Dear Maria,
I can see that others have suggested how to manually change the
secondary structure, but I have one comment:
If a secondary structure detection algorithm doesn't assign those
residues as 'strand' then this is probably (bugs notwithstanding) a
feature of your model and you should
I'd rather not reinvent the wheel if I don't have to. Does anyone
have a version of ccp4.setup which has been converted to Tcl for use
with environment-modules?
More info:
http://modules.sourceforge.net
Sample commands:
module load ccp4 # setup your environment for latest version
module u
Dear Mariah,
You can change the secondary structural elements to the desired helix, sheet or
loop by using the alter command.
for example if you have to change residues from 10-34 in chain A to helices ,
you have to use the following
alter A/10:34/, ss='H'
rebuild
cartoon automatic
show cartoon
Hello Mariah,
Please note that is the CCP4 mailing list. The PyMOL mailing list is at:
http://sourceforge.net/mail/?group_id=4546
In answer to your question, you might first try:
dss
# If thats doesn't solve your problem, then you can use alter to explicitly
assign secondary structure manual
Dear All,
I have a question about PYMOL.
I am trying to make a cartoon diagram of my protein showing the secondary
structural elements. However for some reasons it is not showing the N
terminal strand and showing that as a loop. Is there any command for
selecting a range of residues and showing
I had a similar problem a few months back...
cd $CCP4/src; make lsqkab ; cp lsqkab $CCP4/bin/
Pete
Edward Miller wrote:
> Hey Folks,
>
> I need to recompile lsqkab to increase the parameter NATOM to 8.
>
> What would be the best way to only recompile lsqkab without having to
> recompile al
Hey Folks,
I need to recompile lsqkab to increase the parameter NATOM to 8.
What would be the best way to only recompile lsqkab without having to
recompile all of CCP4?
Cheers,
Ed Miller
UNIVERSITY OF DUNDEE
DIVISION OF MOLECULAR MICROBIOLOGY
COLLEGE OF LIFE SCIENCES
POSTDOCTORAL RESEARCH ASSISTANT
GRADE 7 (£28,839 - £35,469)
SUBJECT AREA: SIGNALLING PROTEINS MUTATED IN METABOLIC/NEUROLOGICAL
DISEASES
A postdoc position is available immediately in the group of Daan van
Aal
Dear BB,
after very quick replies from George Sheldrick and Kay Diederichs we
recompiled shelxh setting JW to 1200 and
IM to 32000 and it worked beautifully. Thank you both very much for
your help, regards, Matt.
--
Matthew Bowler
Structural Biology Group
European Synchrotron Radiatio
Dear Zhongren,
if I remember correctly, mapman from G. Kleywegt can convert from CCP4 map
format to various other formats, including CNS.
Tim
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
On Thu, 28 May 2009, Wu, Zhongren wrote:
De
Maps generated by CCP4 are CNS-formatted and they are
> not accepted with Discovery Studio (DS) and Maestro.
> DS and Maestro use only CNX-generated maps.
There's your problem. CCP4 application do not generate CNS-formatted
maps, they generate CCP4-formatted maps. The two formats are complet
Dear Paul:
Thank you for your input.
Maps generated by CCP4 are CNS-formatted and they are not accepted with
Discovery Studio (DS) and Maestro. DS and Maestro use only CNX-generated
maps.
I did try xdlmapman. No luck. However, I am not sure if xdlmapman is
able to convert maps to CNX-formatted
Dear George
On the contrary, it's being used, it's just that it's rare for something
to go wrong and the documentation is very clear, so there's very little
cause for complaint!
Cheers
-- Ian
> -Original Message-
> From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]
O
Dear Matt,
It is nice to see a message about SHELX on the BB, compared with the
frequency of messages about certain other programs I have the
impression that no-one is using SHELX these days!
You should be using the larger version SHELXH, available from the SHELX
server. If that is still too sma
Matthew BOWLER schrieb:
Dear BB,
I have refined a 1.05A structure with shelxl and would now like to
get some values on the coordinate error by doing a least squares full
matrix cycle, unrestrained. I have followed all the procedures that I
can find, but I keep getting the error message **
Dear BB,
I have refined a 1.05A structure with shelxl and would now like to
get some values on the coordinate error by doing a least squares full
matrix cycle, unrestrained. I have followed all the procedures that I
can find, but I keep getting the error message ** ARRAY B TOO SMALL FOR
TH
Title: [ccp4bb] CCP4 compatability with other software suites
xdlmapman does lots of map conversions. You could try one of the options there.
Best,
Paul..
###
Dr. Paul A. McEwan
Office B55
Centre for Biomolecular Science
University of Nottingham
Nottingham
NG
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