Hi Mike,
My gut feeling is that the accuracy will be around 10%. However it will depend
very much how far the two conformation overlap, or not overlap and how good the
data is. If there are large non-overlapping regions, accuracy may be better.
Best,
Herman
Von: CCP4 bulletin board Im Auftrag
Dear Shenyuan,
I have two suggestions:
1. Is your protein a single or a multi-domain protein? If it is a
multi-domain protein, you should search with the individual domains.
2. Given the low resolution, high anisotropy and expected large number of
molecules in the asymmetric unit, you may
Hi Jiang,
It could have a lot of causes. What I would first check is that the chainID of
the NLE is the same as from the surrounding protein, that the new NLE has the
same residue number as the deleted MET. I would also check that the position
within the coordinate file is the same as the previo
Dear Shawn,
I am not aware of an automated way to merge all fragments into a single
consistent peptide chain. What I would do is to look at the map and the built
fragments in coot and switch the symmetry on with a large radius, e.g. 20-30A
and see if you can find a set of fragments (including s
Dear Martin,
The concept of systematic absences is usually used for absences caused by the
crystal packing, e.g. glide planes etc. I guess that what you meant are
absences due to anisotropic cutoff. In the past, to get an Rmerge is low as
possible, people would cut there data at 2sigma, or even
Hi Prasun,
As others have pointed out, the higher the multiplicity, the better, so I would
be happy about it and not worry.
Concerning the higher Rwork in the inner shell, what are the resolution limits
of this shell? Are there any ice-rings within these resolution limits?
Otherwise I would che
Dear Marion,
If you read in your corrected .cif file in Coot or your refinement program, it
will override the (default) CCP4 .cif file. You can also correct the installed
CCP4 .cif file. I once did this. However, these changes are lost when you
update the CCP4 installation, so best is to ask th
Dear Cryo EM,
In general, if you bring the two atoms at approximatively the correct distance
and do a real space refinement or regularization, a bond should be generated.
However, there are caveats:
1. Do the nucleotides belong to the same chain? If they belong to different
chains, they will
that point group).
>
>Please let me know if any other information is required.
>
>With best regards,
>Sayan Saha.
>
>
>On Thu, Jul 28, 2022 at 1:26 PM Schreuder, Herman /DE <
>herman.schreu...@sanofi.com<mailto:herman.schreu...@sanofi.com>> wrote:
>
>&
: Donnerstag, 28. Juli 2022 15:17
An: Schreuder, Herman /DE
Cc: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] Regarding the correct space group identification
Dear Sir,
The crystal-to-detector distance was set to 190 mm. Yes, multiple diffractions
seem to be present. We have not yet tried Zanuda on
you
complete the refinement in P1?
Best regards,
Herman
Von: Sayan Saha
Gesendet: Donnerstag, 28. Juli 2022 11:43
An: Schreuder, Herman /DE
Cc: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] Regarding the correct space group identification
Dear Sir,
1. There are no ice-rings. However
Dear Sayan,
If a subunit is correctly oriented, but the translation is incorrect, density
for a ligand may still show up in the binding site of the protein. It might be
that one of the 2-fold axes, you think is crystallographic, is in fact non
crystallographic and a few Angstroms away from the
Hi Monika,
I would process the data using the point group information ignoring any
possible screw axes, e.g. in space group P222, where the true space group might
be P212121.
The next step depends on how you plan to solve the structure. You mention that
there is no cryo structure, do you mean
PS: this does not work for very small atoms, e.g. waters. Here I let the
temperature factor take care of the occupancy as well.
Von: Schreuder, Herman /DE
Gesendet: Donnerstag, 3. März 2022 16:23
An: CCP4BB@JISCMAIL.AC.UK
Betreff: AW: [ccp4bb] Ligand occupancy refinement
Dear Ankanksha,
The
Dear Ankanksha,
The ligand is either present, or it is not present. It cannot be that some
atoms are present and others not. For ligands, I always use a single group
occupancy using the program Buster from global phasing. In my hands, this
always works. There is a correlation between occupancy
Hi Shubhashish,
How many molecules do you assume are in the asymmetric unit? You may have a
very high solvent content and by trying to find multiple molecules, you spoil
your solution. Also, did you do a thermal shift assay to make sure your protein
is properly folded?
Best,
Herman
Von: CCP4 b
Hi Yong,
Why make an ensemble when you don't want to search with and ensemble? You could
run separate phaser jobs, one after the other, with your search models. I guess
that this is what is meant by "SERIAL". Maybe Phaser has an option to do this,
but it is also not difficult to write a small s
: Montag, 22. November 2021 22:09
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] AW: [ccp4bb] COOT RSR
What's the difference between a dummy water and a real one?
Paul
On 22/11/2021 14:34, Schreuder, Herman /DE wrote:
Dear Paul,
I agree with Oliver and Norbert, in the early phases of refin
Dear Paul,
I agree with Oliver and Norbert, in the early phases of refinement, when a lot
of rebuilding has to be done, the coot RSR is not very helpful and in general I
leave it to buster do refine the rebuilt regions. Knowing now that (dummy)
waters may be the culprit, I will remove them. How
Hi Adam,
Thank you for your response. Using the pdblocal keyword, I was able to run
MrBUMP. Also the cryo keyword was recognized, but then the mode of operation
was set to "MODELS" and only search models were generated. From your email, I
understand that I will have to wait for ccp4 update 017
Dear Community,
I just came accross a paper on the use of MrBUMP to fit pdb models to cryo-EM
maps: https://scripts.iucr.org/cgi-bin/paper?S2059798321009165
However, it turned out that the program tries to download coordinates directly
from the pdb, which our firewall does not allow. Is there a
Dear Murpholino,
What was the reason of trying all these different processing methods? I, and I
guess most other crystallographers will process the data using a standard
procedure and if the results are good, will not try a myriad of other
processing methods. If it is to get most out of a poorl
Dear Rohit,
Do you mean that the residues after your "C-terminus" have been deleted because
there is no convincing electron density for them?
In that case, a charged carboxylate at the N-terminus is incorrect and you
should delete the OXT atom. Alternatively, you could add one residue at the
C-
It may also be possible to separate the different phosphorylated forms on an
isoelectric focusing gel.
Best,
Herman
Von: CCP4 bulletin board Im Auftrag von Patrick Loll
Gesendet: Mittwoch, 15. September 2021 15:12
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] Phosphatase enzymatic assay
Phos-
adopt the same conformation, I would assume
statistical disorder and not twinning.
My 2 cts,
Herman
Von: mi...@bioc.uzh.ch
Gesendet: Dienstag, 31. August 2021 17:46
An: Schreuder, Herman /DE
Cc: CCP4BB@JISCMAIL.AC.UK
Betreff: Antwort: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb
Dear Nick,
I had just looked at a pdb downloaded from the alphafold server without
problems. However, then I realized that I had looked at the alphafold model
after I had it superimposed on my own structure. Loading the alphafoldmodel
directly in coot failed for me as well.
By looking into the
have different twin fractions, my bet is that the twin supporters
are right.
Best,
Herman
Von: Lijun Liu
Gesendet: Freitag, 27. August 2021 15:57
An: Schreuder, Herman /DE
Cc: ccp4bb@jiscmail.ac.uk
Betreff: Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?
Dear Herman
ecial position. If the swapping of the extra chain
influences the sublattice P32 (or C2 or P1, as pointed out by Kay)
twinned to P3221 might be the better description.
All the best,
Peer
On 27.08.2021 10:56, Schreuder, Herman /DE wrote:
>
> Dear Peer and Eleanor,
>
> This is indeed what
Dear Peer and Eleanor,
This is indeed what I am suspecting: If the "twinning operator" in P32 puts 4
out of 5 protein chains on top of symmetry mates, is the "true" space group
then P32, with 5 twinned chains, or P3221 with 4 normal chains and 1 chain on a
special position? I would vote for the
Hi Peer,
Normally, if one defines some residues with an occupancy below 1.0, the
nonbonding contact restraints with other residues are switched off. It is
already some time ago, but if I recall correctly, I had similar problems that
nonbonding contact restraints were not switched off for residu
Hi Ana,
If this histidine is part of the active site, you may want to look into the
catalytic mechanism to see if this histidine could react with something like a
malonate. Active site residues can do amazing things that normal residues
cannot. If something from your protease inhibitor cocktail
Hi Firdous,
In general, display programs use the HELIX/SHEET records in the pdb and when
these are missing, the programs generate the secondary structure themselves. If
these HELIX/SHEET records are present for some part of the structure, but are
missing for other parts, these other parts will s
Hi Rakesh,
The first question I have is: why do the crystals dissolve after some time? Did
you use a ligand for crystallization that might be turned-over by the protein?
What I would do first in your case is to try to find a stabilizing buffer.
Since you have obtained nice-looking crystals, ther
Rob,
Wat is the Matthews number, would it fit with a very low percentage solvent, or
would it not fit at all? What happens if you superimpose a tetramer on your
dimer?
Best,
Herman
Von: Robert S Phillips
Gesendet: Montag, 5. Juli 2021 16:32
An: Schreuder, Herman /DE
Betreff: Re: Strange
Dear Rob,
Your screen shot shows a large empty region with difference density for the
second half of the tetramer, so the my guess is that you have a tetramer in the
asymmetric unit, but that your molrep program only found a dimer. Would a
tetramer fit in the asymmetric unit?
If you have a tetr
Dear Stefano,
I do not know if it is possible, but as a workaround, you could first expand
your object by crystallographic symmetry and then do the superposition.
Best,
Herman
Von: CCP4 bulletin board Im Auftrag von Stefano Trapani
Gesendet: Mittwoch, 2. Juni 2021 14:31
An: CCP4BB@JISCMAIL.AC.UK
Dear Deepak,
the cryoprotection may destroy the diffraction. I would also try diffraction at
room temperature, using special sleeves to prevent dehydration. With 20%
PEG400, you could also try to freeze the crystals without using additional
cryoprotectant. If you are lucky, it may work.
Best,
H
Dear Sam,
The first thing that would come to my mind would be ice rings, but since you
said you don't have them, there must be another reason for the high Rs.
Zanuda will give you back the space group you used for MR and maybe a higher
symmetry space group, but the program cannot be used to conf
Dear Bulletin Board,
Sorry for the slightly off-topic question, but we are struggling with a
receptor domain that expresses well as a fusion protein, but gets lost the
moment it is cleaved from the fusion partner. It could be that the receptor
domain is not or misfolded, but it could also be a s
Dear Marina,
A lot can happen with twinning andthe crystallization process does not always
adhere to rules written in text books.
The first thing I would do is to look at the predicted spots to see if the
"split" spots are predicted as single spots (and would then really be split),
or if they
Hi Bashir,
At the end of your log file, you get a warning message that you have 87%
solvent, which is highly unlikely and a suggestion to search for more
molecules. Did you try to search for more copies (say 4)?
Best Herman
Von: CCP4 bulletin board Im Auftrag von Muhammad Bashir
Khan
Gesendet:
Hi Suraj,
It is strange that the P3 crystals do not produce a MR solution. Since they all
came from the same crystallization condition, you may want to check that no
proteolytic cleavage of your protein has taken place and that your crystals
only contain a fragment of your protein. You may also
Dear Phil,
0.32 is awfully close to 1/3, which brings a nice mathematical puzzle to my
mind to see if the 1/3 occupancy is somehow related to the 3 fully occupied
monomers... It may also be related to a (trigonal??) space group...
You probably have already tried it, but phaser has the option to
Hi Prasun,
Apparently, when you just mixed the peptide solution with the reservoir
solution, crystals formed. After equilibration, the crystals were gone.
1) what I would try: just mix peptide and reservoir solution, but do not
equilibrate, e.g. do not use a reservoir solution. This is called b
Hi Nika,
Here you need some common sense. The green density in you polder map may just
be the bulk solvent that was removed from the model to generate the polder map.
In this case you have to use common sense and ask yourself a couple of
questions:
* Is the density really from the ligand,
Dear Christian,
We occasionally observe binding to only one monomer of a multimeric complex. I
don’t think this invalidates the biological significance of your finding. I
would superimpose the different monomers to see if they have (slightly)
different conformations that prevent ligand binding.
Looks more like crowd-phishing to me! 😉
The original message did not make it through my spam filter and it may not be a
good idea to open the shared file.
Herman
-Ursprüngliche Nachricht-
Von: CCP4 bulletin board Im Auftrag von Robbie Joosten
Gesendet: Dienstag, 20. Oktober 2020 16:16
An
A practice that was very popular before the Rfree came around was to fit a
water molecule in every noise peak. One would get spectacular low Rfactors this
way, but I cannot imagine that anyone would believe that this would be fitting
and not over-fitting.
Best,
Herman
Von: CCP4 bulletin board
Hi Dhiraj,
you could also consider making a fusion protein of your protein with itself,
with a suitable long linker (gly-ser-gly-ser etc.?) in between. At least that
dimer won't dissociate.
Best,
Herman
Von: CCP4 bulletin board Im Auftrag von Srivastava,
Dhiraj
Gesendet: Mittwoch, 23. Septembe
In theory, one gets one’s own message as well. However, most spam filters, at
least the one I got, block messages sent by the recipient.
Best, Herman
Von: CCP4 bulletin board Im Auftrag von Eleanor Dodson
Gesendet: Montag, 21. September 2020 11:13
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] Re
Dear Andy,
I few thoughts from my side, but no solution I am afraid:
* Your twinning operator -h, -k, l is the standard alternative indexing for
P3x space group, which makes a lot of sense.
* P32 is a low symmetry space group, which makes MR easier, but this is
offset by the NCS.
*
Dear Paul,
I fully agree with Georg and the others. As I said in my first reaction, with
the new coot, the inhibitor or side chain often does not end up a little wrong,
but goes off completely in the wrong direction, which makes me wonder whether I
had somehow selected the wrong map. It might a
them fatter, pinker
and more opaque. If there are still problems and you could somehow make a
screencast available to me that illustrates the problem, then I would be very
interested to view it.
Regards,
Paul.
On 04/09/2020 10:05, Schreuder, Herman /DE wrote:
> Dear Paul,
>
> Here
Dear Paul,
Here I fully agree with Eike. With the real space refinement in the new coot
the ligand often goes everywhere, except where it should go. Changing the Xray
weight helps sometimes, but not always. In many cases I do not real-space
refine and leave it to Buster to do the refinement. It
, because of these
stacked overhangs. The structure was solved by MR using Molrep.
Trials using Phaser were failed. The initial model was obtained by ZN-SAD.
Refinement was dome for space group P43212, with cell parameters
31.96 31.96 95.07 90 90 90, with one duplex molecule per AU.
Schreuder, Herman
Thank you. I think I will then first try to optimize the weight and then
increase the cycles.
Herman
-Ursprüngliche Nachricht-
Von: Tom Burnley - UKRI STFC
Gesendet: Donnerstag, 30. Juli 2020 14:35
An: ccp4bb@jiscmail.ac.uk; Schreuder, Herman /DE
Betreff: Re: [ccp4bb] AW: [EXTERNAL
eer Sheva
Israel
On Jul 29, 2020 18:29, "Schreuder, Herman /DE"
wrote:
Coot does it, but if one wants to do it for a complete protein, it is a lot of
clicking. On the other hand, I have not tried to just select the N- and
C-terminus for real-space refinement to see what happens. I
Gesendet: Mittwoch, 29. Juli 2020 17:23
An: Schreuder, Herman /DE
Cc: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] Re: [ccp4bb] real real-space-refinement
EXTERNAL : Real sender is
eleanor.dod...@york.ac.uk<mailto:eleanor.dod...@york.ac.uk>
Wont coot do that?
Eleanor
On Wed, 29 Jul 2020 at
Dear BB,
I would like to do a real real-space-refinement of a protein against a cryo-EM
map; not the mtz-based Refmac approach. A quick internet search produced a lot
of Phenix hits, but little ccp4 hits. Does somebody know how to do this using
ccp4 programs, or has someone a Coot script to do
Dear Rafal,
At this resolution, one sees many amino-acid side chains with alternative
conformation, so it might be a good idea to test if this is also true for
nucleotides.
Best, Herman
-Ursprüngliche Nachricht-
Von: CCP4 bulletin board Im Auftrag von Rafal Dolot
Gesendet: Mittwoch, 2
Hi Reza,
Since nobody answered your question so far, I will do it now:
In our hands, ArpWARP autoligand is still the best program to automatically
dock ligands into electron density maps. Alternatively, on could also try
Rhofit from Global Phasing or some other docking program.
However, the res
: Schreuder, Herman /DE
Cc: CCP4 bulletin board
Betreff: Re: [EXTERNAL] chirality with electron diffraction
EXTERNAL : Real sender is tim.gru...@univie.ac.at
Dear Herman,
no, I don't think this is routine, yet!
First of all, instrument manufacturers need to catch up. What's on
n of small molecules by
electron diffraction, or is it something that in theory can be done, but only
difficult in practice?
Best,
Herman
-Ursprüngliche Nachricht-
Von: Tim Gruene
Gesendet: Montag, 20. Juli 2020 11:03
An: CCP4 bulletin board ; Schreuder, Herman /DE
Betreff:
Dear Jessica,
Thank you for this positive news on electron diffraction on small molecules. A
point which is still not clear to me: is it possible to determine the absolute
configuration with electron diffraction? Some claim that it cannot be done,
others claim that it can be done using multiple
My guess is that the model no longer superimposed well onto the electron
density map, which should be easy to spot.
Best,
Herman
-Ursprüngliche Nachricht-
Von: CCP4 bulletin board Im Auftrag von Frances C.
Bernstein
Gesendet: Donnerstag, 16. Juli 2020 13:44
An: CCP4BB@JISCMAIL.AC.UK
Bet
I fully agree, I have some old scripts I infrequently use. Making these
programs inaccessible would break these scripts, forcing me to reinvent a
couple of wheels.
My 2 cnts worth of junk to your mailbox,
Herman
Von: CCP4 bulletin board Im Auftrag von Oganesyan, Vaheh
Gesendet: Mittwoch, 8. Ju
. Juli 2020 13:11
An: Schreuder, Herman /DE
Cc: CCP4BB@jiscmail.ac.uk
Betreff: Re: [ccp4bb] AW: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] number of frames
to get a full dataset?
EXTERNAL : Real sender is dgwater...@gmail.com<mailto:dgwater...@gmail.com>
Hi Herman,
I started googling and en
way it will stay.
Best regards,
Herman
Von: David Waterman
Gesendet: Freitag, 3. Juli 2020 10:49
An: Schreuder, Herman /DE
Cc: CCP4BB@jiscmail.ac.uk
Betreff: Re: [ccp4bb] AW: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] number of frames
to get a full dataset?
EXTERNAL : Real sender is dgwater
If you check
https://en.wikipedia.org/wiki/Reflection_(physics)<https://urldefense.proofpoint.com/v2/url?u=https-3A__en.wikipedia.org_wiki_Reflection-5F-28physics-29&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&
Dear Patrick,
if I recall correctly, our systems run at 10-15 ml/min (gas). I will check on
Monday when I am back in the lab.
The original cryostreams would run for several day's on a tank of liquid
nitrogen. However, they had significant hardware to dry the nitrogen and to
ensure a constant flo
Dear all,
While following the development of this thread, I am truly amazed how people
cling to names for the number of measurements per reflection whose meaning:
* Depends on the cultural/engineering/scientific context
* Can only be understood by experts
* Where the experts, as witn
bulletin to think about my proposal as it is, without prejudices.
Best,
Herman
Von: Frank Von Delft
Gesendet: Mittwoch, 1. Juli 2020 09:46
An: Schreuder, Herman /DE
Betreff: Re: [ccp4bb] AW: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to
get a full dataset?
EXTERNAL : Real sender is
ts”, and we are an experimental based
science.
I support it.
Great.
Greetings,
John
Emeritus Professor John R Helliwell DSc
On 30 Jun 2020, at 15:10, Schreuder, Herman /DE
mailto:herman.schreu...@sanofi.com>> wrote:
Dear BB,
Since there does not seem a generally accepted term
Dear BB,
Since there does not seem a generally accepted term for the subject of this
discussions, and since even the IUCR scriptures do not give any guidance, I
would propose to introduce a completely new term:
Measurements per reflection or MPR
This term is politically neutral, should adequat
I had a similar one-sided discussion with FEDEX about their ignoring of our
customs declarations for Switzerland. That was then the last Dewar we sent by
FEDEX.
Best,
Herman
Von: CCP4 bulletin board Im Auftrag von Jan Dohnalek
Gesendet: Donnerstag, 25. Juni 2020 08:34
An: CCP4BB@JISCMAIL.AC.UK
Dear Robert,
In addition to the remarks and suggestions by others: How do your electron
density maps look like? Do they look remotely reasonable, or do they look like
they had gone through a meat grinder? If they look remotely ok, you could also
try manual rebuilding, pruning etc. However, if t
Dear Vito,
I have also worked with iodinated and brominated compounds and in general the
light atoms are not flattened out. As John Helliwell pointed out, you may look
at series termination effects. However, since your map does not appear to be of
extremely high resolution, I guess all useful d
Dear Abhishek,
I did not follow the links given by Paul. However the way I proceeded in these
cases was to first generate an alternative conformation for the problem
residues, save the file and then do the mutation and save the mutated file.
Then, using an editor, I would cut the alternative co
I guess the molecular replacement model has never been refined against this
data set, so there is no reason why the Rfree should be better or worse than
the Rfactor. The difference is larger than I would expect, but it may just be a
statistical fluke. That the Rfree goes up significantly during
This is a very good point. I never was very happy with calculating the average
of all B-factors. E.g. if one adds a lot of high-B water molecules, the average
B goes up, but with the structure itself nothing changes. Instead of
calculating the average B, it would probably better to calculate the
: Schreuder, Herman /DE ; CCP4BB@JISCMAIL.AC.UK
Betreff: Re: AW: [EXTERNAL] Re: [ccp4bb] on-topic: your opinions requested!
EXTERNAL : Real sender is
frank.vonde...@sgc.ox.ac.uk<mailto:frank.vonde...@sgc.ox.ac.uk>
I meant: complain to the editor for accepting a paper without released
coord
Dear Frank,
here I disagree. I think it is bad practice to complain to the editors or start
naming and shaming before asking the authors first. Only if they do not want to
cooperate, it would be time to bring the flame-throwers in position.
However, I think the situation is more subtle and that
button and a 2-button) configured to work properly with
Wincoot in Win10.
Roger Rowlett
Gordon & Dorothy Kline Professor, Emeritus
Colgate University
On Mon, Mar 23, 2020, 11:56 AM Schreuder, Herman /DE
mailto:herman.schreu...@sanofi.com>> wrote:
Hi Arne (and others),
I am using Win
: Schreuder, Herman /DE
Cc: CCP4BB@jiscmail.ac.uk
Betreff: [EXTERNAL] Re: [ccp4bb] Wincoot middle-mouse button does not work
EXTERNAL : Real sender is
arne.raasa...@gmail.com<mailto:arne.raasa...@gmail.com>
Hi Herman,
which version, OS and mouse are you using? I can confirm that middle mouse
Dear community,
Courtesy to the Corona crisis, I am now separated from my Linux workstation and
I am trying to get everything working from home. Running coot remotely via a
low-speed internet connection was no option so I had Wincoot installed on my
laptop. Everything appears to work fine with
cleaved by a protease, you may also try to get
some cocrystal structure with the protease. There are quite a few tricks
available to achieve this.
Best, Herman
Von: chitra latka
Gesendet: Donnerstag, 12. März 2020 12:59
An: Schreuder, Herman /DE
Cc: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [EXTERNAL
Dear Chitra,
There usually is a reason the C-terminus is disordered. Either it needs to bind
a ligand to get ordered, or it needs to bind to some other protein. You have to
check the literature. If the C-terminus binds a ligand, you have to add this
ligand to your crystallization experiment. If
Dear Gerhard,
By clicking on the "Actions" button, I discovered that the contribution comes
from Brian McMahon. Maybe you could contact him about this?
Best regards,
Herman
-Ursprüngliche Nachricht-
Von: CCP4 bulletin board Im Auftrag von Gerard Bricogne
Gesendet: Dienstag, 10. März 20
I fully agree with this!
Best, Herman
-Ursprüngliche Nachricht-
Von: CCP4 bulletin board Im Auftrag von Phoebe A. Rice
Gesendet: Freitag, 28. Februar 2020 17:03
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] Re: [ccp4bb] What resolution - X-ray diffraction round this
time
EXTERNAL : Rea
Dear Rajnesh,
My experience with molecular replacement is that when you don’t have a model,
you don’t get density. Only in exceptional cases (crystals with a very high
solvent content) I see density for missing loops or domains, so missing density
is very inconvenient, but no reason to be worri
Hi Daniele,
I agree with Wim that the first thing you should check is your space group and
especially whether a ncs symmetry element has been mistakenly identified as
being crystallographic. Since your Patterson peak is along w (c-axis), you have
to change the space group for processing such, t
Dear Bärbel,
this is a good point. Last fall, I attended the bachelors ceremony for
informatics students for my daughter. I was somewhat surprised to see that most
German graduates were male, but that most Indian graduates were female. At the
reception afterwards when talking to some people I d
Dear Thomas,
The asymmetric unit of the bovine pTAFI structure (3dgv) contains one regular
dimer and one somewhat disordered monomer. However there is no domain-swapping
of alpha-helices or other special things.
Best regards,
Herman
Von: CCP4 bulletin board Im Auftrag von Kluenemann,
Thomas
Hi Katrin,
First, I think you meant that the green density disappears after contouring at
6 Sigma and not 6 A?
That you ligand is only partly visible due to disorder and has partial
occupancy happens often and is no reason for concern. Of course, you could try
soaking with a 10-fold higher liga
Dear Ishan,
A structural alignment should be independent of the software used.
However, the residues being selected for the alignment can make a big
difference and different programs have different selection criteria.
There are two cases:
1. Different proteins. Here one needs to decide what t
: Samstag, 30. November 2019 11:00
An: Schreuder, Herman /DE
Cc: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [EXTERNAL] [ccp4bb] 8/ 2263 spots indexed XDS
EXTERNAL : Real sender is maps.fa...@gmail.com<mailto:maps.fa...@gmail.com>
Hi Herman,
thank you for your answer. Yes, my data were collected
Dear Almu,
were your data collected at a synchrotron? Many synchrotrons run automatic
processing of the data being collected and it is worth looking if there is some
processing directory between the frames you collected. If so, these data may
already be quite decent, and in any case, the XDS.IN
Dear Matthias,
I have the impression that you have set FRIEDEL'S_LAW= FALSE in your input,
which means that CORRECT will print the anomalous completeness. If you plan to
solve your structure with molrep, you can set FRIEDEL'S_LAW= TRUE, which
should give a much better completeness.
Best,
Herm
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