Re: [ccp4bb] 3D structure based alignment

Hi Tania, A classical way of superimposing two structures is to use lsq_e and lsq_i commands in O . You can specify the regions that you want to match and visualize the superimposed structures right away to see if they make sense or not. O will also give you a pairwise sequence alignment and RM

[ccp4bb] Microsymposium 9 at Osaka IUCr Congress

Dear Colleagues, Here is an update on Osaka IUCr Congress MS9 ie http://www.iucr2008.jp/scientific_program99.html#MS MS9 Macromolecular structural studies by powder diffraction, AFM etc. MS9 Titles and Speakers confirmed thus far:- "Seeing the first stages of protein crystal nucleation through

Re: [ccp4bb] MolRep of coiled coils

MR on CCs is generally a pain. The problem is that sliding any CC along its own supertwist (say by one heptad) will give you a solution that lines up very well with the "right" model. There are a lot of solutions of this type, so you basically have a multitude of models that are all "okay" an

Re: [ccp4bb] 3D structure based alignment

Hi, You can use Chimera to do the work . Good Luck! liu Tânia Oliveira wrote: Hello, I´m having a problem that I would like to know if someone could help me. I want to do a 3D structure based alignment of my protein with another one. The problem is that my protein has 2 domains, and the stru

Re: [ccp4bb] 3D structure based alignment

Hallo Tânia, you can try 'Rapido' by R. Mosca and T. Schneider at EMBL Hamburg. It is available as a web application under: http://webapps.embl-hamburg.de/rapido/ Best wishes, Gerrit Langer. Tânia Oliveira wrote: Hello, I´m having a problem that I would like to know if someone could help

Re: [ccp4bb] problem with Coot and ccp4mg

Uma Katre schrieb: Dear all, I recently installed CCP4 suite on a DELL workstation running Red Hat Enterprise Linux 5. CCP4 seems to be working fine, however, Coot and ccp4mg fail to open. This is what I get when I try to run Coot: current_exe_dir is /usr/local/ccp4/ccp4-6.0.2/Coot-0.3.3/bin

Re: [ccp4bb] program to draw 2D image of a peptide

I want to draw a picture of the contact of a 22-mer peptide with a protein in a 2-D perspective. Would be basically be what Ligplot does, however I don`t like the output of this program. I know that using programs like ChemDraw I can do it manually but decide to see if anyone knew about a progr

[ccp4bb] 3D structure based alignment

Hello, I´m having a problem that I would like to know if someone could help me. I want to do a 3D structure based alignment of my protein with another one. The problem is that my protein has 2 domains, and the structure that I want to superimpose just have one. I can do the structure superimposit

Re: [ccp4bb] program to draw 2D image of a peptide

I have a perl script to do this. It creates a pymol script and runs pymol to generate the view you are looking for. Thanks Abhinav Stanford Synchrotron Radiation Laboratory Joint Center for Structural Genomics Mail Stop 99 Phone: (650) 926-2992 Fax: (650) 926-3292 -Original Messa

Re: [ccp4bb] Model ensemble for x-ray crystallography

Have a look at this: Acta Cryst. (2007). D63, 597-610 Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models T. C. Terwilliger, R. W. Grosse-Kunstleve, P. V. Afonine, P. D. Adams, N. W. Moriarty, P. Zwart, R. J. Read, D. Turk and L.-W. Hung Pavel. O

Re: [ccp4bb] Model ensemble for x-ray crystallography

Something to think about in using ensembles for refinement: Even in ultra high resolution crystal structures, usually only a single conformation for MC (maybe dual in some places) is seen and maybe 2-3 conformations for many SCs. Occupancies of these SCs can be adjusted during refinement with ev

[ccp4bb] Abstract submission deadline

Dear Colleagues, This is a friendly reminder that the abstract submission deadline for IUCr Congress in Osaka, Japan is March 31st. One of the many interesting sessions is entitled "Recent progress in synchrotron data collection" (Session number is MS65). This session will cover new development

Re: [ccp4bb] MolRep of coiled coils

Hi Thomas, MR of coiled coils can be quite tricky including considerations of being curved, etc. If conventional MR is failing (assuming you have tried different kinds of parameter and search model tweaks, you can also play around with the search thresholds in phaser), you may try the followi

[ccp4bb] problem with Coot and ccp4mg

Dear all, I recently installed CCP4 suite on a DELL workstation running Red Hat Enterprise Linux 5. CCP4 seems to be working fine, however, Coot and ccp4mg fail to open. This is what I get when I try to run Coot: current_exe_dir is /usr/local/ccp4/ccp4-6.0.2/Coot-0.3.3/bin COOT_PREFIX is /usr/lo

Re: [ccp4bb] Model ensemble for x-ray crystallography

PDB entries 1LYZ, 2LYZ, 3LYZ, 4LYZ, 5LYZ, 6LYZ all have the same reference: Diamond, R. (1974) Real-space refinement of the structure of hen egg-white lysozyme. J.Mol.Biol. 82: 371-391 I believe they are independent refinements using the same experimental data. I do not have access to the jo

[ccp4bb] program to draw 2D image of a peptide

Does anyone know of a program, different from Ligplot, that can draw 2D image of peptides out a pdb file? It would be a plus if it can establish and draw contacts between this peptide and the neighbors residues. thanks in advance for any input. Sandra

Re: [ccp4bb] Model ensemble for x-ray crystallography

At 10:13 AM 3/28/2008, Lucas Bleicher wrote : Some time ago I've heard about the idea of proposing an ensemble of models (as in NMR), instead of a single model for x-ray crystallography structures. If I remember correctly, this idea has been published somewhere. Can anyone tell me what article

Re: [ccp4bb] Model ensemble for x-ray crystallography

Hi, This idea was rejuvenated recently in the follg. work from 2007. I believe the article you are looking for is: Ensemble refinement of protein crystal structures: validation and application. Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN Jr. Structure. 2007 Sep;15(9):1040-52. Regards

Re: [ccp4bb] Model ensemble for x-ray crystallography

have fun ... http://mordred.bioc.cam.ac.uk/~nick/files/Furnham-Structure-2006.pdf http://mordred.bioc.cam.ac.uk/~nick/files/Furnham-NSMB-2006.pdf M.A. DePristo, P.I.W. de Bakker, T.L. Blundell (2004) Heterogeneity and inaccuracy in protein structures solved by X-ray crystallography. Structure

Re: [ccp4bb] Model ensemble for x-ray crystallography

Didn't that trick very successfully lower the R-factors of the completely wrong models that led to the Great Pentaretraction? Unless you have stunningly high resolution, beware. Phoebe At 10:13 AM 3/28/2008, you wrote: Some time ago I've heard about the idea of proposing an ensemble of m

Re: [ccp4bb] Model ensemble for x-ray crystallography

On Fri, March 28, 2008 10:13 am, Lucas Bleicher wrote: > Some time ago I've heard about the idea of proposing > an ensemble of models (as in NMR), instead of a single > model for x-ray crystallography structures. If I > remember correctly, this idea has been published > somewhere. Can anyone tell m

[ccp4bb] Model ensemble for x-ray crystallography

Some time ago I've heard about the idea of proposing an ensemble of models (as in NMR), instead of a single model for x-ray crystallography structures. If I remember correctly, this idea has been published somewhere. Can anyone tell me what article is that? Lucas Abra sua conta no Yahoo! M

Re: [ccp4bb] MolRep of coiled coils

My short experience with coiled-coil is that molecular replacement can be difficult for "classical software" (due to the very anysotropic shape of the protein). In our case (a short parallel dimeric coiled-coil), molecular replacement trials using AMoRe or MOLREP were unsuccessful. We solved the st

Re: [ccp4bb] MolRep of coiled coils

Sorry - I should have added that, yes, there are 2 identical peptide chains that should be parallel coiled-coil. Any advice gratefully received. Ed -Original Message- From: cockburn [mailto:[EMAIL PROTECTED] Sent: Fri 3/28/2008 1:35 PM To: Thomas Edwards Subject: Re: [ccp4bb] MolRep of c

Re: [ccp4bb] too good R/Rfree with resolve

make sure that you are using the original observation (Fobs and corresponding sigmas) not that produced by density modification (e.g. solve resolve) programs. Garib On 28 Mar 2008, at 10:43, stefano ricagno wrote: Dear CCP4bb readers, this is my problem: I solved a structure by MR: the sol

[ccp4bb] MolRep of coiled coils

Dear BB, I am attempting molecular replacement with a 2.8A data set from crystals of a coiled coil of about 150 residues. Probably p21212 but maybe p2221. So far, Phaser, MolRep, Amore, Mr Bump, have not provided a good solution as judged by Z-scores, CCs, Rfactors, and whether there is any den

[ccp4bb] too good R/Rfree with resolve

Dear CCP4bb readers, this is my problem: I solved a structure by MR: the solution was easily found (molrep, phaser and balbes found always the same one), density looked generally reasonable (however in several places it was dubious) but R/Rfree were stuck at 42/47%. Then I tried some density modi

Re: [ccp4bb] Placing an EM map in a large P1 box

Hi Larry, here is how I'd do it: mapmask MAPIN MAPOUT << EOF SYMMETRY 1 XYZLIM CELL PAD 0.0 END EOF Good luck with it! Ciao Pietro -- Pietro Roversi Sir William Dunn School of Pathology, Oxford University South Parks Road, Oxford OX1 3ER, England UK Tel. 0044-1865-275385