Fpocket and CAVER are good.
Yarrow
On Friday, September 19, 2014, Faisal Tarique
wrote:
> Dear all
>
> Please tell me the names of good servers / tools which calculate the
> size and surface area of the active site pocket of a protein..
>
> --
> Regards
>
> Faisal
> School of Life Sciences
> JN
Hello CCP4 users.
I noticed a discrepancy between the estimated wilson B reported by XDS and
that reported by truncate. As far as I know XDSconv and truncate use the French
and Wilson (K.S. Acta. Cryst. (1978), A34, 517-525.) method for converting
to structure factors. However, the result below is
Hey Jeff,
Why not try the command line version of CAVER. It is easily adjustable and
provides nice figures of solvent accessibility for Pymol. It also prints
out a ton of stats in the log files if you want numbers.
-Yarrow
On Wed, Jun 25, 2014 at 1:10 PM, Jeff Holden wrote:
> Experts,
>
> I w
You can use CAVER but you would have to make all the symmetry mates as one
chain in order to fool it. Still better to just do the experiment I think.
Either it will work or it won't, regardless of what any software tells you.
Just a wild idea : )
On Fri, Jun 27, 2014 at 5:06 PM, Yarrow Ma
ry refining to a less ambitious resolution to start,
> assuming anisotropy will affect the higher resolution to a greater degree.
>
>
>
> Hope this helps.
>
>
>
> Brent
>
>
>
> *From:* yarrowmadr...@gmail.com [mailto:yarrowmadr...@gmail.com] *On
> Behalf Of
>
>
>
> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of
> *Yarrow
> Madrona
> *Sent:* Thursday, May 08, 2014 10:12 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] stalled refinement after MR solution
>
>
>
> Hello CCP4 commun
our search model is so good, why not go down to p1 to see what’s
> going on, then re-merge if necessary?
>
>
>
> JPK
>
>
>
> *From:* yarrowmadr...@gmail.com [mailto:yarrowmadr...@gmail.com] *On
> Behalf Of *Yarrow Madrona
> *Sent:* Thursday, May 08, 2014 4:29 PM
>
atology, University of Cambridge
> Cambridge Institute for Medical ResearchTel: +44 1223 336500
> Wellcome Trust/MRC Building Fax: +44 1223 336827
> Hills Road
> E-mail: rj...@cam.ac.uk
> Cambridge CB2 0XY, U.K.
> www-structmed.cimr.cam.ac.uk
>
>
roject onto the
> BB there is little we can do for you.
>
> Dale
>
> On 05/08/2014 10:11 AM, Yarrow Madrona wrote:
> > Hello CCP4 community,
> >
> > I am stumped and would love some help. I have a molecular
> > replacement solution that has Rfree stuck a
Hello CCP4 community,
I am stumped and would love some help. I have a molecular replacement
solution that has Rfree stuck around 40% while Rwork is aorund 30%. The
model is actually the same enzyme with a similar inhibitor bound. Relevant
information is below.
-Yarrow
I have solved a structure i
Thanks Pavel. I was a little tired from an overnight Synchrotron run when I
wrote that. Lesson: Stay off the internet when you are tired. Haha. I
forgot that the TLS groups would be assigned per chain not per molecule.
Thanks for the correction. I didn't know you could run find TLS groups as
part o
Hi Vipin,
I'm not sure what software you are running or your refinement strategy.
However, in some refinement software (phenix.refine), if you run TLS
refinement and you don't specify the TLS groups, the entire structure is
considered one TLS group which is not helpful. This may be why the
annotat
: ++972-3640-8723
> Fax: ++972-3640-9407
> Cellular: 0547 459 608
>
> On Mar 19, 2014, at 18:37 , Eleanor Dodson
> wrote:
>
> How pretty - I love circular molecules!
> Eleanor
>
>
> On 19 March 2014 15:58, Yarrow Madrona wrote:
>
>> Thank you to everyone f
ckstraat 35, 9000 Ghent, Belgium
> Tel/SMS/texting +32 (0)472 928 519
> Skype: savvas.savvides_skype http://www.LProBE.ugent.be/xray.html
>
>
>
> On 19 Mar 2014, at 16:58, Yarrow Madrona wrote:
>
> Thank you to everyone for their input. I am posting a picture to some of
> th
g of the latest structure we solved. :)
> https://dl.dropboxusercontent.com/u/5116503/4J05.png
>
> best
> -Bjørn
>
> --
> Bjørn Panyella Pedersen
> Macromolecular Structure Group
> Dept. of Biochemistry and Biophysics
> University of California, San Francisco
>
&g
o 3.2 angstroms. Thank you!
https://www.dropbox.com/s/r01u37owbkz9pon/donut.png
-Yarrow
On Wed, Mar 19, 2014 at 6:59 AM, Yarrow Madrona wrote:
> Yes in the first couple of rounds of refinement it refines very well for a
> 3.2 angstrom structure (Now at 30%/24% Rfree/R). Everything Packs
not another molecule.
> Does it refine? If you look at the maps following refinement any missing
> features should become more obvious.
> Solvent content of 65% is not uncommon.
> Eleanor
>
>
> On 19 Mar 2014, at 03:46, Yarrow Madrona wrote:
>
> Hello CCP4 Users,
>
>
Hello CCP4 Users,
I recently collected data in-house on an Raxis IV and am trying to solve a
3.2 angstrom structure.
I have obtained only "partial solutions" using Phaser and would like some
help. I believe I only have two molecules in the ASU instead of three as
suggested by the mathew's calcula
lt will be a complete
> merge.mtz with all original data plus phase information. This will assure
> you do not loose anything on the way.
>
> Good luck,
>
>
> Yury
>
>
>
> From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf o
how to get
this info?
-Yarrow
--
Yarrow Madrona
Graduate Student
Molecular Biology and Biochemistry Dept.
University of California, Irvine
Natural Sciences I, Rm 2403
Irvine, CA 92697
labels:
H K L I FOM PHI SIGI
Thank you
Yarrow Madrona
--
Yarrow Madrona
Graduate Student
Molecular Biology and Biochemistry Dept.
University of California, Irvine
Natural Sciences I, Rm 2403
Irvine, CA 92697
labels:
H K L I FOM PHI SIGI
Thank you
Yarrow Madrona
Fax: +44 1223 336827
> Hills Road
> E-mail: rj...@cam.ac.uk
> Cambridge CB2 0XY, U.K.
> www-structmed.cimr.cam.ac.uk
>
> On 15 Oct 2013, at 22:31, Yarrow Madrona wrote:
>
>> Thank you Dale,
>>
>> I will "hit-the-books" to better the rotation
t; of about 31 A along x so if your A cell edge is about 62 A you have
> a 2_1 screw.
>
> Dale Tronrud
>
> On 10/15/2013 12:29 PM, Yarrow Madrona wrote:
>> Hi Phil,
>>
>> Thanks for your help.
>>
>> I ran a "Find-NCS" routine in the phen
of the P21 asymmetric unit if it was really
> P212121 and you could overlap the maps corresponding to the different
> monomers using those programs.
>
> Phil Jeffrey
> Princeton
>
>
--
Yarrow Madrona
Graduate Student
Molecular Biology and Biochemistry Dept.
University of California, Irvine
Natural Sciences I, Rm 2403
Irvine, CA 92697
ssed in P2
Refinement without twin law:
Rwork = 0.3387
Rfree = 0.3650
~85% Ramachandran favored (+ missing part of helix)
Refinement with twin law:
Rwork = 0.2994
Rfree = 0.3214
--
Yarrow Madrona
Postdoctoral Scholar
Ortiz De Montellano Lab
Pharmeceutical Chemistry Dept.
Univ
(+ missing part of helix)
Refinement with twin law:
Rwork = 0.2994
Rfree = 0.3214
--
Yarrow Madrona
Postdoctoral Scholar
Ortiz De Montellano Lab
Pharmeceutical Chemistry Dept.
University of California, San Francisco
Genentech Hall, Rm N556
--
Yarrow Madrona
Graduate Stud
(+ missing part of helix)
Refinement with twin law:
Rwork = 0.2994
Rfree = 0.3214
--
Yarrow Madrona
Postdoctoral Scholar
Ortiz De Montellano Lab
Pharmeceutical Chemistry Dept.
University of California, San Francisco
Genentech Hall, Rm N556
actor of 80, then suddenly 78
> vs 83 doesn't seem all that different (only a 10% change). Basically, a
> difference that would be "significant" in a high-resolution structure is
> "washed out" by the overall crystallographic B factor of the
> low-resolution struc
ge B-factors, because
> you won't have the exact same number of atoms.
>
> Best, Manfred
>
> On 25.02.2013 21:08, Yarrow Madrona wrote:
>> Hello,
>>
>> Does anyone know a good method to compare B-factors between structures?
>> I
>> would like to compar
happy to make additions or modifications to this, but
> so far I haven't received much feedback.)
>
> -Nat
>
> On Mon, Feb 25, 2013 at 12:08 PM, Yarrow Madrona wrote:
>> Hello,
>>
>> Does anyone know a good method to compare B-factors between structures?
>&
your help.
--
Yarrow Madrona
Graduate Student
Molecular Biology and Biochemistry Dept.
University of California, Irvine
Natural Sciences I, Rm 2403
Irvine, CA 92697
--
Yarrow Madrona
Graduate Student
Molecular Biology and Biochemistry Dept.
University of California, Irvine
Natural Sciences
your help.
--
Yarrow Madrona
Graduate Student
Molecular Biology and Biochemistry Dept.
University of California, Irvine
Natural Sciences I, Rm 2403
Irvine, CA 92697
he phenix log-file to
>> figure out why it calculates the completeness so low.
>>
>> Regards,
>> Tim
>>
>> On 12/04/2012 11:55 PM, Yarrow Madrona wrote:
>>> Hello CCP4 users,
>>>
>>> My column labels from scala include:
>>>
>
factors?
I don't need the anomalous data so I don't need to keep it separate.
Thanks.
-Yarrow
--
Yarrow Madrona
Graduate Student
Molecular Biology and Biochemistry Dept.
University of California, Irvine
Natural Sciences I, Rm 2403
Irvine, CA 92697
: 972-8-647-2992 or 972-8-646-1710
>
>
>
>
>
>
> From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Yarrow
> Madrona [amadr...@uci.edu]
> Sent: Saturday, October 06, 2012 4:48 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] calculating di
Hello CCP4 list readers,
Does anyone know how to calculate the dielectric properties of an enzyme
active site? I would like to compare the polarity/hydrophobicity of
similar proteins and different mutants.
Thank you.
--
Yarrow Madrona
Graduate Student
Molecular Biology and Biochemistry Dept
I have a buried active site and would like to determine if there is room
for a water molecule in various mutants. Does anyone know of a good
program to calculate this? I have heard of GRID and VOID but have never
used them.
Thanks.
--
Yarrow Madrona
Graduate Student
Molecular Biology and
> Try manually purging the pump with a syringe.
> I have had some success running hot water followed by NOAH and guanadine
> when the pump was clogged with a buffer that crapped out in the pump. If the
> pump is really clogged the pressure should spike when you try to run it. If
> not somethin
> Subject: Re: [ccp4bb] offtopic: packing gel filtration columns
>
> We do it pretty routinely in our lab with great results. To do it right you
> have to invest in a reservoir sold by GE. It screws onto the end of the
> column. It allows you to pour the entire slury (resin and water) into the
> From: Yarrow Madrona
> Date: July 12, 2012 7:39:57 PM PDT
> To: Peter Hsu
> Subject: Re: [ccp4bb] offtopic: packing gel filtration columns
>
> It is also likely that the clogging due to NAOH is due to crapped out
> protein. Try cleaning with guanadine.
>
>
&g
la, although I have never tried that myself.
>
> Good luck
>
> Carsten
>
>
> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Yarrow Madrona
> Sent: Tuesday, December 06, 2011 11:04 AM
> To: CCP4BB@JISCMAIL.AC.UK
anyone know if this is correct?
Also I wondered if there is any way to get a redundancy dependent R value
from scalepack. Thank you.
-Yarrow
--
Yarrow Madrona
Graduate Student
Molecular Biology and Biochemistry Dept.
University of California, Irvine
Natural Sciences I, Rm 2403
Irvine, CA 92697
0:1 5ms DVI VGA 3D Black
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> Account Executive
> ASI- Atlanta
> Phone: (800) 746-6274 x 343
> Fax: (678) 502-1392
> Email and MSN: oliver@asipartner.com
>
>
>
>
>
>
>
>
>
>
>
> On 5/30/11 12:38 PM,
gt; Hi,
> How sure are you about that Zalman is no longer producing 3D monitors?
> There is plenty of stock of the 24-inch 3D model ZM-M240W in Europe at
> least.
>
> Cheers,
>
> Maritn
>
> On May 30, 2011, at 6:38 PM, Yarrow Madrona wrote:
>
>> Hello CCP4 mail subs
are looking for a less expensive
alternative to the SGI work station that just blew-up. We are thinking of
buyng a mac and using something like a Zalman monitor. Alternatively we
are thinking of running Fedora with a Zalman monitor. Thank you for your
help.
-Yarrow
--
Yarrow Madrona
Graduate
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