Re: [ccp4bb] Multiple NCS relations

Or download the latest refmac 6.6, and it will do NCS fully automatically, and handle conformational flexibility too. David Schuller wrote: I think you should be able to specify two different NCSR lines, one to cover chains AA' and CC', and another to cover chains BB'. On 06/23/10 18:51,

[ccp4bb] molecular replacement

Dear All, I am trying to resolve a protein structure with the use of Molecular Replacement. However, some part of protein are overlap in the interface of homodimer. Would someone please give me suggestions? Thank you! -- Best regards, WuXH

Re: [ccp4bb] Multiple NCS relations

If this is happening something is wrong! REFMAC can certainly use multiple NCSR requests.. I usually check the agreement with the Superpose molecules task (Coordinate utilities) matching all atoms just to make sure that AC does match A'C' and B matches B'. If the RMS difference is greater

Re: [ccp4bb] model refinement (corrections, apologies!)

Rfactors can vary a lot for equally good results it seems. You need to look at your Rfactor v resolution to see if there are any problems - ice rings? low resolution stuff? etc etc Have you used TLS sensibly - this can help.. etc etc But if the maplooks good you should be happy. Eleanor Tim

Re: [ccp4bb] molecular replacement

Hi there, If there are a few clashes (acceptable - usually surface loops that enter the surface part of another molecule or subunit) then you can delete the parts of loops that usually have poor density and that clash, refine, compute a new map and see if the loop can be traced (usually it

Re: [ccp4bb] Merohedral twining for P212121. -

Matheus, Ian, Frank, Jonathan Thanks for all the comments. It is easy to calculate the amount of splitting of the spots once the cell dimensions of each component are known. For the P212121 case, with a-b twinning, splitting will be zero in the c* direction. The splitting will increase as h and k

Re: [ccp4bb] How to run UPPSALA-mapman in PBS?

On Thu, Jun 24, 2010 at 4:15 AM, Hailiang Zhang zhan...@umbc.edu wrote: Hi Tim: Thanks a lot for suggeting exec in my shell script. It really works under both shell and PBS; however, the running was just terminated right after exec ${DIR}/lx_mapman was excutated. I am not sure why this

[ccp4bb] Fellowship available

GRADUATE PROGRAMS IN BIOLOGICAL SCIENCES: BIOCHEMISTRY-IMMUNOLOGY PHYSIOLOGY-PHARMACOLOGY Institute of Biological Sciences – Universidade Federal de Minas Gerais - Brazil Fellowship available The coordinators of the Graduate Programs in Biochemistry-Immunology and Physiology-Pharmacology of the

[ccp4bb] older ACA Transactions available

If anyone can use any of these, please let me know. The only thing I ask is postage reimbursement. Vol. 16 1980Structure and Bonding Relationships Between Quantum Chemistry and Crystallography, T.F. Koetzle, Ed. Vol. 17 1981Diffraction Aspects of Orientationally

[ccp4bb] Another scaling question

Dear CCP4bb, I am still playing around scaling two datasets together and have noticed another interesting behavior in scala. If I scale all my data (from 1.5A to 51A) I get 100% completeness in my outer shell, 98% in my inner shell and 99.9% overall, stats that I am normally quite happy

[ccp4bb] Improved Version of ADIT Available

Improved Version of ADIT Available An updated and enhanced version of ADIT is now available for depositing new entries at http://deposit-beta.rcsb.org/adit/. We encourage depositors to use this new tool and send feedback to depo...@deposit.rcsb.org. ADIT is used to validate and submit

Re: [ccp4bb] older ACA Transactions available

That was quick. They are all taken. Frances = Bernstein + Sons * * Information Systems Consultants 5 Brewster Lane, Bellport, NY 11713-2803 * * *** *Frances C.

Re: [ccp4bb] Stuck refinement

Francis E Reyes wrote: Sorry a late comer to this thread but the OP mentioned tweaking the error model in HKL2000. I have heard this before.What's the validity in this? Does it actually help or does it only help the integration numbers but you'll pay for it during refinement? FR There is no

Re: [ccp4bb] Another scaling question

It might be instructive to draw a precession-like diagram of your reflections in reciprocal space. Remember that reciprocal space dimensions are generally in reciprocal Angstrom and volumes raise those dimensions to the third power. Thus (1/12)^3 to (1/15)^3 is not a big volume. How many

Re: [ccp4bb] How to run UPPSALA-mapman in PBS?

Hi Ian: There was an issue with the environment setup of my PBS script, which has just been fixed and everything back to normal. Anyway, thanks a lot for all the help! Best Regards, Hailiang On Thu, Jun 24, 2010 at 4:15 AM, Hailiang Zhang zhan...@umbc.edu wrote: Hi Tim: Thanks a lot for

[ccp4bb] error in running Phaser NMA mode

I am getting an error in running Phaser in NMA mode based on the usage in the Phaser document. pre BFONT COLOR=#FF html!-- CCP4 HTML LOGFILE -- !--SUMMARY_BEGIN-- #

[ccp4bb] Postdoctoral position in Houston

Dear all, A position has become available for a Post-doctoral Refsearch Fellow in the Department of Pharmacology, at Baylor College of Medicine in Houston. The focus of our work is on structural and biochemical characterization of Serine/Threonine protein kinases. The successful candidate will be

[ccp4bb] LINK option during refinement

Dear Dr. Murshudov, I am working on the heme protein with a surface Cys residue covalenlty linked to another molecule through its SG atom. Here is a part of log file. -- INFO: link is found (not be used) dist= 2.188 ideal_dist= 2.300 ch:AA res: 400

Re: [ccp4bb] LINK option during refinement

In your run with the option residues are close only refmac also should generate a pdb file with link records added. In very simple form you can edit this pdb file and remove all unnecessary links and leave link you want. Then you can rerun with normal options and generated library. Better

Re: [ccp4bb] error in running Phaser NMA mode

Hello, I used this script once just to have a look at some NMA-moved structures: --- #!/bin/bash if [ $# -ne 1 ] ; then #0 1 echo usage: phaser_nma.sh INPUT.PDB exit 1 fi name=`echo $1 | sed s/\.pdb$//g` phaser EOF TITLE moved by some low frequency normal

[ccp4bb] Matthews coefficient

hi CCPeers The Matthews coefficient of my protein is 3 calculated with matthews-cell content analysis CCP4 programe with 87% confidence , but when doing the refinement the third molecular couldn't get into the unit cell because of too many clashes.Deletion of the clashed AA did not work well,

Re: [ccp4bb] Matthews coefficient

Hi everyone: Thanks for all the responses. The Matthaws-cell content analysis programe in CCP4 package gives the results: 47% solvent content and 3 molecules in asu with 87% confidence. the space group is P3121. how to carry out self rotation function? can phaser do that work? If there