l, are mixtures in terms of chain
> length.
>
> Boaz Shaanan, Ph.D.
> Dept. of Life Sciences
> Ben Gurion University
> Beer Sheva, Israel
>
> On Feb 3, 2025 19:12, Dale Tronrud wrote:
> Looks like a pretty good PEG fragment to me.
>
> Dale Tronrud
>
> On 2/3
Hi Sam,
Perhaps the Modeller service is what you’re looking for?
https://salilab.org/modeller/
Best wishes,
Chris
On Fri, 6 Aug 2021 at 07:42 Sam Tang wrote:
> Dear all
>
> Sorry for an off-topic question here. I wonder if anyone may be aware of
> any search program which allows one to 'blas
Hi Richard,
I recently observed the sulfenic acid derivative of a cysteine residue
(S-hydroxy-Cys, ligand ID CSO) in one of my high-resolution maps. Could it
be possibly be this, H-bonded to a nearby water molecule?
Best wishes,
Chris
On Fri, Mar 27, 2020 at 21:33 Paul Emsley wrote:
>
> On 27
ly-To: *Christian Roth
> *Date: *Wednesday, January 22, 2020 at 12:17 PM
> *To: *"CCP4BB@JISCMAIL.AC.UK"
> *Subject: *Re: Unusual monomer-monomer interface in crystal
>
>
>
> Hi Chris,
>
>
>
> it could be all Ni besides Zn. I've seen Ni carried ov
Thanks to Guenter and Eleanor for their replies. I mentioned that there is
not adequate space for a metal ion at the described interfaces.
Nevertheless, placement of a metal ion, followed by refinement in Phenix,
repositions the side chains significantly so as to make room for the ion
without disto
Dear CCP4BB Users,
I've recently solved the ~2.2 angstrom structure of a protein. In my
electron density there are unusual monomer-monomer interfaces involving
pairs of His and Cys residues (see https://ibb.co/wdWBcdk). Note the
positive Fo-Fc density between the four side chains. As there is not
/3 if it is on 3-fold axis and so on
>
> ср, 6 нояб. 2019 г. в 11:18, Chris Fage :
>
>> Dear BB Users,
>>
>> Within my unit cell, I see overlapping spherical blobs of Fo-Fc and
>> 2Fo-Fc density in Coot. These blobs appear directly at the symmetry
>> boundary, s
Dear BB Users,
Within my unit cell, I see overlapping spherical blobs of Fo-Fc and 2Fo-Fc
density in Coot. These blobs appear directly at the symmetry boundary, such
that building a water molecule at the position results in overlaid
symmetry-related molecules (see water 420, between three copies o
2019 at 9:02 PM Murpholino Peligro
wrote:
> I think this is part of the problem.
> https://pymolwiki.org/index.php/Normalize_ccp4_maps
>
> El lun., 30 de sep. de 2019 a la(s) 10:09, Chris Fage (fage...@gmail.com)
> escribió:
>
>> Hi Paul,
>>
>> After exp
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On Mon, Sep 30, 2019 at 3:04 PM Paul Em
9FDF2>
On Mon, Sep 30, 2019 at 1:26 PM Robbie Joosten
wrote:
> Hi Chris,
>
> You made an Fobs map not a 2Fo-Fc map. You can leave sigma empty if you
> want to make a map in this case.
>
> Cheers,
> Robbie
>
> > -Original Message-
> > From: CCP4 bull
re that you
> uncheck it before loading your map in Pymol.
>
> I hope that above suggestion works for you.
>
> Regards,
> Santhosh
>
> On Mon, Sep 30, 2019 at 4:06 PM Chris Fage wrote:
>
>> Dear All,
>>
>> I recently obtained structures of a protein
Dear All,
I recently obtained structures of a protein bound to two different small
molecules. When viewing the structures in Coot with a similar contour
setting, the 2Fo-Fc map around ligand 1 is clearly much weaker than that
around ligand 2.However, after generating 2Fo-Fc maps in FFT and loading
Dear All,
Pymol seems to ignore the HELIX and SHEET records in my coordinate file,
and instead assigns secondary structural features according to the default
method. Unless my understanding is flawed, these records should override
Pymol's assignment...?
I generated the records with the Stride Web
Hi Laurent,
I seem to recall being able to click on outliers in the output of the
phenix.refine GUI, which links to a Coot window. This would, however,
require refinement in the Phenix suite rather than the CCP4 one.
Best,
Chris
On Thu, Mar 22, 2018 at 10:27 AM, maveyrau
wrote:
> Hi all,
>
> I
20 AM, Eugene Osipov
wrote:
> Hi, try to add 1-5 mM EDTA, because trace amounts of metals cause
> precipitation of tagged proteins.
>
> 14 июля 2017 г. 1:40 пользователь "Chris Fage"
> написал:
>
> Dear CCP4BB Community,
>>
>> This week, I purified a nicely
Dear CCP4BB Community,
This week, I purified a nicely overexpressing protein by Ni-NTA followed by
gel filtration. In a 4 C centrifuge, I concentrated my gel filtration
fractions to ~1 mL, transferred the spin filter to ice, and then collected
2 uL for measurement on the Nanodrop. Sadly, the prote
Hi Stephen,
I've had some luck calculating ligand-binding cavity volume with the 3v
website (http://3vee.molmovdb.org/). You might want to give it a shot.
Best,
Chris
On Wed, Jun 14, 2017 at 12:42 PM, <
stephen.c...@rc-harwell.ac.uk> wrote:
> Dear ccp4bb,
>
> I am trying to compare the shape o
Hi Eike,
I wouldn't necessarily let the morphology deter you. While working on my
PhD, a colleague collected beautiful data from hollow crystals.
If the crystals collapse while looping, is it possible for you to perform
"micro-surgery" on the crystal so that you only have a single face?
Sometimes
Sorry--I think you were referring to phasing, not refinement. I hope my
message is still relevant.
Cheers,
Chris
On Tue, Oct 11, 2016 at 10:39 AM, Chris Fage wrote:
> Dear Jacob,
>
> I'm not an expert on the topic, but from my experiences with twinning I
> can agree with you.
Dear Jacob,
I'm not an expert on the topic, but from my experiences with twinning I can
agree with you. I recently solved my second twinned structure by MR (twin
fraction of 0.43, as estimated by Xtriage). Performing twin refinement in
Refmac or phenix.refine dropped the R-factors, as expected, bu
Hi Ayan,
Try 3V:
http://3vee.molmovdb.org
It has worked nicely for me. You'll need to delete the substrate/inhibitor
from your coordinate file for one of the runs.
Cheers,
Chris
On Saturday, January 10, 2015, Bio Physics
wrote:
>
> Hello CCP4bb:
>
> Help me to advice any program/server to cal
Hi Mark,
I recently ordered "HD Clear Sealing Tape, 3 inches wide" from Jena:
http://www.jenabioscience.com/cms/en/1/catalog/287_sealing_tape.html
Best,
Chris
On Mon, Dec 1, 2014 at 12:18 PM, Mark J van Raaij
wrote:
> you are right, I must have been looking with my ears when I checked this
> m
Hi Bernie,
I agree with Herman. I think you will be all set if you simply change the "no"
twin refinement option near the top of the Refmac interface to "intensity
based" or "amplitude based" twin refinement. Refmac will determine the
appropriate twin operators/fractions and refine.
Best,
Chr
Hi Prashant,
I typically stop the centrifuge once in awhile and pipet up/down to prevent
the sample from over-concentrating. Depending on how sensitive the sample
is, you may want to do this once every 10-60 min.
Hope this helps,
Chris
On Tue, Aug 19, 2014 at 1:42 PM, Prashant Deshmukh <
prasha
Hi Rhys,
Have you tried quick back-soaks into solutions lacking the heavy atoms? This
can reduce radiation decay caused by absorption of X-rays by overabundant heavy
atoms.
Best,
Chris
> On Jul 27, 2014, at 4:48 PM, RHYS GRINTER
> wrote:
>
> Hi All,
>
> I thought I might put a question t
Hi Catherine,
If they are indeed salt crystals, have you tried preparing different
truncations of the gene encoding your target? I've seen a number of
successes in which, after a codon or two was added to the termini of the
gene being overexpressed, the target crystallized beautifully.
Best,
Chri
leaving my PEGS and PEG screens at RT in the
> light.
>
> Nick
>
>
> On Mon, Jul 14, 2014 at 12:32 PM, Chris Fage wrote:
>
>> Hi Jerome,
>>
>> -I have heard that PEG solutions can become unstable in light. We usually
>> store our block in the fridge, whe
Hi Jerome,
-I have heard that PEG solutions can become unstable in light. We usually
store our block in the fridge, where photons are scant anyway. For any
stocks that I prepare, I wrap the tube/bottle in aluminum foil. I'm not
sure about freezing them.
-Some labs (not ours) evidently prepare buff
do
> not waste time on ZANUDA.
>
> If you have pseudo-translation, try to refine the model output by ZANUDA in
> P212121.
>
> Best,
>
> Misha
>
>
> From: Chris Fage [cdf...@gmail.com]
> Sent: 12 July 2014 00:33
> To: Isupov, Michail
> Cc: CCP4BB
ZANUDA has resolved several similar cases for me.
>
> Misha
>
>
> From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Chris Fage
> [cdf...@gmail.com]
> Sent: 10 July 2014 01:14
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp
Hi Everyone,
Despite modelling completely into great electron density, Rwork/Rfree
stalled at ~38%/44% during refinement of my 2.0-angstrom structure
(P212121, 4 monomers per asymmetric unit). Xtriage suggested twinning,
with <|L|> = 0.419, = 0.245, and twin fraction = 0.415-0.447.
However, there
im
>
> On 05/08/2014 07:26 PM, Chris Fage wrote:
>> Hi Everyone,
>>
>> Thank you for the advice, especially Pavel's. My issue has been
>> resolved. I lowered the occupancy and B-factors of the metal ions in
>> the .pdb and ran phenix.refine for 10 cycles. This
s was also effective, dropping Rwork and Rfree by ~1% each. To
do this, I edited the "Individual B-factor refinement" values as
follows.
Isotropic atoms: not (element Zn)
Anisotropic atoms: element Zn
Best,
Chris
On 5/6/14, Chris Fage wrote:
> I have used CNS before, but not for this
n.
> So, I soaked in the appropriate amount of Ca2+ to see the residue in
> both positions. There was a high correlation between the asp residue
> orientation and the Ca2+ ion occupancy.
>
> Steven Herron
> sherron_...@yahoo.com
>
>
>
>
> On 5/6/2014 11:02 AM, Chris Fage
Hi Everyone,
In my 2.5-angstrom structure, there is negative Fo-Fc density
surrounding a metal ion after refining in Phenix. From anomalous
diffraction I am certain of the metal's identity and position in each
monomer. Also, the ion is appropriately coordinated by nearby side
chains. Should I be r
up
> CSIRO, CMSE
> 343 Royal Parade
> Parkville, VIC, 3052
> +613 9662 7304
> +614 57 539 419
> tom.p...@csiro.au
>
> From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Chris Fage
> [cdf...@gmail.com]
> Sent: Tuesday, April 22, 201
Hi Everyone,
I am trying to refine a structure with a phosphorylated amino acid. After
refining in Phenix, the Fo-Fc density (green) overlaps the 2Fo-Fc density
for all atoms of the derivatized amino acid in Coot, almost as if I had not
built in the residue. I am loading a .cif for the derivative
;m not sure why this
dataset in particular was less complete than the others.
Thanks,
Chris
On Fri, Feb 21, 2014 at 6:41 PM, Chris Fage wrote:
> Dear CCP4BB Users,
>
> I recently collected a number of datasets from plate-shaped crystals
> that diffracted to 1.9-2.0 angstroms and
Dear CCP4BB Users,
I recently collected a number of datasets from plate-shaped crystals
that diffracted to 1.9-2.0 angstroms and yielded very nice electron
density maps. There is no major density unaccounted for by the model;
however, I am unable to decrease Rwork and Rfree beyond ~0.25 and
~0.30,
I am grateful for all of the suggestions. I think I have enough tricks to
try at this point, but I may check back with this group if things don't
work out.
Many thanks once again,
Chris
On Sat, Jan 18, 2014 at 11:14 AM, Chris Fage wrote:
> Hello Everyone,
>
> I am currently try
eedle-like crystals.
Any further input is greatly appreciated!
Regards,
Chris
On Sat, Jan 18, 2014 at 11:14 AM, Chris Fage wrote:
> Hello Everyone,
>
> I am currently trying to phase a structure with an asymmetric unit
> predicted to contain 20-24 monomers (space group P1). Th
Hello Everyone,
I am currently trying to phase a structure with an asymmetric unit
predicted to contain 20-24 monomers (space group P1). The native crystals,
while beautiful in appearance (see attached), only diffract to ~3.4-3.0
angstroms at best, and SeMet-derived crystals grow with poor morphol
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