Hi all.
I'm rather surprised that Jalview has yet to be mentioned:
http://www.jalview.org/
Although I've heard that ESPript can make the best looking figures, Jalview
is also capable of generating very beautiful output, and I've found it
reasonably intuitive and plenty powerful.
I'm not fond of
Dear James:
This is really the easiest and a very smart way to get around this
problem. I generated a PDB only only my interest region, which serves to
produce a mask encomprassing only this region. The last "Total" line in
the output should be it. Everything is cool except that some terminal
resi
The easiest thing to do is to make a PDB file that contains ONLY the
residues you are interested in and set all the residue numbers to "1".
Use this PDB file to calculate the "MODE ATMMAP" and the "MODE ATMMAP
RESMOD" maps with SFALL. Then OVERLAPMAP (in "correlate residue" mode)
will give yo
Hi Pavel:
This is actually something I am doing right now. Yes, sometimes it is
always better to try it practically.
Best Regards, Hailiang
> Hi Hailiang,
>
> On 5/25/10 8:14 PM, Hailiang Zhang wrote:
>> Have seen the real-space correlation used widely judging the map
>> quality.
>> Generally or
Hi James:
Actually I did OVERLAPMAP calculation in this way. I first flagged the map
grid points by using the provided pdb information, which serves as
"mapin3" for the OVERLAPMAP calculation. However, the calculated CCs or
RSRs are either based on each individual atom, residue or map section, but
Hi Hailiang,
On 5/25/10 8:14 PM, Hailiang Zhang wrote:
Have seen the real-space correlation used widely judging the map quality.
Generally or empirically, in order to say an map (area) has "good"
quality, how large should the real space correlation coefficient be? Say,
is 0.8 good enough on a re
OVERLAPMAP will do this, but you need to calculate a "label map" with
SFALL first and provide that to OVERLAPMAP as "mapin3", as MW and others
have pointed out already.
RTFM:
http://www.ccp4.ac.uk/dist/html/overlapmap.html#notes_mapin3
http://www.ccp4.ac.uk/dist/html/sfall.html#mode_atmmap_resm
Hailiang Zhang wrote:
Hi Eleanor:
Do you have some references in mind that discussed the value of CC (say
0.5) to be able to build the structure? Didn't find one for right now:-(
Lunin and Woolfson, (1993)
http://scripts.iucr.org/cgi-bin/paper?he0076
Hi Eleanor:
Do you have some references in mind that discussed the value of CC (say
>0.5) to be able to build the structure? Didn't find one for right now:-(
By the way, probably a "weak" question, In the case "a lousy model will
give poor CCs even if the map is brilliant", we still accept this m
Dear Eleanor:
Yes, this is something I want to do (RSR and CC). But I just want to do
the calculation based on a group of residues or atoms, and it seems
OVERLAPMAP doesn't do it, so I think I have to find other ways.
Hailiang
> mapdump does this if you select the right flags. But as Ian says yo
I see. It is like the CC for each "slide" along the Z direction. But, do
you know does CCP4, or any other programs, calculate CC for a group of
residues at all?
Thanks!
Hailiang
> You might find some useful examples in $CCP4/examples/unix/runnable
> OVERLAPMAP is used in mapcorrelation_procedure
Dear Rex,
It might still be while before a structure of a full-length voltage-gated
sodium channel (or voltage-gated calcium channel) comes along. Keep an eye
on the NaChBac channel (originating from Bacillus species), as this
prokaryotic sodium-selective channel will likely be the first to repre
Hello all
I am novice to this field and trying to crystallize a protein-protein
complex verses DNA i.e a ternary complex of protein complex and DNA, which
stochiometry is 2:!.
I am wondering
1-what should be the DNA and protein ratio for the ternary complex like this
typically for binary complex i
PISA's interface area is 1/2 of sum BSAs for the interfacing
structures. If you go to
interface details, you also get total area of structures and their
individual BSAs.
The latter I should think would be an overinterpretation if used.
Eugene.
On Wed, May 26, 2010 at 1:45 PM, Sollepura Yogesha
You should take a look at DIFFMODE COMPARE keyword in AREAIMOL manual,
it allows for buried surface area calculation (you have to prepare the
two pdb files with complex and receptor only). If you can easily use
command line and scripts (i.e. you are running CCP4 on non-micro$oft
OS), try the follo
Dear All,
I am trying to calculate BSA (Buried surface area) for a protein complex. I am
using CCP4 AreaIMol.
I used Accessible surface area module and calculate areas for " protein atoms
only"
I know that the buried surface area (BSA) can be calculated as: BSA = ASA(A) +
ASA(B) - ASA(AB)
I believe SSM does just that:
http://www.ebi.ac.uk/msd-srv/ssm/
Eugene
On Tue, May 25, 2010 at 7:39 PM, Muhammed bashir Khan
wrote:
> Dear All;
>
> Can some body tell me a website for structure based sequence alignment,
> which can also pin point the similar and identical residues in different
Does anyone know of the existence of a structure for a voltage gated Na (not K)
channel?
Rex Palmer
Birkbeck College, London
If you ask for CORR SECTion then overlapmap does just that - the CC will
have a certain value for each section regardless of the CHAIN
parameters. If you want correlation residue by residue you must ask for
CORR RESI
As someone said - a lousy model will give poor CCs even if the map is
brilli
mapdump does this if you select the right flags. But as Ian says you
will get a LOT of numbers. You dont say why you want this information,
but if it is to find the electron density at an atom site overlapmap
will do that if you ask for "real space rfactor"
eleanor
Hailiang Zhang wrote:
Hi,
Muhammed bashir Khan wrote:
Dear All;
Can some body tell me a website for structure based sequence alignment,
which can also pin point the similar and identical residues in different
colors.
regards
Bashir
PISA does just this - go to the ebi web site and select pisa
You might find some useful examples in $CCP4/examples/unix/runnable
OVERLAPMAP is used in mapcorrelation_procedures, overlapmap.exam,
waterpeaks.
As I understand it, CORR SECT does a map correlation by map section, so
you get a single CC value per map section.
This mode does not use MAPIN3, and do
Thanks Roger,
that worked perfectly!
I'll try and have fun with aline now.
ciao,
s
On May 25, 2010, at 7:56 PM, Roger Dodd wrote:
> Hi there,
>
> I just got this working a couple of days ago under Mac OS X 10.6.3. I
> manually compiled and installed Perl-Tk from CPAN. Steps taken:
>
> 1. Down
Another tool you can use is RAPIDO (http://webapps.embl-hamburg.de/rapido). It
identifies rigid bodies between the two structures and already produces pyMol
scripts for the superposition both on the entire structure and on the single
rigid bodies.
A more complete list of the tools you can use c
Another alignment tool worth to keep an eye on is this one:
http://foldit.wikia.com/wiki/Alignment_Tool
They are still debugging, but the plan is to release a standalone
version after CASP9. Or at least a version that runs in a standalone
FoldIt version.
On Tue, May 25, 2010 at 15:18, Victor A
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