Yanming Zhang schrieb:
Hi, All,
After lunching pymol, if I drag the Xterm window produced by PYMOL using
mouse, my computer will suddenly freeze, the keyboard seems no longer
functioning. The only thing I can do is to re-boot my Linux system. This
problem makes it almost impossible for me to
Dear ccp4bb readers,
Two research positions funded by the Norwegian Research Council will be
available starting in January 2008 at the University of Tromsø, Norway. A PhD
student and a postdoctoral scientist will study structural selectivity
determinants of protein kinase ligands and ramificati
You need the atom name CA and CL moved one space to the left relative to
C O N etc..
And correct the atom type in cols 76?? from C to CL and CA ( again moved
one space to left)
Eleanor
Vineet Gaur wrote:
Hi all
i am having Ca2+ and Cl- as hetroatoms in my protein structure. while doing
refin
Hi there!
here's my original post:
Hi all,
I'm starting using pymol to generate movies to show my structure.
While its seems fairly easy to generate simple movies with rocking
or rotating molecules, I have been finding some difficulties
understanding how to generate more complex movies.
For i
Dear CCP4 Users,
I'd like to solve the structure of the protein-protein complex. I
intend to purify and incubate the complex then run gel-filtration
before setting crystal.
I'd like to know your experience about the Kd value of the interaction
in order to get the complex after running the gel-filt
Dear ccp4BB,
Sorry for the non-ccp4 post.
I have been using a NEC DVD_RW ND-2500A drive to archive onto DVD-Rs
(using 'mkisofs' and 'dvdrecord' commands) from our RH linux system.
This has worked very well with 8x compatible DVD-R disks, but doesn't
recognise the newer 16x disks that only seem t
Hello,
I wonder if there was any direct answer to the question that Lari made a
couple of days ago.
Sorry if I missed it, but I believe there wasn't any response to the
ccp4bb...
thanks
Alejandro
Lari Lehtio wrote:
Dear All,
I just came back from the beam line and started to continue
I think this isn't a problem in the latest version of Refmac (0040 I think), so
try downloading it from the York site.
-- Ian
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of Alejandro Buschiazzo
> Sent: 19 September 2007 13:20
> To: Lari Lehtio
>
Hi Dave,
I have found in the past that some DVD writers need a bios / firmware
upgrade to be able to cope with the faster DVD's. Usually this is a
windows program you run which overwrites something inside the DVD
hardware itself, which will then work fine for writing. This is unlikely
to be helpfu
Hi,
Indeed, I just tested version 5.3.0040, and there the ANISO seems to work.
~L~
___
Lari Lehtiö
Structural Genomics Consortium
Medical Biochemistry & Biophysics Dept.
Karolinska Institute
Stockholm, Sweden
__
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of Victor Lamzin
> Sent: 18 September 2007 12:48
> To: [EMAIL PROTECTED]; CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] arp/warp in p22121
>
> Dear Florian,
>
> ARP/wARP supports 65 space groups where pr
Sounds like an OpenGL graphics driver misconfiguration to me. What is the
graphics card and driver, and like Kay asked, how was the driver configured?
A friend's computer at one of the lab's here had similar issues, turns out
the NVidia driver was severly misconfigured. Fixed following the re
Dear all,
we are in the progress of 'collecting data' on a sealed
tube machine which we want to buy. I know that this issue
was handled several times here and I also looked through
older mails. However, my impression is that the generators
that are offered change quite quickly according to recent
Acording to the product specs from NEC that drive model is only designed to
write up to 8X speed, it was never intended to write any faster. Nothing
wrong with the drive, it just is not designed to burn any faster. For
burning 16X discs at 8X speed, maybe a firmware update, or maybe it is a
s
I used Refmac 5.3.0037 to refine a structure. Is there a problem with this
version too?
Thank you in advance,
Madhavi
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Ian Tickle
Sent: Wednesday, September 19, 2007 8:21 AM
To: CCP4BB@JISCMAIL.AC.UK
Subje
Hello,
The Macromolecular Structure Database (MSD) group
(http://www.ebi.ac.uk/msd/) is currently looking for suitable candidates
to fill in three job vacancies (Scientific Database Curator, Scientific
Programmer and Software Engineer) at the EBI, Hinxton (near Cambridge,
UK). Interested candi
The problem is specifically that ARP/wARP *doesn't* support the IUCr
convention as given in IT (Vol. A, >= 1983 edition, Table 9.3.4.1, p.758
in 5th ed.) regarding choice of cell in primitive orthorhombic space
groups, and I suspect in centred monoclinic ones also. AFAIK ARP/wARP
and pointless ar
I'm confused now, sticking to the IUCr convention should not require any
axis permutation. My beef is specifically against unnecessary axis
permutations! Surely it's when the program doesn't support the
convention that you are forced to permute the axes?
Besides I did solve a structure in P22121
Dear all,
just checking my cofactor dictionary produced with prodrg in refmac I
realized that the torsion restraints are not taken into account with my
default settings. I noticed the old posting from 2001, that "var_" is
not used, but if I input an additional line by hand with
restr tors inc
Hi Sue
It's certainly true that the convention in the 1935 and 1952 editions of
IT Volume 1 *appeared* to be the 'standard setting' convention that you
describe because only the 'standard' settings were listed, and this was
the way that many crystallographers interpreted it (actually only
macromol
On second reading maybe I misunderstood what you were saying. If Phaser
reads an MTZ file which doesn't conform to the convention (e.g. a<=b<=c
NOT true in primitive orthorhombic) then it certainly should not by
default permute the axes on output, I agree that that certainly would
cause confusion.
I do not know about the affinity required for gel filtration, but I have
had success crystallizing a number of protease-inhibitor complexes just
by incubating and setting up drops with equimolar amounts of the two
components. It is probably to our advantage that we have functional
inhibition ass
Dear TriNgo,
The Kd is only 1/2 of the picture. You also should contemplate the
consequences of the on and off rate for the complex formation. If the off
rate is in the range of minutes then you can have successful purification
over size exclusion even though the Kd may be high micromolar.
Other
Hello,
This density is the 'evil sausage-like blobule' that tends to crop up
whenever something ill-defined (but sausage-like) binds weakly to the
surface of the protein. It could be almost anything - something from the
polyacrylic acid, something from Triton (it has lots of sausage-like
shapes),
So I vote for a default of preserving the input convention whatever it
is, and I definitely vote against all axis permutations unless a) it's
absolutely necessary (e.g. for consistency with other datasets), and b)
the user specifically requests it (and really really means it!).
Phew! It makes
Joe,
I think this is neither a constructive or accurate statement. I
have collaborated with the PDB (both the RCSB and the EBI) for many
years and I believe that they are doing a very good job under very
difficult circumstances. They have been tasked with curating an ever
increasing vol
Nevertheless, there is a huge problem with interoperability between
software packages, and this core issue greatly frustrates everyone, not
only Joe.
Frankly, it is a disgrace that even in 2007, software users in
structural biology and computational chemistry still cannot reliably
exchange basic m
Dear Colleagues,
Warren makes a good point, but let me recast it slightly. We are
all part of the structural biology community, and we, as a community,
need to get together and explore our options for interchange of
information. Some of us already have a proposal pending with the
NSF for a co
By the way, I would like to mention that I was sloppy with the language in
the original reply - I was referring to complex half-life (T1/2) which is
expressed in direct units of time, not the kon or koff, which are expressed
in inverse units of time. Thank you Raji Edayathumangalam for pointing thi
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