[ccp4bb] Career opportunity at Ambry Genetics

Hi, We would like to draw your attention to a new career opportunity in structural biology at Ambry Genetics. Please see the link below: https://recruiting.ultipro.com/AMB1001AMGEN/JobBoard/bcdd10b1-192e-e264-1203-f18eb6dd40c1/OpportunityDetail?opportunityId=6a66793e-789c-4857-b14a-cc50cbdd1d1

Re: [ccp4bb] AW: [ccp4bb] Cleaved peptide density!

l > form. You may also want to scan the literature to see if some non-cleavable > substrate-analog (inhibitor) is available. > > On the positive side: your structure with the cleaved peptide is also > interesting, since it represents the product complex! > > Good luck! >

Re: [ccp4bb] Best method for weighted averaging of Friedel pairs?

+ + I- ) sigImean = 0.5 * sqrt( sigI+^2 + sigI-^2 ) The only CCP4 program I found that actually does this is mtzMADmod. This method also has the advantage that the original intensity values of I+ and I- can be reconstructed from the mean and the anomalous difference (albeit with the loss of the ori

Re: [ccp4bb] From non-twinned to twinned?

I wouldnt expect radiation damage to cause twinning! 1) maybe you have different indexing for the 2 passes? Have you used pointless to check if this could happen (depends on SG and cell dimensions) Ask for "match reference set in input and give it sca1 as input 1, then check sca2 2) use pointle

Re: [ccp4bb] chirality problem

alformed >> geometry, typically flattening of of the group. This means that a >> computational chirality problem can lead to a 'real' chirality problem. >> In >> Refmac, this will not happen for LEU or VAL, but it will happen for >> things >> like SO4, GOL

Re: [ccp4bb] on water picking

I am not sure what you mean by clashing at 0.4A - such a site must mean something is wrong. coot will select resasonable waters for you - it is very conservative. refmac and other software lists clashes and you should do something about them - move protein - delete water - worry! Eleanor On Fri

Re: [ccp4bb] Help with deleting reflections from an mtz file

Thanks Clemens - I knew it should be possible! Documentation didnt exactly help.. Eleanor On Wed, 17 Aug 2011 19:20:21 +0100, Clemens Vonrhein wrote: > Dear Eleanore, > > Ooops - the ccp4bb rejects attachements with *.sh ending? Let's try it > again with *.sh.txt ... > > The attached script wo

[ccp4bb] Coot for Virtalis Immersive VR Display System

ified Coot for this system? (Or any other molecular graphics programs that have been?) Cheers, Jan White (jan.wh...@shef.ac.uk) -- ***** CCP4 Account *** * Molecular Biology, Sheffield University * * Phone: +44 114 222 2741 FAX: 222 2800 * * E-Ma

Re: [ccp4bb] cTruncate fails after Scala - clipper::Message_fatal

gt; running through it looks like the problem is name truncation on the output > columns. Whether it is the > total name, /crystal/dataset/column , or just the column name I do not > know. If I reduce the length of > colout it runs through successfully > Charles Ballard > CCP4 &

Re: [ccp4bb] adding side-chains to a backbone model (without introducing clashes in the process)

such task > (http://www.pirx.com/pulchra/index.shtml). > > I wonder if there is another tool in the CCP4 treasure chest > for the same kind of task (preferably open source). > > Regards, > F.

Re: [ccp4bb] No reflections in resolution bin???"

Oh dear - how did you lose it! It isworth hunting back through the data files - all data processing software I know of outputs both F and SigF and I and SigI .. nt Remember - it is good practice to ALWAYS use that first merged data set as the input to refinement Eleanor On Thu, 4 Aug 2011 08:10:1

Re: [ccp4bb] Sodium ion vs. Water

:31:09 -0500, Jacob Keller wrote: > I asked the CCP4 experts this question a while back--maybe try > searching the archive? There were some very helpful comments. > > Jacob > > On Tue, Aug 2, 2011 at 1:24 PM, Young-Jin Cho wrote: >> Dear CCP4 experts, >> >> I w

Re: [ccp4bb] ARP/wARP install on 6.2.0 & RHEL 6?

seemed to have worked.. Can someone - either CCP4 or arp-warp people check this out? Eleanor On Wed, 27 Jul 2011 20:35:50 -0700, Ethan Merritt wrote: > On Wednesday, 27 July 2011, you wrote: >> Hi Jonathan, >> seems to be a UW centered day today on the BB (Eric, Jan, you, m

Re: [ccp4bb] I/sigma for h+k=2n+1 and h+k=2n

>From memory - check the documentation mtzutils hklin1 data.mtz RZONE 1 1 0 2 0 lists reflections with h+k = 2n END mtzutils hklin1 data.mtz RZONE 1 1 0 2 1 lists reflections with h+k = 2n+1 END Eleanor This will list all On Tue, 26 Jul 2011 09:51:47 -0400, zhang yu wrote: > H

Re: [ccp4bb] Non-crystallography symmetry operator

; molecules in ASU. Is that right or I missed something? > > In "SUPERPOSE" of CCP4, How to ask the program to calculate the NCS > operator? It asks me to input two structures and will output another pdb > file. > > Yu > > 2011/7/25 Frederic VELLIEUX > >&g

Re: [ccp4bb] Phaser and Molrep gave different solutions

That looks very hopeful. Do you know how the two molecules are related to each other? Do they form a dimer or have some interesting relationship? I would keep on improving the model - possibly use COOT to average the density and build into that for a start. I presume there are still side chains to

Re: [ccp4bb] Phaser and Molrep gave different solutions

Did you test other possible space groups? >> Choosing >> the wrong space group could exactly lead to the results you observe. >> >> Best, >> Herman >> >> >> -- >> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMA

Re: [ccp4bb] low resolution refinement

Roberto steiner has told you how to use these new REFMAC5.6 features, Rob Nicholls has suggested how to generate secondary structure restraints, and Martyn Winn given a page to install a new interface to make it easier to use them.. But with such limited data it isnt surprising that the FreeR c

Re: [ccp4bb] abnormal I/Sigma over phi rotation range

This seems somewhat weird - your Rmerge values increase with more frames as explained by Tim, but I cant see why the I/SigI should increase sharply for the 180 degree set then fall off again. if you have run Scala look at the scaling plots v batch, and resolution to see if there are any weird outli

Re: [ccp4bb] Same protein, different molecule numbers per ASU

PM, Alexandre OURJOUMTSEV > wrote: > >> Dear Ferrol, >> >> ** ** >> >> Could you let us know the unit cell parameters for both these crystals ? >> (did I miss them somewhere in your previous mails?). I wonder if in fact >> this is not the same pack

Re: [ccp4bb] occupancy-refinement

You are right that refining occupancy and B value at the same time cant be done with REFMAC, and probably wouldnt work anyway at 2.9A However, if you set the ligand occupancy to 0.7 say, and refine the residue B factors, the occupancy should not be set back to 1.0. It certainly isnt in the local

Re: [ccp4bb] how to combine the experimental phase and molecular replacement phase

I would run DM first to extend the experimental phases to the limit of your resolution.. Then if you run REFMAC to refine your MR model, using the experimental phases as part of the input the output phases from REFMAC will include contributions from both the MR and the DM/experimental phasing. Thi

Re: [ccp4bb] large R-Rfree difference in "final" structure

jelly-body restraints, although they may not work at your resolution. >> >> >> >> Cheers, >> >> Robbie >> >> >>> Date: Wed, 13 Jul 2011 08:38:38 -0700 >>> From: careinaedgo...@yahoo.com >>> Subject: [ccp4bb] large R

[ccp4bb] Stereo 3D LCD is coming for gamers

ces will tumble. Then maybe us oldies will be able to have lovely stereo again, and even the kiddies may see the light. Cheers, Jan -- * CCP4 Account (Jan White) * Molecular Biology, Sheffield University * * Phone: +44 114 222 2741 FAX: 222 2800 * *

Re: [ccp4bb] Cocrystals - should they pop up under native conditions?

Dear Brenda, I am running co crystallisation experiments and have thus far been trying under oil screens with some success (i.e. various hits in various conditions resulting in crystal growth). These conditions have varied from the native condition up until now. Do you already have the s

Re: [ccp4bb] Characterization of common salt crystal forms?

Dear Joe, working with divalent ions, I often get salt crystals (most surely phosphate). I do not have any table available, but can give you the commercial kits & numbers going with it. Just let me know. On Jan 22, 2008, at 6:12 PM, Joe Krahn wrote: Salt crystals are common in macromolecu

Re: [ccp4bb] salt sensitive complex

Dear Jerry, Are there some better ways that I can validate the binding affinity? I think it is possible to calculate the interacting energies by APBS... once you have the complex structure this is! Would be interesting to compare the values of the constants you get from ITC and SPR with

[ccp4bb] CCP4mg Molecular Graphics v1.1 now released

Hello CCP4BB, We are pleased to announce the release of CCP4mg v1.1 which is now available from http://www.ysbl.york.ac.uk/~ccp4mg ... also, please follow the link from the home page to sign up for the CCP4MG bulletin board. New features: Picture wizard which will set up complex scenes quickl

[ccp4bb] New CCP4 Molecular Graphics (1.1beta2)

Hello CCP4bb, CCP4mg version 1.1 (beta2) is now available from http://www.ysbl.york.ac.uk/~ccp4mg New features include: Picture Wizard - set up standard scenes automatically (and easier labeling) Less automatic superposition to complement the SSM automatic tools Lipid cartoons Editable picture