Good morning CCP4 members
I have a question about a 2F0-Fc difference map that I calculated with Refmac.
In some instances it gives me negative (red) density around part of a side
chain and no positive density in sight. Furthermore the entire residue fits
well into the blue density of the compl
Dear Ian,
I installed the fonts from the link
http://www.scripps.edu/~arvai/adxv.html.Everything works now on my linux
system.There was no need of extra fonts on my xming (I had already installed
extra fonts from the link you have suggested) and it works just fine.
Thanks to your time to help.
On 22 November 2011 22:04, Pius Padayatti wrote:
> Rajesh,
> The fonts error please follow the guidelines from following link
>
> http://www.scripps.edu/~arvai/adxv.html
OK the fonts you need are the ones mentioned above (in
http://www.scripps.edu/~arvai/adxv/fonts.tar.gz), BUT the installation
i
Rajesh,
The fonts error please follow the guidelines from following link
http://www.scripps.edu/~arvai/adxv.html
see relevant parts under the heading questions
it did solve issues for me
cheers
psp
On Tue, Nov 22, 2011 at 10:37 AM, Rajesh kumar wrote:
>
> Dear All,
>
> All the suggestions helpe
Mark may or may not have meant what I think he meant, but it did remind
me of the following passage from Blundell and Johnson (1976):
"The chain reaction initiated by fee radical formation probably accounts
for the common observation that radiation damage effects in protein
crystals continue, ev
Filip Van Petegem wrote:
In a case I'm currently looking at, I'm particularly dealing with cryo-EM data,
not X-ray structures, but with the same underlying principles: what are the
odds that all pixels of the map move together in the same direction?
I suspect you may be better off asking an
On 22/11/11 00:31, Santarsiero, Bernard D. wrote:
I just installed CCP4-6.2.0 and COOT on a Red Hat v6.1, x86, linux
workstation. Some of the menus, along the right edge, are gray buttons on
gray background. Where is the preferences file to change the colors of the
menu buttons? The menus across
Hi Rajesh
The fonts have to be installed where they are needed, i.e. where the
display of the GUI is happening, on the X server (e.g. your Windows
PC), not on the compute server (your Linux box). I had problems with
missing fonts in Cygwin when I first installed it. Cygwin doesn't
install all th
It is hard to make sensible comments without seeing your maps.
In these cases I use coot to validate.
Run the ramachandran check - click on all outliers and see if what the
electron density looks like. Sometimes you do see indicators on how to
make corrections. Sometimes you have a CIS peptid
Dear all,
A brief email to let you know that registration for this meeting will close on
Friday 2 Dec, so if you would like to attend you have a week and a bit to
register.
Registration details and a full program can be found at the meeting webpage
http://www.diamond.ac.uk/Home/Events/BCA.html
Hi Rajesh,
That is a very old version (1.9.4) of ADXV.
Try the current version from here
http://www.scripps.edu/~arvai/adxv/
version 1.9.8 works fine for us and opens Pilatus data without modifying
the files.
Hope this helps.
Andrew Purkiss
--
X-ray Laboratory Manager,
London Research Inst
Hi Rajesh,
A simple thing I would try first is to try to open a different image. I'm a
bit suspicious about yours given the error messages you sent. Is this from
a Pilatus detector? The line "pixelsize = 0.172 mm" suggests this is so,
but at the bottom below all the warnings it looks like this val
Rajesh,
I think there is a simpler explanation to your problems but we need to
go back to the installation of adxv on your linux machine.
How did you extract adxv binary from the *.gz file?
I've actually learned yesterday that if you use graphic tools to
extract the binary the resulting f
Rajesh
I use adxv (as well as xemacs, xdsview, imosflm, hklview, ipdisp etc)
over ssh/Cygwin X11 from Windows XP to a Centos (like RedHat) server
with no problems at all.
I suspect your xming either just doesn't have the requisite X11 libs
or somehow they have not gotten installed on your system
Dear Tim,
Yes, I have windows 7 computer and use ccp4 and phenix through xming/putty and
I run them over linux lab computer.Sorry if I have confused you all with
insufficient information.On the lab linux system, I installed everything you
suggested in BASH and it works but not completely.Core
Dear Prof Dodson,
I agree with you. Instead of further refining mutant structure, right now I am
looking in to Apo structure. Which is at 2.74A and has R/freeR 22.7/27.9. But
I have a molprobity profile like this
Clashscore, all atoms: 33.73 50th percentile* (N=185, 2.740Å ±
0.25Å)
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Rajesh,
are you saying that the computer you are sitting in front of is a
windows computer?
Are you sure you have been using CCP4 and phenix through an
ssh-connection and not the respective windows-binaries?
I am not familiar with windows and th
I don't know if I need that installed on my windows computer terminal.On the
server also I could run adxv. Thought of using other ccp4 utilities.
Thanks for everyone for the help. I give up.
Regards,Rajesh
> Date: Mon, 21 Nov 2011 11:36:14 -0500
> From: ber...@upstate.edu
> Subject: Re: [ccp4bb]
Dear Filip
'Annoying' MR problems for which the answer often lies in relatively small
differences between the search model and 'RB-shifted' domains and/or subdomains
in the actual structure, are I think a good experimental indication of the
significance of such issues.
To extrapolate from this,
On 22/11/11 00:16, Jan van Agthoven wrote:
Hi everyone!
Does anyone know if there is a way of auto-refining a sugar in Coot?
Such a tool (if I understand correctly what you want) does not yet
exist. However, I believe that things are not in as poor a state as one
might infer from other posts
If you run scala after data integration, ( and thats a good idea whether
you have used any integration software - just get out the unmerged
scaled file - feed it through pointless to get useful info there, and
then scala/truncate to get more useful graphs and analysis) there isa
an option to
You can also try Jligand to generate your cif file
J
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jan van
Agthoven
Sent: Tuesday, 22 November 2011 1:17 p.m.
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] sugar and coot
Hi everyone!
Does anyone know if there is a way of auto
** Sorry for posting again, but I wanted to replace the subject by the
specific topic (my former subject was due to the dact that I use the
CCP4BB digest only) **
Dear Filip,
as Roberto mentioned earlier, our program Escet, respectively the RAPIDO
web server - http://webapps.embl-hamburg.de/r
Dear Filip,
as Roberto mentioned earlier, our program Escet, respectively the RAPIDO
web server - http://webapps.embl-hamburg.de/rapido/ - is taking
coordinate errors (as derived from DPI- or empirically scaled B-factors)
into account when judging the significance of structural invariance
(th
http://agoni.es/zine/wp-content/plugins/extended-comment-options/chivpld.htm
Hi Filip,
Would it be a worth-while exercise to make a histogram of the absolute
values of atomic displacements ? If the distribution is bimodal (as you
indicated that it may), then indicating statistical significance should be
much easier (and convincing ?).
My twocents,
Nicholas
On Mon, 2
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