Thank you Sir.
With Regards
Kavya
> So there is a CCP4 GUI
>
> Just prepare a txt file with the relevant occupancykeywords and use it in
> the GUI under 'Refmac keyword file'
>
> Best
> R
>
> From my iPhone
>
> On 12 Apr 2013, at 19:50, "Kavyashree Manjunath"
> wrote:
>
>> Respected Sir,
>>
On 04/12/2013 06:03 PM, Nat Echols wrote:
On Fri, Apr 12, 2013 at 2:45 PM, Boaz Shaanan
mailto:bshaa...@exchange.bgu.ac.il>> wrote:
Whichever way the input file for the run is prepared (via GUI or
command line), anybody who doesn't inspect the log file at the end
of the run is doome
On Fri, Apr 12, 2013 at 2:45 PM, Boaz Shaanan
wrote:
> Whichever way the input file for the run is prepared (via GUI or command
> line), anybody who doesn't inspect the log file at the end of the run is
> doomed and bound to commit senseless errors. I was taught a long time ago
> that computers a
Waters are moved during annotation using the perceived space group's
symmetry operation. So if the authors give the wrong space group, then the
annotation pipeline understandably messes things up. If the originally
uploaded PDB file was kept by PDBe, then the problem can be recovered quite
easily b
Hi Nat,
Whichever way the input file for the run is prepared (via GUI or command line), anybody who doesn't inspect the log file at the end of the run is doomed and bound to commit senseless errors. I was taught a long time ago that computers always do what you
told them to do and not what yo
My experience is also that the bulk solvent model sometimes makes the mask
exclude internal large cavities.
Laurie Betts
On Fri, Apr 12, 2013 at 12:03 PM, Pavel Afonine wrote:
> P.S.: you are not alone having such R-factors
>
> On Fri, Apr 12, 2013 at 9:50 AM, Jan van Agthoven wrote:
>>
>>> Co
In this particular case attempting to calculate R-factor using data and
model files and making sure that the R you get is not twice as large as
published one would entirely suffice -:)
Pavel
On Fri, Apr 12, 2013 at 12:42 PM, Eugene Osipov wrote:
> In my opinion pdb must perform more strict chec
It is typo:
R factor for p212121 - 0.4
for p21212- around 0.18
Although water seem to have been moved around using p212121
On 12 Apr 2013, at 16:33, Phoebe A. Rice wrote:
> Looks like a typo to me: if you change the CRYST space group record from
> P212121 to P21212, as th
i meant to say P21212
On 12 Apr 2013, at 21:47, Savvas Savvides wrote:
> The CRYST1 in the pdb header is problematic.
> CRYST1 95.520 47.815 88.570 90.00 90.00 90.00 P 21 21 218
> it looks like the number '1' was paired to the space group rather than the
> space grop number (i.e.
The CRYST1 in the pdb header is problematic.
CRYST1 95.520 47.815 88.570 90.00 90.00 90.00 P 21 21 218
it looks like the number '1' was paired to the space group rather than the
space grop number (i.e. nr. 18 for P21212)
Table 1 in the paper specifies P212121 as the space group.
In my opinion pdb must perform more strict checks of structures. I can
remember at least 2 structures without OXT entry for C terminal tail . Of
course rcsb won't accept my fixes. As graduate student I am not sure that
I can point out mistakes to unknown author
12.04.2013 23:34 пользователь "Eugen
This explains why I cannot reproduce published R-factors (with files from
PDB I get ~40%). If I force my favorite refinement program to use P21212
then I get R close to reported in PDB file header.
This makes it worth reminding that it's rarely a good idea to edit PDB file
out of refinement.
Pavel
Not only 118, look at 119 . It seems also that residues 82-88 incorrectly
placed . I think that authors (if they are reading this board ) must fix
errors. To be honest this is not first time I see such models.
12.04.2013 23:17 пользователь "Michel Fodje"
написал:
By the way, you will need to sho
Looks like a typo to me: if you change the CRYST space group record from
P212121 to P21212, as the paper says it is, the packing problem goes away.
++
Phoebe A. Rice
Dept. of Biochemistry & Molecular Biology
The University of Chicago
773 834 1723; pr...@u
By the way, you will need to show symmetry atoms to see the problem.
>-Original Message-
>From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
>Michel Fodje
>Sent: April-12-13 1:14 PM
>To: CCP4BB@JISCMAIL.AC.UK
>Subject: [ccp4bb] Puzzling Structure
>
>Has anyone else notic
Has anyone else noticed a problem with the structure of the N-terminal capsid
domain of HIV-2 PDB 2wlv.
Load it up to in coot and navigate to residue B118.
/Michel.
On Apr 12, 2013, at 12:44 PM, eugene.krissi...@stfc.ac.uk wrote:
> What, I'm afraid, people rarely realise these days, is that their desktops
> are, essentially, GUIs to various OS features, so they obviously use GUI more
> frequently than they think :) After all, this is all matter of habits an
What, I'm afraid, people rarely realise these days, is that their desktops are,
essentially, GUIs to various OS features, so they obviously use GUI more
frequently than they think :) After all, this is all matter of habits and
training, and the reality is that people get more and more GUI-orient
So there is a CCP4 GUI
Just prepare a txt file with the relevant occupancykeywords and use it in the
GUI under 'Refmac keyword file'
Best
R
>From my iPhone
On 12 Apr 2013, at 19:50, "Kavyashree Manjunath" wrote:
> Respected Sir,
>
> I saw this option in refmac5 - 5.6.0037, (I use
> refm
I agree with Nat. There are good GUIs and bad GUIs, just like there are
good command-line programs and bad command-line programs. Bad programs
are easy to write and good ones are hard. Conservation of "work" I think.
-James Holton
MAD Scientist
On 4/12/2013 10:38 AM, Nat Echols wrote:
On F
Respected Sir,
I saw this option in refmac5 - 5.6.0037, (I use
refmac5-5.6.0117), but is this option present in
GUI?
Thanking you
With Regards
Kavya
> Dear Kavya
>
> What about using occupancy refinement in refmac?
> link http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/ follow occupancy
> refinem
On Fri, Apr 12, 2013 at 10:27 AM, James Holton wrote:
> But, when it comes to GUIs, I have always found them counterproductive.
> In my humble opinion, the purpose of computers and other machines is to DO
> work for me, not create work for me, and I already have enough buttons to
> push each day
Alright, alright,
I should thank Eugene for being such a good sport. And I should also
apologize for all the work I just created for him!
I fully appreciate all the years and years of effort and struggle that
has gone into making ccp4i and other crystallographic GUIs the
accessible tools
Measuring Angles is another matter, but the superposition services of
the DrugSite will align an arbitrary selection of DNA residues (the
moving molecule) onto a target residue selection on another
structure. The selection can include a duplex, or even a duplex and
some protein residues.
P.S.: you are not alone having such R-factors
On Fri, Apr 12, 2013 at 9:50 AM, Jan van Agthoven wrote:
>
>> Could this be due to an excessive low R
>> factor that phenix.refine has generated: R=17.9 and Rfree=23.3 at a
>> resolution of 2.85 A?
>
>
Histogram of Rwork for models in PDB at resolutio
Hi,
not knowing other details, the most naive guess is that this may be a
footprint of mask-based bulk-solvent model. Next one is that you are
contouring at too low/high level (note, sometimes, if, for instance,
solvent content is high, you need to look above/below 3sigma). Of course,
there could
Dear Kavya
What about using occupancy refinement in refmac?
link http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/ follow occupancy
refinement.
R
On 12 Apr 2013, at 17:12, Kavyashree Manjunath
wrote:
> Dear users,
>
> Is it advisable to refine the occupancy of
> a ligand for a 2.0Ang data by
Dear users,
Is it advisable to refine the occupancy of
a ligand for a 2.0Ang data by approximately
changing the values of occupancy based on
its b-factor?
After refinement, there were some negative
densities appearing in some parts of the
ligand, like at the centre of a pyrimidine
ring, so I expec
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Peer,
can you send the output of the command
ls -l /share/prog64/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif
Best,
Tim
On 04/12/2013 04:11 PM, Peer Mittl wrote:
> Dear Colleagues,
>
> For some reason Refmac refuses to read the file "mo
Dear Colleagues,
For some reason Refmac refuses to read the file "mon_lib_list.cif" athough the
file exists. The error message is as follows:
Open failed: Unit: 7, File:
/share/prog64/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif (logical:
/share/prog64/ccp4-6.3.0/lib/data/monomers/l
LSQMAN aligns just about anything, incl. DNA and RNA -
http://xray.bmc.uu.se/usf/lsqman_man.html
There's a ready-to-use macro that will do all the hard work for you -
ftp://xray.bmc.uu.se/pub/gerard/omac/align_rna.lsqmac - there's one line that
may need editing, it defines the name of the nomi
Doesn't lsqkab work? It just needs proper atom matching.
Coot definitely does superimpose DNA. One problem is that simple-lsq works on
a single chain, but you can trick it by changing chain id and renumbering the
other strand.
As for helix rotation, you can derive it from rotation reported by
Hi,
This questionnaire is designed to test the hypothesis that developments in
Structural Biology methods are creating a need for new forms of facility
access, processing and modelling software, and data archives:
http://www.surveymonkey.com/s/ZH565SN
We would be very grateful for your input
Hi Phil,
Since these will be mostly used for numbers, and supplied only if BBSRC change
their mind about wanting to see the specific letters, I would say that people
doing high impact research (which should include anyone who has been funded),
might contribute their penny's worth. We will be
Dear BBer,
As I hope you are all aware CCP4 has been well supported throughout its
existence by BBSRC grant income. This Research Council funding is vital for the
continued success of the CCP4 collaboration and to support its software
development, distribution, and out-reach activities. This
Hi
I'd second NX; you can install a free server for one or two (I think - I only
use one at a time ;-)) concurrent connections and a local client, then it's
almost "like being there".
On 11 Apr 2013, at 22:54, Dyda wrote:
> Or nx, which works very well, although the server has to be installed
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