Hi Jae,
Try resetting the MAXJNT parameter (increase the set value). I had problems
with MAXA and other
parameters and I suspect your problem has the same solution. You might need
root access for the same.
Also, make sure that you are specifically asking to read the topology and
parameter file
Try elbow.builder and phenix.refine in the phenix package. It will make
your life much easier.
Jae Hyun wrote:
> Dear all,
>
> I have a decavanadate anion in my structure, and want to refine it. For
> that, I got parameter and topology files from HIC-Up website, and used in
> CNS. But, it gave t
Dear all,
I have a decavanadate anion in my structure, and want to refine it. For
that, I got parameter and topology files from HIC-Up website, and used in
CNS. But, it gave the error message as follows:
Program version= 1.1 File version= 1.1
Torsion Topology>
Torsion Topology> fix gr
I'll revise my last after running my own newly-installed CCP4 on Fedora
Core 6. You will definitely need to include the 127.0.0.1 loopback entry
in your /etc/hosts file to make this error go away. The problem is that
the ::1 entry is ipv6-format, and the 127.0.0.1 is ipv4 format. CCP4
obviously req
We are pleased to announce the release of the rampage module as part of
the CCP4 6.0.2 public release. The rampage program is a validation tool
that in particular produces high quality ramachandran plot. Rampage is
part of the Rapper package http://mordred.bioc.cam.ac.uk/~rapper/ , and
is kindly pr
Both of these issues are related to the proper definition of the local
host in your /etc/hosts file. Check this file to make sure local host is
defined. You should see a line like either of the following:
::1 localhost.localdomain locahost
or
127.0.0.1 localhost.localdomain localhost
I just bui
I understand this surprising feature now ..
The atomic density is being smeared by the BADD 100 to cover a volume >
3A from the atomic centre. (3.2A to be more precise..)
But the limit on the map sections to be included in the inverse fft is
calculated without that BADD - in fact you use the
I now have my own issue with in stalling CCP4 6.0.2 on Fedorea core 6. when
I start a job I get this error:
ERROR running script can not connect to server port (RunNotification)
SERVER_HOST localhost SERVER_PORT 4441
Message: "couldn't open socket: host is unreachable"
Any clues? Naturally, I ju
Hi Sebastiano,
Can you send me the problematic PDB (offlist) and we'll take a look?
Thanks,
Dave
On Jun 25, 2007, at 8:50 AM, Sebastiano Pasqualato wrote:
Hi all,
despite using the latest version of pdb2pqr ( http://
agave.wustl.edu/pdb2pqr/server.html) and having downloaded the
late
Hi all,
despite using the latest version of pdb2pqr
(http://agave.wustl.edu/pdb2pqr/server.html) and having downloaded
the latest version of the apbs plugin for pymol, I still do not
manage having it work with all the pdbs, most of the time getting an
error while using the apbs plugin inparsi
Hi all,
here's the original post:
At 10:55 AM 6/19/2007 +0200, you wrote:
Hi all,
a few days ago I sent a post in which I was asking if anybody knew a
program to automatically define the hydrophobic core of a protein,
given the pdb.
Unfortunately I got no answers, and indeed a more thorough
For Stereophiles and Xineramaphiles,
for those that asked me for our Xorg.config file (see below) for running a two
screen setup (requires Nvidia Quadro card).
This file is set up for a stereo beamer and a LCD.
You have to do some editing of your xorg.conf file (do that by creating
a copy and
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