First suggestion - use WEIGHT AUTO in REFMAC - you may have restrained
the geometry too tightly..
And have you tried TLS ?
And at what level do you see no density - remember sigma levels in
maps need to vary with B factor - very easy to achieve this with COOT..
Eleanor
JOE CRYSTAL wrote:
Q2
Copy the MAL entry into your own directory
cp $CLIBD/monomers/m/MALcif ./
Then correctt it in your directory
And assign LIBIN ./MAL.cif
The program will read your corrected version and ignore the distributed
one.
Q1
If you run REFMAC the GUI under review restraints, it will detect and
There is a collection of posts (unfortunately with a number of spam
messages) at
http://wwpdb-remediation.rutgers.edu/mail-archive/
with various comments. Although I'm not familiar with the internal
workings of this remediation program, it seems indeed that the PDB
format is now largely auto-ge
Hmmm - ccp4bb doesn't allow an attachement ... so script comes here:
-- cut here ---
#!/bin/sh
[ $# -eq 0 ] && echo " ERROR: give some PDB identifier as argument"
type tkdiff >/dev/null 2>&1
[ $? -eq 0 ] && diff=tkdiff || diff=diff
for id in $@
do
i
Yes, this is how a wiki page for CCP4 might look like. However, to make a
wiki successful we have to make sure it is secure and that there is a
dedicated core team to maintain it. Kevin was asked by the CCP4 to lead
the wiki project and while he is setting things up, it would be
counterproducti
Our AKTA FPLC has been trouble-free for 9 years, and we bought one of
the early models. It has lived in a cold room, withstood periods of
heavy use, periods of inactivity, and ham-handed undergraduates without
incident. I think we have replaced only the injector channels and the
solvent filters
Hey,
When was the announcement made? I can't claim to read all the CCP4 mail
very carefully, so I probably missed the it...
The wiki I've set up is essentially a sandlot - something to play with and
something to give people ideas (in other terms, not intended as a final
product), but I'll gladly
Hi all,
I am trying to use the new ARP/wARP to build a model starting from a
partially refined structure for the phases using the "Use pdb file as it is"
option. When I run the program it quits after/during the first REFMAC cycle
with the following message:
ERROR ('IndexError', ('list index out o
I like to think structural biologists are more than just another user
group, they FEED the PDB!
Their needs should first and foremost be taken care off, I would think.
Also, it would indeed be a great loss if legacy programs can not be used
anymore.
- Jeroen -
Clemens Vonrhein wrote:
Th
Hi Artem,
There was a decision by the CCP4 Executive at the last CCP4 developers
meeting in March to develop the wiki. Kevin was asked to coordinate this
after his presentation of the wiki proposal and analysis of the issues
involved, based on the experience gained from the York wiki. The
deve
Would a "CCP4 wiki" be different from a general crystallography wiki? Would it
reflect, for instance, the breadth of topics on the CCP4BB?
On Monday 23 July 2007 09:57, [EMAIL PROTECTED] wrote:
> Contributions from volunteers to establish and maintain the CCP4 wiki will
> be definitely appreciat
Thanks to all those who replied to my query about purification of protein-DNA
complex for
crystallization. I figured out that extraction from native PAGE is the best
way to purify duplex DNA.
Does any one have a protocol that had worked for you.
I found the following protocol that I am plannin
If you're worried about UV all you need to do is to run multiple lanes of
the same stuff, shield all but one with some sort of UV-opaque material
(many kinds of plastics work very well), and cut the shielded lanes based on
what you see on the illuminated lane. In a properly cast gel, all the lanes
Hi all,
Resolution doesn't matter when solvent accessible surface area(SASA) is
calculated?
If resolution is poor, I think that the SASA is not likely to be
reliable. Then, is there any resolution cut-off for SASA calculation?
Also, when you calculate SASA, do you include NMR data, too?
Any co
I am interested in the SASA per residue.
On Tue, 2007-07-24 at 14:43 +0900, Hyunchul Kim wrote:
> Hi all,
>
> Resolution doesn't matter when solvent accessible surface area(SASA) is
> calculated?
>
> If resolution is poor, I think that the SASA is not likely to be
> reliable. Then, is there any
Hello Hyunchul Kim,
I found this paper very interesting:
Novotny M, Seibert M, Kleywegt GJ.
On the precision of calculated solvent-accessible surface areas.
Acta Crystallogr D Biol Crystallogr. 2007 Feb;63(Pt 2):270-4. Epub 2007 Jan
16.
PMID: 17242521 [PubMed - indexed for MEDLINE]
http://www.n
Hello Miguel,
Thank you for your reply.
It's related to the total SASA of a protein structure but not that of
per residue. However, it still give me a hint. :)
Best,
Hyunchul Kim
On Tue, 2007-07-24 at 08:12 +0200, Miguel Ortiz-LombardÃa wrote:
> Hello Hyunchul Kim,
>
> I found this paper very
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