As Joel has suggested before, alphafold on an IDP would be interesting
and would seem like a zero-cost starting point - perhaps one you have
tried already.
Sent from ProtonMail mobile
Original Message
On 15 Aug 2021, 15:53, Scott Horowitz < scott.horow...@du.edu>
This is precisely why SHELX always used the coordinates of the general
position (LATT+SYMM) to define the space group rather than a name or number.
George
On 22/07/20 14:15, Ian Tickle wrote:
Hi David
The problem is that the PDB incorrectly used the H lattice symbol
(without consulting any
Dear Matthias,
That is very strange. First please repeat the shelxl refinement with the
occupancy of the offending chlorine(s) in the .ins file changed from 11
(i.e. fixed at 1.0) to 1.0 (i.e. freely refined starting from 1.0). If
that does not help I would be happy to look at it in
As explained in the attached email from Peter Keller, I was deliberately
preparing the binary Linux SHELX distribution using older (2011) system
libraries so that the programs would run on older systems that many
users are still using. Unfortunately this means that they do not run on
some
I'm afraid that I have to disagree with Eleanor, a very rare event. Both
pure SIR and pure SAD give you only half of the necessary phase
information. The initial map will in both cases be a double image. One
then tries to improve it by density modification. For pure SAD one image
is positive
. for sulphur-SAD phasing. Although shelxd
is still used it has not been changed for decades and needs to be
brought up to date. Anyone interested should contact me by email.
George Sheldrick
--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry
University of Goettingen
Tammannstr. 4s
SHELXE 2019-1 may now be downloaded from the shelx server at
shelx.uni-goettingen.de. With default parameters this version traces
structures with good resolution and phasing power faster, for difficult
structures see 'recent changes' on the shelx homepage or the summary
printed when the
To put the record straight, despite our efforts SHELXE is not currently
multiply threaded, but ARCIMBOLDO is able to run several copies of
SHELXE simultaneusly (which can be more effective). On the other hand
SHELXL, SHELXD and SHELXT (widely used to solve small molecule
structures) are
A particularly useful command line option in SHELXT for such cases is
-L15 to try all trigonal and hexagonal space groups. SHELXT is included
in recent CCP4 distributions and is also available with documentation
from shelx.uni-goettingen.de
George
On 02.08.2018 15:53, Aaron Finke wrote:
Hi
there are/were even more prolific candidates
Best, BR
*From:*George Sheldrick
*Sent:* Wednesday, July 4, 2018 16:17
*To:* b...@hofkristallamt.org; ccp4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] Oxford University Press
Dear Bernhard,
I agree with you sentiments, but was wondering which 'poor Russian
/wiki/Elsevier#cite_note-28>
A complaint about Elsevier/RELX was made to the Competition and
Markets Authority
<https://en.wikipedia.org/wiki/Competition_and_Markets_Authority>.^[29]
<https://en.wikipedia.org/wiki/Elsevier#cite_note-29>
On 2 July 2018 at 08:01, Georg
Since neither I nor my university can afford Elsevier journals, I have
no access to papers published in them. In view of their excessive
profits, for some years I have not submitted papers to them and have
declined all requests to referee for them. If everyone did that, they
might reconsider
For small molecules, programs such as SHELXT move the structure to be as
near as possible to the center of the unit-cell, not the origin. Failure
to do so may cause a 'checkCIF alert'.
George
On 06/21/2018 09:34 PM, John Berrisford wrote:
From a PDB deposition point of view, I echo Paul’s
This discussion has not convinced me to stop using Fortran. FORTRAN66
programs such as SHELX76 still compile and run unchanged with modern
Fortran compilers, though I do use a few useful features introduced in
FORTRAN77 and FORTRAN90 such as character handling and run-time memory
allocation.
Dear Charles (and CCP4 users),
I was delighted to see that CCP4 update 057 at last includes Anna
Luebben's pdb2ins, which we had been requesting for months and is very
useful for preparing the two input files needed to run shelxl.
Unfortunately you were too modest to mention this in your
Dear Rafal et al,
With some help from Kay I think that I could find out what is happening
here. SHELXT finds the space group Ibca and solves the structure easily
with default parameters but has difficulty in assigning the elements
because it was not expecting arsenic (!). The data are not very
Here is another attempt from my old email address. I was not registered
to use the email lists from my
new address, but please use it in future!
New versions of SHELXE, SHELXL and SHELXT and also Anna Luebben's
program pdb2ins that provides
a quick way of setting up a shelxl refinement given a
Dear Abhishek,
Maybe Paul had forgotten that shelxl was designed to read 80 column
punched cards.
To check against overrun it was checking that column 80 is a blank. I
may be able to fix
this in the next version of shelxl. For the moment you will have to do
some hand editing,
e.g. using
Dear James.
What small molecule programs report often looks like:
R1 = 0.1550 for 17413 Fo > 4sig(Fo) and 0.2058 for all 23715 data
R1(Free) = 0.2208 for 1938 Fo > 4sig(Fo) and 0.2766 for all 2635 data
from a well-known small molecule program being (mis)used to refine a
protein.
Over 50 years ago, a Toepler pump that I had glass-blown myself
developed a crack that caused several kilos of mercury to hit tha
ceiling and give me a shower. Fortunately I did not then know how
poisonous it was and suffered no ill-effects
George
On 12.09.2017 19:46, James Holton wrote:
Dear Carlos,
You are correct. I reinstalled CCP4 two days ago and also got version
0044 and that did not incude the new shelxe_2017-1. However the new
shelxe is definitely on the shelx server. It is a single statically
linked executable with no dependencies (!) so you can simply replace the
Dear Graeme,
The WIGL instruction in SHELXL does exactly that, and has some useful
options.
http://shelx.uni-ac.gwdg.de/SHELX/shelxl_html.php#WIGL
Best wishes, George
On 08/17/2017 05:17 PM, Graeme Winter wrote:
Dear All,
Is there a protocol out there to gently perturb atomic positions so
A new version 2017-1 of SHELXE is available for downloading from the
SHELX server. See /recent changes/ on the SHELX homepage at
shelx.uni-goettingen.de for details. The most important changes
(contributed by Isabel Uson) should extend the chain tracing to lower
resolution. Since this requires
Just to confirm what Eleanor said: all SHELX programs prefer to be given
intensities but can accept F if the intensities have been lost.
Converting intensities to F (e.g. with ctruncate) and back again
degrades the statistics for the weak reflections and is discouraged. The
same applies to
Dear Murpholino,
I must apologize, there was a mistake in may last email. The critical
parameter is, as you correctly pointed out, DSCA not RIPW and it is
necessary to try a range of values for DSCA. For this reason I am CCing
this to CCP4bb.
As you will be discovering, RIP phasing is not
Dear Murpholino,
I suspect that the pipelines in CCP4i and CCP4i2 do not include RIP
phasing (perhaps they should) but you can also run the SHELX programs
from a command line since you don't like black boxes. SHELXC reads
XDS_ASCII.HKL files and has some special facilities for RIP, you can
Dear Paul,
As you suggest, small molecule crystallographers are used to such
complicated situations and often use SHELXL for the purpose. Since you
fortunately have 1.0A data you could do the same, first using pdb2ins to
convert your PDB file to a SHELXL .ins file. You will need to use PART
Dear Bernhard,
After Kay showed me how to do it by making SHELXL parallel, I was able
to make SHELXD, ANODE and SHELXT (my current small molecule direct
methods program) highly parallel. I'm still working on SHELXE because it
requires major changes. In principle chain tracing is difficult to
Dear Francis,
You need to put the atoms starting with CG into PART -1 to prevent them
clashing, and reset the occupancies to 10.5 (i.e. fixed at 0.5). There
must be another disorder component pointing somewhere else (also with
half occupancy).
SHELXPRO has been made obsolete by Anna
ch"
resolution-extended data.
Best wishes, George Sheldrick
On 28.12.2016 11:43, 张士军 wrote:
Dear Kay
You mean after convert .phs to .mtz ,use the .mtz file refine the initial
structure model? By the way , what's the difference between this density map
with the density map modified af
best wishes
Phil
On 25 Oct 2016, at 20:31, George Sheldrick<gshe...@shelx.uni-ac.gwdg.de> wrote:
SHELXL may be used to refine both small and macromolecular structures against
X-ray or neutron diffraction data, including non-merohedral twins. A new
version 2016/6 of SHELXL may now be dow
SHELXL may be used to refine both small and macromolecular structures
against X-ray or neutron diffraction data, including non-merohedral
twins. A new version 2016/6 of SHELXL may now be downloaded from the
SHELX server. It has been well tested by about 20 volunteers to whom I
am very
Just for the record, the Fortran sources for all the SHELX programs are
identical for Windows (32 or 64 bit), Linux (32 or 64 bit) and MacOSX
(always 64 bit) except for one line that I need to comment out for
Windows. I use the Intel ifort compiler for all these platforms. I pay
the commercial
Dear Dale,
Isabel Uson's ARCIMBOLDO-LITE works well for coiled coils and has the
same resolution
requirements (2.1A or better) as AMPLE because both use SHELXE to expand
the solution.
It also employs PHASER to place a small fragment but it is often
sufficient to let it search for
just two or
Dear Tom,
Please go to the SHELX homepage (Google knows where that is) and
'register'. You will then immediately
receive an email with downloading instructions (free for academic use).
Sometimes this email lands in the
trash folder.
Best wishes, George
On 04/18/2015 11:40 AM, Tom Wong
Dear Finke,
SADABS and similar programs work best when given scans about several
axes relative to the crystal. Scanning about a single axis can do more
harm than good especially if the symmetry is low. SADABS can also do a
face-indexed numerical absorption correction too, but this assumes
Dear George and Patrick,
It is particularly tricky to do such a search for SHELX because there
are different ways of referencing it for refinement (SHELX, SHELX-76,
SHELXL, SHELXL-97, SHELXL-2014 etc.) and there are other ways of using
SHELX, in particular SHELXD for finding the heavy atom
Immediately after the DGK Meeting in Goettingen, there will be an IRTG
Methods Course
on Macromolecular Applications of SHELX there on the afternoon of
Thursday March 19th.
See: http://shelx.uni-ac.gwdg.de/SHELX/workshops.php for details.
George
--
Prof. George M. Sheldrick FRS
Dept.
Dear Georg,
When you start SADABS, the first question is whether you rquire 'expert
mode'. This mode asks more questions to set additional parameters. If
you select expert mode, the second question is the maximum number of
reflections. 200 is merely the default value. I would be
Dear Georg,
Since you collected your data on a Bruker machine and integrated them
with SAINT you should simply scale the .raw files with the Bruker
program SADABS and then read them into into XPREP. This can scale the
two datasets together and produce either merged or unmerged but scaled
Dear Ian, Kay et al.,
The omnipotent CheckCIF program that is used to check all small molecule
structures submitted to /Acta Cryst./ and many other journals requires
(a) the H-M space group name, (b) the Hall symbol and (c) the list of
equivalent positions, and checks that *all three* are
Since this discussion doesn't want to end. I should point out
(a) The IUCr has, in its wisdom, decided to use the */Hall space group
symbols/* to settle the matter. See International Tables for
Crystallography, Vol. B (2001), Chapter 1.4, Appendix 1.4.2//and /Acta
Cryst./ (1981). A*37*,
The strange thing is that small molecule crystallographers do not suffer
from this problem, because they don't use space group numbers! This is
just as well, because instead of just 8 combinations of primitive
orthorhombic space groups and settings, they have to consider 111 (if I
have
Dear Alistair,
Erratic behaviour is often caused by the antibumping restraints because
they get switched off and on, and riding hydrogens and changes in the
occupancies can affect their action. This probably applies to both programs.
Any suggestions for improving the bulk solvent model in
You might consider using AnoDe (J. Appl. Cryst. 44 (2011) 1285-1287).
This program and its documentation are available via the SHELX homepage.
You will need a PDB file name.pdb of the native structure and a file
name_fa.hkl that contains the anomalous differences. You can use SHELXC
or XPREP
Dear Kristof,
Have you tried to solve it with the new SHELXT? You can force it to
consider only chiral (Sohnke) space groups by putting -c on the command
line.
Best wishes, George
On 13.08.2014 11:00, Kristof Van Hecke wrote:
Dear,
I’m struggling with the following (small molecule)
Dear Frances,
I don't think that you can put the blame entirely on the 80 column
limitation.
The program SHELX76 was limited to 80 columns because the input came as
punched cards. It introduced a simple concept, the /free variables/,
that are frequently used to represent occupancies and can
I think that 'observed' goes back to whether it was possible to see a
reflection (and estimate its intensity by eye) on the photographic FILM.
In small molecule crystallography it is usually understood to mean
F4sigma(F) (or I2sigma(I)).
George
On 07/15/2014 07:02 PM, Edward A. Berry wrote:
I agree with Pavel. Even for accurate small molecule data with R-values
below 3% the differences are hardly significant, the 'B-factors'
compensate so well. The large majority of small molecule structures are
refined with neutral atom scattering factors even if ions are present.
The calculated
Dear Roberto,
If you are using shelxc/d/e, it is best to read the XDS.ASCII.HKL file
DIRECTLY into shelxc. This is what hkl2map does.
When you run shelxe (from the command line or hkl2map), you usually need
to try both hands of the heavy atom substructure. If the 'contrast' for
one hand is
Dear Alastair,
As you point out, SHELXL allows atom names, RESIdue numbers and PARTs
(=Altlocs) to be used in any combination. The only rule is that no two
non-hydrogen atoms may have the same settings for all three. Other
refinement programs may be more restrictive.
Best wishes, George
In my program documentation I usually call these 65 the Sohnke space
groups, as defined by the IUCr:
http://reference.iucr.org/dictionary/Sohnke_groups
George
On 05/02/2014 02:35 PM, Jim Pflugrath wrote:
After all this discussion, I think that Bernhard can now lay the claim
that these 65
Dear Chen,
If you don't know how many sites to expect - and in some cases, e.g. an
iodide soak, this is inevitable - I recommend trying different numbers
(FIND N in shelxd) and choosing the one where the occupancy of peak N
comes out as about 0.2. If it is higher you need a higher N and vice
There are good arguiments for using quaternions rather than Eulerian
(or other) angles anyway, this is very well explained in the paper
*Quaternions *in *molecular modeling*
Indexing involves storing all the reflection positions in orthogonal
reciprocal space and then finding a reciprocal lattice that fits most of
them.
For a 10 degree frame all we know is that a reflection lies somewhere on
a sort of 10 degree arc; only two of the three coordinates are
precisely
Abbas Ourmazd who is physics professor at Milwaukee has asked me to post
this job advert on CCP4bb:
http://jobs.sciencecareers.org/job/325225/assistant-or-associate-professor-in-biophysics/
George
--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
I think that more people read wikis than contribute to them, so this
'experiment' (see below) is
a little biased. On the other hand, it is often easier to put a question
to CCP4bb than to search
for the answer in wikis and other documentation, however well organized
they are.
Kay: can you see
It would be so nice to have a 'sister CCP' for questions aboud wet-lab
problems that have nothing to do with CCP4 or crystallographic computing,
The is clearly a big need for it, and those of us who try to keep out of
wet-labs would not have to wade though it all.
George
On 02/12/2014 03:05
Adapting programs to make optimal use of modern multicore chips is
non-trivial and depends very much on the algorithms employed,
there is no magic bullet. First one needs to understand Amdahl's law.
Assume we have a chip with four cores such as the widely used
Intel i7, amd the program consists
(+) and I(-) SIGI(-)
But as George says Why do you want it? That will change the way you proceed.
Eleanor
On 14 Nov 2013, at 21:08, George Sheldrick wrote:
I'm not sure why you want to do that. If you wish to look at a map or poly-Ala
trace from SHELXE, just read the .pdb and then .phs files
I'm not sure why you want to do that. If you wish to look at a map or
poly-Ala trace from SHELXE, just read the .pdb and then .phs files into
Coot directly. If you want to use them to make pictures with PYMOL, use
Tim Gruene's SHELX2map. For further information please go to the SHELX
homepage
Dear Yafang,
If radiation damage is not a major problem, MAD should give you more
phase information than SAD, i.e. better maps, especially
at low resolution. If SAD works but MAD doesn't, there are several
possible explanations:
1. (most likely) your datasets are inconsistently indexed. This
The flexibility of CIF is indeed infinite. Even the names of the
unit-cell dimsnsions are different in mmCIF and (small molecule) core CIF.
One of the main reasons why I had to bring out a new version of SHELXL
recently (SHELXL-2013 to replace SHELXL-97) was that in the
meantime COMCIFS
Dear Peter,
i am planning to produce a new pdb2ins containing several improvements,
but until this is ready please continue to use the old shelxpro.
Best wishes, George
On 17.06.2013 16:57, Peter Moody wrote:
At the risk of (more) people pointing at me and laughing...
I used to use
The title of my PhD thesis was NMR of inorganic hydrides but I soon
realized that I was out of my depth with
the theory so switched to something easier to understand (gas phase
electron diffraction). However this involved
taking the (somewhat dangerous) samples by train to Durward
Dear Olga,
I always run SHELXC/D/E from hkl2map because of the nice graphical
diagnostics while the programs are running.
If you start hkl2map, give any project name and choose 'more options'
you will be able to specify that you need more memory.
From your comment I suspect that you are
One day many years ago, my Ph.D. students all appeared wearing T-shirts
with the logo
We want more redundancy. They had clearly got the message about how to
do sulfur
SAD phasing, but were completely unaware of the usual meaning of the
word in the UK!
George
--
Prof. George M. Sheldrick FRS
Dear Frank,
We did extensive testing of this approach at the beginning of this
millenium - see
Acta Cryst. D59 (2003) 393 and 688 - but never claimed that it was our idea.
Best wishes,
George
On 05/14/2013 06:50 AM, Frank von Delft wrote:
Hi, I'm meant to know this but I'm blanking, so I'll
Dear Wei,
There is a new SHELX homepage with extensive documentation and downloading
instructions at: http://shelx.uni-ac.gwdg.de/SHELX/
SHELXE requires reflection files name.hkl (native) and name_fa.hkl (data
for phasing) and
and the heavy atoms in SHELX format in name_fa.res. I recommend
or P6522, then you should
run shelxe twice, once with and once without -i (which would invert the
space group and atom
coordinates). It is usually worth trying different solvent contents (-s).
George
On 03/15/2013 11:09 AM, George Sheldrick wrote:
Dear Wei,
There is a new SHELX homepage
' commands).
(also see my blog article http://grauonline.de/wordpress/?p=71 )
Is it possible to build one for Mac 10.5.8?
Thanks!
Guangyu Zhu
On 2/26/13 3:32 AM, George Sheldrick
gshe...@shelx.uni-ac.gwdg.de wrote:
As some of you have already discovered, there is a major new
release
As some of you have already discovered, there is a major new release of
the whole
of SHELX (the first since 1997) complete with a new homepage that should
make
downloads easier. To obtain the programs, please point your browser to:
http://shelx.uni-ac.gwdg.de/SHELX/
and then 'register' (top
Dear Huw,
It looks as though you have correctly diagnosed a problem with AMPLE.
For expansion from borderline partial structures, I recommend the latest
SHELXE (on my beta-test server since Jan. 20th) and experimenting with
the -O and -F switches, e.g.
-F0.9 -O100 -a30
However SHELXE is
Correct, shelxe does not use the free -R flags, and works just
as well with the original unmerged unctruncated intensities.
George
Hi Ronan,
On 28 Jan 2013, at 12:18, ronan.kee...@stfc.ac.uk wrote:
Well spotted! We originally gave structure factors to SHELXE in our testing as for most
of
I have now looked at James's two challenges to see what I could learn
from them, and will try to give enough details so that less experienced
readers of this list can repeat what I did and apply the experience
thereby gained to solving their own structures. For those who are not
interested
Dear James,
I agree with Pavel that your example is not very realistic. In practice
one would start from the heavy atom positions. As well as providing
starting phases, they are useful in other ways. For example. shelxe
(and probably most other tracing programs) adds them to a 'no-go'
map so it
James,
I had in fact just come to the conclusion that the indexing was
consistent with 3dko for 'possible' but not for 'impossible',
which I suppose was logical.
George
Woops! sorry folks. I made a mistake with the I(+)/I(-) entry. They
had the wrong axis convention relative to 3dko and
A computationally elegant and probably faster approach is to use
quaternions, proposed by MacKay in Acta Cryst. A40 165-166. For a recent
description of this method see
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2958452/
George
On 12/27/2012 09:09 PM, Dale Tronrud wrote:
If you just
Punched cards, stored in a sealed dry box, and perhaps irradiated to
kill off any bacteria, should long outlive any magnetic or capacitive
storage medium. If it is difficult to find a working card reader, they
could always be read by eye, though that might be tedious. Their EBCDIC
code is not
is
as good as any and you clearly already know how to use it. The older
shelxs has further Patterson options, as do many other programs such as
the CCP4 program FFT.
Best wishes, George
On 12/07/2012 11:31 AM, ccp4...@hotmail.com wrote:
Dear professor George Sheldrick,
I am sorry to bother you
That is a list of the strongest Patterson peaks, the ones marked with
'*' are used
as translation search vectors to kick-start the heavy atom location.
x,y,z are the
crystal coordinates of the peaks, height is the peak height, mult
indicates how the
peaks have coalesced because they are on
shelxl-2012 does include the space group in a way that Coot understands
when it writes a .pdb file. This version is in the final beta-testing
stage with a lot of new features (mainly for small molecules) and no
known bugs, so I hope to release it soon. If anyone would like to try it
now please
shelx .hkl files often have a blank line or a line filled out with zeros
at the end as a terminator. This is useful if you wish to edit in extra
information such as the cell dimensions after this line, but is not
obligatory. However if you concatenate the files with cat or a text
editor you
It is the lack of compatibility between different versions mentioned by
Ethan that really put me off learning PYTHON. In contrast, the
FORTRAN-66 program SHELX76 still compiles and runs correctly with any
modern FORTRAN compiler. The only significant 'new' features that I now
use are dynamic
Dear Annette,
I suspect that a trivial error like confusing F and intensity is the
cause of your problem. You would probably get a better response if you
sent your message to the very informative Bruker mailing list or asked
one of the Bruker applications scientists. If you wish to send me
Which programs require that the data be the 'standard' a.u.? None of
mine require this.
George
On 05/29/2012 03:44 PM, Ian Tickle wrote:
Mark, thanks for pointing that out, I see it now:
In P321 the only possible alternate indexing is (-h, -k, l): this is a
2-fold || c which is an operator
In SHELXL. a refinement program sometimes used by small molecule
crystallographers, all Fourier map for at least the last 20 years were
weighted by Ic^2/(Ic^2+sigma^2(I)), where Ic is the calculated squared
structure factor and sigma(I) is the square root of 1/w. w is the weight
assigned to a
You probably need to insert the space group name into the CRYST1 record.
Tthe version of SHELXL that I am planning to release this summer already
deduces the space group name from the LATT and SYMM cards and puts it
there. If you read the .res file into Coot instead of the .pdb, Coot can
I think that anything that irrevocably modifies the experimental data
should be avoided whenever possible. Since anisotropic scaling is a
relatively fast calculation and there are several ways of doing it, it
is better to apply it locally when it is needed, e.g. in phasing (where
it is applied
Dear Gerard,
That will be an extremely useful facility. Is a 'regrading' of the
monomer library planned, at least for common cofactors and
crystallization additives?
Best wishes, George
On 03/19/2012 06:22 PM, Gerard Bricogne wrote:
Dear all,
The generation of reliable restraints
Dear Lu Yu,
SHELXL is usually very stable so there must be an error in your .ins
file, but it is difficult fo us to guess what it is without seeing the
full file. A common error that can cause such instability is caused by a
long-standing bug in Coot, which sets some occupancies in the .ins
for any such
purposes.
I got the number 140A^3/a.a. from George Sheldrick who told me where he
got this number from, but I do not remember for sure - it could be Kevin
Cowtan, but George may update my memory in order to pay proper credit.
Cheers,
Tim
On 03/12/2012 08:48 PM, Bernhard Rupp
Dear Lu Yu,
Most readers of this list will only be familiar with the use of SHELXD
to find heavy atom sites for experimental phasing, but it appears that
you are using it for small molecule direct methods, which in fact is
what the program was originally written for. For small molecule direct
Dear Brennan,
Since you accidentally sent your request to the CCP4bb rather than the
Phenix email list, I suggest that you try SHELXC/D/E, e.g. using Thomas
Schneider's HKL2MAP, to see if it gets the same answers. These programs
have solved lysozyme hundreds of times. HKL2MAP will also
It depends a lot on which home source and which synchrotron, there are
enormous differences. Goettingen is uniquely well placed because we can
reach four synchrotrons in a few (3-7) hours by high speed train and in
theory at least five more with a longer train journey, trains are very
From the rather non-technical inofrmation available so far, it seems to
me that it is like leaving out all but the strongest reflections (or
perhaps the strongest normalized structure factors). This is unlikely to
improve the quality of structure refinement, the importance of using as
much
SHELXD does not use the solvent content. However since you know how many
seleniums it found and presumably know how many methionines are in the
sequence, you can use that to estimate the number of molecules is the
asymmetric unit. Note that an N-terminal selenomethionine is often
disordered
The pseudo-free CC in SHELXE is not a very decisive figure of merit. By
far the best way is to run the autotracing (e.g. with -a5) and to look
at the CC for the trace against the native data. A value of more than
25% is almost always solved.
George
On 12/06/2011 10:02 PM, Tiruttani
Dear Yuri,
The new program ANODE (J.Appl.Cryst. (2011) 44, 1285-7, Open Access) is
designed for this and is very simple to use. It may be downloaded from
the SHELX beta-test server (please email me if you require downloading
intructions).
George
On 11/26/2011 06:05 AM, Yuri Pompeu wrote:
As Mark says, structure solution of smallish peptides is not usually as
easy as one might expect. A number of the small (say up to 50 residue)
peptides in the PDB were solved by direct methods, but these require
native data to 1.2A or (preferably) better. If sulfur is present in the
molecule,
100 matches
Mail list logo
