate model. Balbes found a structure with 29%
> identity, but no solution. Now I am running molrep with the
> Phyre is a fold-recognition server...
And one might argue that "recognising the fold", getting the
loops/boundaries in the right place is the first step towards getting
MR to work properly - which is what I think Phyre does rather well.
But I absolutely agree that an approach like this requires
Thank you all for your quick answers. I already tried the phyre server but
could not find a appropriate model. Balbes found a structure with 29%
identity, but no solution. Now I am running molrep with the model balbes
found...
2010/5/23 Nathaniel Echols
> On Sun, May 23, 2010 at 12:57 PM, David
On Sun, May 23, 2010 at 12:57 PM, David Briggs wrote:
> I like to generate some models using the "Phyre" server
>
> ( http://www.sbg.bio.ic.ac.uk/~phyre/ )
>
> Feed the best .pdbs into Mr Bump.
>
> Go and get coffee. Come back and find a solution with post-refmac
> R/Rfree in the mid-30s.
>
> IMHO
Try balbes. It needs only your sequence and your mtz file.
http://www.ysbl.york.ac.uk/~fei/balbes/
Maia
Paul Lindblom wrote:
Hi everybody,
I just crystallized a new project protein. How can I find a possible
model for using molecular replacement? I have the sequence of my
protein. Is it e
tramural AIDS Research Fellow,
> Structural Immunology Section,
> Laboratory of Immunogenetics,
> NIAID/NIH
> Twinbrook II, Rm 108,
> 12441 Parklawn Drive,
> Rockville,
> MD 20852, USA
>
> Office Phone: 301 594 0242
> Lab Phone: 301 496 3792
> ---------
,
12441 Parklawn Drive,
Rockville,
MD 20852, USA
Office Phone: 301 594 0242
Lab Phone: 301 496 3792
---
-Original Message-
From: Miri Hirshberg [mailto:m...@ebi.ac.uk]
Sent: Sunday, May 23, 2010 3:35 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Finding best model
XtalPred
http://ffas.burnham.org/XtalPred-cgi/xtal.pl
or if you have data already let Balbes do the job.
Jürgen
On May 23, 2010, at 3:34 PM, Miri Hirshberg wrote:
> Sun., May 23rd 2010
> EBI
>
> Paul,
>
> 1. yes you can run your sequence against all PDB.
>
> 1. http://www.ebi.ac.uk/pdbe-srv/
Sun., May 23rd 2010
EBI
Paul,
1. yes you can run your sequence against all PDB.
1. http://www.ebi.ac.uk/pdbe-srv/view/
drop the one letter sequence in the sequence box
and search
2. http://www.ebi.ac.uk/Tools/fasta33/index.html
From the Databases protein you pick
Protein structure Sequence
Hi everybody,
I just crystallized a new project protein. How can I find a possible model
for using molecular replacement? I have the sequence of my protein. Is it
enough to make a sequence search in the pdb? Or is there another approach I
can use?
Thanks a lot,
Paul
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