Dear All,
Some more details.
I am running a Ubuntu 11.04 system. The ccp4i is recently installed.
I looked into our previous posts and tried to locate the ccp4.LOCK
file, but I cannot find one in my system.
Also tried to reinstall the whole ccp4i but hasn't solved the issue.
Also tried to delete t
Dear All,
I am getting the following error message when trying to execute any program.
Database Access Failure
This instance of CCP4i no longer has control of the current database..
It is recommending to close the interface and restart, but it is
coming back with the same error even after r
On 10/05/2011 07:25 AM, Jun Liao wrote:
Dear All,
These days, I want to calculate the surface curvature for my proteins in
a quantitative way and show the results in a graphics software such as
Pymol. Does someone have a good idea of which program will do a nice job?
If you are a C++ expert an
> Maybe it's just a sequencing glitch?
Not so--BLAST showed there are a whole cadre of these things in
various genomes. Go figure.
JPK
>
> JPK
>
>
> On Tue, Oct 4, 2011 at 4:05 PM, Jacob Keller
> wrote:
>> Thanks everybody, I tried using
>>
>> --toolkit tuebingen mpi
>> --Scanprosite
>>
>>
Just for kicks, check out this sequence I found in the process
(conjecture: maybe when the virus causes its synthesis, it uses up all
the cysteines/methionines!):
>sp|Q69566|U88_HHV6U Uncharacterized protein U88 OS=Human herpesvirus 6A
>(strain Uganda-1102) GN=U88 PE=4 SV=1
MYVSVSVHVSVHVSVRVSVRVS
Dear All,
These days, I want to calculate the surface curvature for my proteins in a
quantitative way and show the results in a graphics software such as Pymol.
Does someone have a good idea of which program will do a nice job?
Thanks in advance,
Best,
Jun Liao
Dept. of Physiology
UTSW medica
Dear all,
I tend to use Google's cached versions or
The web archive
http://www.archive.org/web/web.php
leading to
http://web.archive.org/web/20100814204611/http://www.bioscreencastwiki.com/Crystallography_Howtos/Installing_ccp4-6.0.99e_on_64_bit_Ubuntu
Hope this helps someone...
Best regards,
Hi,
On Tue, Oct 4, 2011 at 1:55 PM, Brigitte Ziervogel wrote:
> (...)
> Any suggestions or ideas of better ways to score ligand fits are
> appreciated, thanks.
>
another alternative:
phenix.model_vs_data model.pdb data.mtz comprehensive=true
will list triplet of numbers: {map CC, 2mFo-DFc val
Thanks everybody, I tried using
--toolkit tuebingen mpi
--Scanprosite
I think my regex syntax was different from the Tuebingen site's, but
scanprosite worked well and found many hits, although without really
hitting paydirt. I think both of these programs would do the job well,
though.
Thanks ve
Hi folks,
Anyone know if this site is temporarily down or is it more permanent?
http://bioscreencastwiki.com/Crystallography_Howtos/Installing_ccp4-6.0.99e_on_64_bit_Ubuntu
Cheers
Joel
_
Joel Tyndall, PhD
Senior Lecturer in Medicinal Chemistry
National School
Hi,
I am using the program Overlapmap to calculate real-space R-factors and
correlation coefficients in order to find ligand conformations that fit best
within the density.
I'm confused by the Overlapmap output, which includes "Fobs" and "Fcalc" values
that are used to calculate the R-factors
Hi Jacob,
SCAN PROSITE
http://prosite.expasy.org/scanprosite/
will do precisely what you want.
C-X-C-X-C-X-C
or
C-X-C-X-C
would be the pattern using Prosite syntax.
Cheers,
Dave
David C. Briggs PhD
Father, Structural Biologist and Sceptic
=
Thanks Ian, I'll keep posting :)
Brigitte
Original message
>Date: Tue, 4 Oct 2011 21:19:40 +0100
>From: Ian Tickle
>Subject: Re: [ccp4bb] Calculate real-space R-factor/corr coeff for ligand
>To: bkziervo...@uchicago.edu
>Cc: Adam Ralph , CCP4 bulletin board
>
>
> On Tue, Oct
Dear Crystallographers,
I cannot get BLAST to find all proteins with the motif cxcxcxc or at
least cxcxc. It seems to think of "x" as an actual amino acid rather
than a wildcard. There must be some easy way to do this? Ordinarily to
find a short motif, I would just paste the sequence and get the
a
On Tue, Oct 4, 2011 at 7:14 PM, wrote:
> Hi Adam and Ian,
>
> Thanks for your help. If I re-calculate the R-factors with the correct
> absolute values I get more reasonable values. However, I'm still a bit
> confused because the output given by the Overlapmap program is structure
> factor value
At first glance, it looks like it could be
modeled by a partially reduced carboxylate (to aldehyde or
carbonyl radical). Is there any precedent for such a
radiation-induced photoelectron reduction? Like you, I only
remember seeing decarboxylations of Asp and Glu.
Thank you all. I had forgotten about checking pdb record formats..
Eleanor
It works when you follow the rules!
On 10/04/2011 05:05 PM, Frances C. Bernstein wrote:
I checked back and the 1992 format decscription did not use
columns 77 - 80 for ATOM/HETATM records. But the 1996 document
did use
I checked back and the 1992 format decscription did not use
columns 77 - 80 for ATOM/HETATM records. But the 1996 document
did use them. I then checked the old Newsletters and the proposed
use of columns 77 - 80 was discussed in April 1995.
Frances
===
On Tue, Oct 4, 2011 at 4:41 PM, Eleanor Dodson wrote:
> OK
>
> So the ATOM TYPE has ZN O C S etc in column 77/78 and the +2 etc in 79/80
>
> Is there any documentation for this?
>
> E
Yes, see:
ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v33_A4.pdf
Though this has been the forma
I think it is a pdb rule. Here are some of the rules:
http://www.wwpdb.org/documentation/format33/sect9.html
Charges (confusingly) could be 2+ etc.
Regards
Garib
On 4 Oct 2011, at 16:41, Eleanor Dodson wrote:
> OK
>
> So the ATOM TYPE has ZN O C S etc in column 77/78 and the +2 etc in 79/80
OK
So the ATOM TYPE has ZN O C S etc in column 77/78 and the +2 etc in 79/80
Is there any documentation for this?
E
On 10/04/2011 03:56 PM, Garib N Murshudov wrote:
If you will put element names in correct positions then refmac may have a
chance to find it. Here is corrected positions:
AT
*CALL FOR PROPOSALS FOR ESRF BEAM TIME WITH ONLINE MICROSPEC*
Proposal Deadline *21st October 2011*
There will be beam time available at the ESRF for MX data collection
with a setup that allows online monitoring of UV/VIS absorbance or
fluorescence spectral changes of the crystal during the X-
If you will put element names in correct positions then refmac may have a
chance to find it. Here is corrected positions:
ATOM 1893 O HOH A 258 -8.934 52.268 49.467 0.00 66.53 O
ATOM 1894 ZNZN B 1 -10.456 38.580 26.267 1.00 57.36 ZN+2
ATOM 1895 O
Can anyone advise me how to get the Zn+2 formfactor from atomsf.lib
The input coordinate is given atom type ZN+2 but the formfactor is that
for Zn:
I changed the atom name to Zn+2 but that made no difference...
ATOM 1893 O UNK A 258 -8.934 52.268 49.467 0.00 66.53
O
ATOM 1
Ooops (.03+.01+.01+.01)/(.19+.01+.09+.09) = .16
-- Ian
On Tue, Oct 4, 2011 at 12:22 PM, Ian Tickle wrote:
> On Tue, Oct 4, 2011 at 11:21 AM, Adam Ralph wrote:
>
>> Dear Brigitte,
>>
>>
>> Looking at the formulae it could be possible to get those results.
>> Take an example
>> below
>>
>>
On Tue, Oct 4, 2011 at 11:21 AM, Adam Ralph wrote:
> Dear Brigitte,
>
>
> Looking at the formulae it could be possible to get those results.
> Take an example
> below
>
>
> Rho_cal = -0.11, 0.0, 0.05, 0.05
> Rho_obs = -0.08, 0.01, 0.04, 0.04
>
>
> R-fac = 0.02/0.0 = undefined
Dear Brigitte,
Looking at the formulae it could be possible to get those results. Take an
example
below
Rho_cal = -0.11, 0.0, 0.05, 0.05
Rho_obs = -0.08, 0.01, 0.04, 0.04
R-fac = 0.02/0.0 = undefined
Correl = 0.0032 - (-0.0025*0.0025)
-
Beryllium chloride is very toxic. More care is needed when preparing it.
在 2011年10月4日 上午7:35，Peter Hsu 写道：
> Sorry for the very off topic and dumb question, but does anyone know if BeCl2
> needs to be prepared fresh for use (making BeF3) or can it be stored as a
> solution stock at room temp
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