Dear All,
I am trying to use pdbset from the terminal and am constantly getting an
error:
[XYZ@NCCS3 110613]$ pdbset XYZIN input.pdb XYZOUT output.pdb B_reset
MINIMUM 0
CCP4 library signal ccp4_general:Use: logical name file name
(Error)
raised in ccp4fyp
pdbset: Use: logical name file
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Dear Swastik Phulera,
after the word 'output.pdb' you must first hit the Enter-key which
takes you into the program pdbset.
Then you type
B_reset Minimum 0
END
and the program runs.
If you wish to do it without interaction, e.g. in a script, you
Hi Wei,
if you tried both P3 and P6 and all subgroups, the right space group should
have been in there. By the way, the number of monomers in the a.u. will depend
on the exact space group (e.g. 1 in P622, 2 in P6 or P321, 4 in P3). There
might be a conformational change, which causes the MR
H..the real message from figure 3. The protein concentration.
seems to be that 70% of proteins do NOT crystallize in the 10-12.5 mg bin,
i.e. the 'right' concentration is an individual protein-in-that-buffer
property - and
all one can say is that the concentration needs to be high enough
-- Forwarded message --
From: Swastik Phulera swastik.phul...@gmail.com
Date: Tue, Jun 11, 2013 at 1:51 PM
Subject: Re: [ccp4bb] pdbset
To: Tim Gruene t...@shelx.uni-ac.gwdg.de
Dear Tim, Miguel
Thanks for your suggestions, the program does work now, but it seems that
it cant
What about getting rid of the ANISOU records before processing the pdb
file, with
grep -v ANISOU input.pdb output.pdb
?
If a program complains about ANISOU records then you use the isotropic
approximation...
That's what I would do as a quick and dirty fix.
Fred.
On 11/06/13 10:22,
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Dear Swastik Phulera,
unless you need the ANISOU cards, you can first remove them with e.g.
grep -v ^ANISOU youfile.pdb yournewfile.pdb
before running pdbset.
(I hope you don't work on a Windows machine, then you would probably
first find a way
In Windows:
findstr /b /v ANISOU input.pdb output.pdb
Cheers,
Robbie
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Tim Gruene
Sent: Tuesday, June 11, 2013 10:40
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Fwd: [ccp4bb] pdbset
Dear Tim,Fred
Negative B factors and occupancies higher than one came in from shelxl,
Also getting rid of Ansiou at first would lead me to an additional step of
placing them in their right place later on (is there a short cut that I may
take).
On Tue, Jun 11, 2013 at 2:09 PM, Tim Gruene
Postdoctoral Research Assistant
Sir William Dunn School of Pathology, South Parks Road, Oxford, UK
Salary Grade 7: £29,541 - £36,298 p.a.
A position is available in the DNA Damage Response group led by Dr Ivan Ahel
investigating DNA damage response mechanisms. This post is for up to 36 months
Two postdoctoral research opportunities in X-ray crystallography at Umeå
University, Sweden
Several positions are open for postdoctoral candidates interested in doing
research in the highly interactive and multidisciplinary research environment
UCMR - Umeå Centre for Microbial Research at Umeå
If you are resetting B factors you must recalculate the AniosUs later
But if you are getting negative B values something in your procedure is
less than optimal!
Are you refining aniso Us with too limited data? You need high resolution
data to attempt this.
Are you trying to refine B factors and
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Dear Swastik Phulera,
if your res-file sports negative U-values, your model has room for
improvement. You really should go back to the ins-file and make the
appropriate modifications in order to get rid of negative U-values
(the do not make chemical
Bernhard,
I'm often amazed at how forgiving protein crystallization is, or to put it
another way, how efficient screens are at picking up crystallization hits
even when you do everything wrong.
However if you do go down to 20 + 20 nl drops you have to remember that
probably 3/4 of your protein
Dear Bulletin board,
I am looking at protein complexes with ligands containing non-natural amino
acids. When I run PISA, I get the total area of the ligand, as well as the area
of the ligand-protein interface, but hydrogen bonds and salt links are not
recognized. I therefore do not think the
Dear Herman,
I am looking at protein complexes with ligands containing non-natural amino
acids. When I run PISA, I get the total area of the ligand, as well as the area
of the ligand-protein interface, but hydrogen bonds and salt links are not
recognized. I therefore do not think the
We have an MSC Cryo-Xe-Siter that won't fit in our refurbished X-ray
laboratory. If it can't find a new home it will be disposed of. We're
offering it free of charge to any interested UK organisations on the condition
that the recipient pays for its transport. It's currently in central
Hi Theresa,
Here is a comparison between both methods (Table under 6-Summary):http://www.cryst.bbk.ac.uk/pps97/assignments/projects/ambrus/html.htm
If you would like to have an idea about structures of membrane proteins (why was NMR used and what answers they got etc) solved by NMR to
Dear Colleagues,
On behalf of Rigaku, I'm very pleased to introduce a new Rigaku Crystallization
Webinar series. As crystallization of biological molecules continues to remain
the bottleneck in structural biology, we would like to provide the community
educational materials and a discussion
This message is posted for Eric Olson, Ph.D. (Chair of Molecular Biology), who
is looking for a postdoctoral fellow to join his lab to work on a novel
membrane protein (first described in Nature, in press). See project description
below and if interested please contact him at:
Email:
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