Hi Andrew,
yes, exactly as you describe: set distance_ideal to a meaningful value
(approx. distance between density peaks, doesn't have to be very accurate),
and set sigma to some large number, say 1 or so.
Pavel
On Mon, Dec 19, 2016 at 7:40 PM, Andrew Marshall <
andrew.c.marsh...@adelaide.edu.a
Hi Pavel,
To define a weak bond, would you use "geometry_restraints.edits { ... bond
{... " , and just set a rough distance_ideal and a very high sigma (like
say 5A)?
Or are you referring to something different?
Andrew Marshall
PhD Candidate
Laboratory of Protein Crystallography
Dept. of Molecula
Hi Perdo,
technically this should work too with the caveat that non-blanc altid will
trigger occupancy refinement for corresponding atoms which may not be
desired.
Pavel
On Mon, Dec 19, 2016 at 12:54 AM, Pedro Matias wrote:
> Hi Andrew,
>
> The simplest way would be to place the "offending" a
Hi Andrew,
you can define a weak bond between clashing atoms which will disable
repulsion. A weak bond should not introduce any bias.
Pavel
On Sun, Dec 18, 2016 at 9:39 PM, Andrew Marshall <
andrew.c.marsh...@adelaide.edu.au> wrote:
> Hi all,
>
> I have a structure of a condensing enzyme with s
Could this be a covalent interaction?
Difficult to judge without seeing anything
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Andrew
Marshall
Sent: Tuesday, 20 December 2016 2:48 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Atom clashes in active site?
Hi all,
Th
Hi all,
Thank you for your suggestions. I tried the pdb file edit (making the
offending atoms of both the ligand and the protein 'B' altconf), but it
didn't seem to make any difference to their positions after a single round
of refinement..?
The atoms in the active site concern two acetyl groups -
Hi All,
I am asking if anyone used Ubuntu Mate operating system and is this system
good for Pymol and Coot 3D?
On 12/19/16 11:25, herman.schreu...@sanofi.com wrote:
Dear Andy,
I don’t think you will solve this pre-Xmas
...
There is hope of a pre-Christmas solution. Convert to Eastern Orthodox;
that will provide an extra two weeks margin, due to the Orthodox use of
the Julian calendar.
--
=
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Dear Andrew,
did you remove all cysteins, and all methionines with the mutations? Your
resolution is about 2A, if I understand correctly. This may be suitable for S-
SAD. I would try to get access to a modern inhouse machine to get high quality
data at high multiplicity. Some modern synchrotron
Dear All,
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To apply, please browse to the Structural Biologist and Principal Structural
Biologist
Thanks again Herman,
The protein is a two domain protein (approx 40aa, 350aa split) - searching with
either is proving fruitless.
Original, wild-type cell = 49 x 75 x 80 P212121
This painful mutant = 39 x 157 x 75 beta=98.26 P21
(so one can say that there seems to be a relationship there, wt b
Dear Andy,
I don't think you will solve this pre-Xmas, but here are some more suggestions:
-is there any relationship with the unit cell of the parent, unmutated protein?
This might give some ideas of the packing of the problem crystals.
-are some promising solutions being rejected due to clashes
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Hi All
OK sorted, I need:
tccif CCIFIN ./4j8q.cif
Cheers
-- Ian
On 19 December 2016 at 13:14, Ian Tickle wrote:
>
> Oooops sorry last email is incomplete:
>
> Im trying to read CCIF files using a simple Fortran program. Essentially
> this is all it is:
>
> REAL CC(6)
> CALL CCP
Hello All,
We are looking for recommendations/reviews of alternative 48 well hanging
drop plates. We had been using Hamptons HR3-275 VDX48 Plate with sealant,
but are looking for more affordable alternatives. Do you have suggestions
as to other good brands of plates to use/what you use in your lab
Oooops sorry last email is incomplete:
Im trying to read CCIF files using a simple Fortran program. Essentially
this is all it is:
REAL CC(6)
CALL CCPFYP
CALL CCP4CCIF_INIT
CALL CCP4CCIF_ROPEN('CCIFIN','',ID)
CALL CCP4CCIF_GETCELL(ID,CC,VC,IE)
PRINT *,CC
Hello All
Im trying to read CCIF files using a simple Fortran program. Essentially
this is all it is:
CALL CCPFYP
CALL CCP4CCIF_INIT
CALL CCP4CCIF_ROPEN('CCIFIN','',ID)
CALL CCP4CCIF_GETCELL(ID,CC,VC,IE)
PRINT *,CC
END
Dear All,
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Thanks Herman. In short:
-no twinning suggested from xtriage etc
-P2 doesn't give a solution either
-monoclinic cell would have 2 (60% solvent) or 3 (40% solvent) copies
-I originally thought the zanuda P1 route would be the way to go, but phaser
was still churning away after running overnight an
Hi Andrew,
in the past I solved this problem by either switching off certain van der Waals
repulsions, or by specifying a very small van der Waals radius for certain
atoms. In Xplor/CNX this was rather easy. I do not know how this is with phenix.
Best,
Herman
Von: CCP4 bulletin board [mailto:CC
Dear Andrew,
Just a few questions:
-Do the processing/refinement programs suggest twinning?
-Are you sure your space group is P21 and not P2? Did you try MR in P2?
-How many protein molecules do you expect in the asymmetric unit?
P2(1) is a very low symmetry space group. In this case I would not
Dear Dhaval,
To check whether your compound precipitates, you could set up crystallization
drops with everything (buffer, precipitant, compound), but without the protein.
If the precipitates still form, it’s your compound.
Remember, getting cocrystals with your ligand of interest might be as dif
Hi Andrew,
The simplest way would be to place the "offending" atoms in separate
conformers as used to refine alternate conformations. This is a 1-letter
code that goes just before the 3-letter residue name:
> ATOM139 SG *B*CYS A 21 -20.620 4.518 34.501 0.39
> 12.23 AS
Thi
Dear All,
I have just collected data on a mutant of a protein that should be facile to
solve by molrep (one residue/320 changed, approx 2Ang resolution) but is
proving problematic. Data merging stats look good.
The spacegroup is monoclinic, P21, the cell:
a=39.47 b=157.36 c=74.9 beta=98.26
I
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