Re: [ccp4bb] calculation of active site area

Fpocket and CAVER are good. Yarrow On Friday, September 19, 2014, Faisal Tarique faisaltari...@gmail.com 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

[ccp4bb] wilson B in xds vs. truncate.

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

Re: [ccp4bb] Solvent channels

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 Madrona

Re: [ccp4bb] solvent exposed

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 hold...@uci.edu wrote:

[ccp4bb] stalled refinement after MR solution

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

Re: [ccp4bb] stalled refinement after MR solution

. 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 around 40% while Rwork is aorund 30%. The model is actually the same enzyme with a similar inhibitor bound

Re: [ccp4bb] stalled refinement after MR solution

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 On 8 May 2014, at 18:11, Yarrow Madrona amadr...@uci.edu wrote: Hello CCP4 community, I am stumped and would love some help. I have

Re: [ccp4bb] stalled refinement after MR solution

...@janelia.hhmi.orgwrote: Since your 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 *To:* Keller, Jacob

Re: [ccp4bb] stalled refinement after MR solution

:* 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 community, I am stumped and would love some help. I have a molecular

Re: [ccp4bb] stalled refinement after MR solution

the higher resolution to a greater degree. Hope this helps. Brent *From:* yarrowmadr...@gmail.com [mailto:yarrowmadr...@gmail.com] *On Behalf Of *Yarrow Madrona *Sent:* Thursday, May 08, 2014 1:50 PM *To:* Segelke, Brent W.; CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] stalled

Re: [ccp4bb] regarding TLS records

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

Re: [ccp4bb] regarding TLS records

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

[ccp4bb]

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 On 03/19/2014 08:58 AM, Yarrow Madrona wrote

[ccp4bb]

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 amadr...@uci.edu wrote: Thank you to everyone for their input. I am posting a picture to some of the symmetry related molecules shortly. There are six

[ccp4bb]

-3640-9407 Cellular: 0547 459 608 On Mar 19, 2014, at 18:37 , Eleanor Dodson eleanor.dod...@york.ac.uk wrote: How pretty - I love circular molecules! Eleanor On 19 March 2014 15:58, Yarrow Madrona amadr...@uci.edu wrote: Thank you to everyone for their input. I am posting a picture to some

[ccp4bb]

. 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, I recently collected data in-house

[ccp4bb]

. Thank you! https://www.dropbox.com/s/r01u37owbkz9pon/donut.png -Yarrow On Wed, Mar 19, 2014 at 6:59 AM, Yarrow Madrona amadr...@uci.edu 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

[ccp4bb]

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

[ccp4bb] [CCP4] Converting ShelX .phs to mtz

labels: H K L I FOM PHI SIGI Thank you Yarrow Madrona

[ccp4bb] shelx anamalous data

this info? -Yarrow -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

Re: [ccp4bb] [CCP4] Converting ShelX .phs to 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 of Yarrow Madrona [amadr...@uci.edu] Sent: Thursday, November 14, 2013 3:43

Re: [ccp4bb] A case of perfect pseudomerehedral twinning?

a translation 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 phenix package. It came up with what I pasted below: I am assuming

[ccp4bb] A case of perfect pseudomerehedral twinning?

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

[ccp4bb] A case of perfect pseudomerehedral twinning?

(+ 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 Student Molecular

[ccp4bb] A case of perfect pseudomerehedral twinning?

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. University

Re: [ccp4bb] A case of perfect pseudomerehedral twinning?

Jeffrey Princeton -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

Re: [ccp4bb] A case of perfect pseudomerehedral twinning?

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 phenix package. It came up with what I pasted below: I am assuming the the first rotation matrix is just

Re: [ccp4bb] How to compare B-factors between structures?

% difference is significant depends on how accurate you think your B factors are. If you kick your coordinates (aka using noise in PDBSET) and re-refine, how much do the final B factors change? -James Holton MAD Scientist On 2/25/2013 12:08 PM, Yarrow Madrona wrote: Hello, Does anyone know a good

[ccp4bb] How to compare B-factors between structures?

for your help. -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

Re: [ccp4bb] How to compare B-factors between structures?

for 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

Re: [ccp4bb] How to compare B-factors between structures?

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 amadr...@uci.edu wrote: Hello, Does anyone know a good method to compare B-factors between structures? I would like to compare mutants to a wild-type

Re: [ccp4bb] How to compare B-factors between structures?

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 compare mutants to a wild-type structure. For example, structure2 has a higher B-factor

[ccp4bb] Does Scala merge anomalous/non-anomalous?

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

[ccp4bb] calculating dialectric properties of enzyme active site

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

Re: [ccp4bb] calculating dialectric properties of enzyme active site

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 dialectric properties of enzyme active site Hello CCP4 list readers, Does anyone know how

[ccp4bb] Calculating water accessible volume in active site

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

[ccp4bb] offtopic: packing gel filtration columns

From: Yarrow Madrona amadr...@uci.edu Date: July 12, 2012 7:39:57 PM PDT To: Peter Hsu hsuu...@u.washington.edu 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

[ccp4bb] Fwd: [ccp4bb] offtopic: packing gel filtration columns

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

[ccp4bb] scalepackvirus rejections and Rrin

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

Re: [ccp4bb] scalepackvirus rejections and Rrin

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 I, Rm 2403

[ccp4bb] New or alternative to 3D Zalman monitor for coot/pymol?

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

Re: [ccp4bb] New or alternative to 3D Zalman monitor for coot/pymol?

, Yarrow Madrona amadr...@uci.edu wrote: Hello CCP4 mail subscribers, I know there have been previous threads regarding the use of a Zalman monitor for using coot and pymol on these message boards. I am wondering if there is a new alternative since the Zalman monitor is no longer being produced. I