[ccp4bb] Mtz2various

Hi: I'd use Mtz2various to convert .mtz file to .phs format. The format of .phs file is like below: 0 0 9 29.5 0.14 220.00.00.00.00.0 0 0 12 160.5 0.97 109.0 -4.52.4 -0.91.2 0 0 15 72.6 0.87 56.0 36.5 10.5 -12.6 -7.9 0 0 1

Re: [ccp4bb] shelxl/missing residues

Hi Sam, Ideally, with the R factor you are at, you should be able to build these residues in, using Coot/Ono/xtalview and then refine with shelxl. If you want to go to shelxl straightaway, you might want to refine res 9-86 as one chain and res 94-last residues as another. I guess you could mutate a

[ccp4bb] shelxl/missing residues

Hi I would appreciate few things for my protein structure. Data is 1.5A. This protein is of 400 residues. 2 molecule in the asymm unit. Missing residues are : N-terminal 8 residues, C-terminal 5 residues and in the middle residues 87-93. Final R(working) = 21% after refmac refinement. Some (not a

[ccp4bb] stereo glasses thread

Does anyone have a synopsis of the recent (last few months?) discussion about stereo glasses? I've been using cross-eyed stereo, but my mom says that my eyes will stick that way... Thanks, Pat --- Patric

[ccp4bb] Please take me off the list

Hi there, Could you please either take me off thelistof CCP4BB or instruct me how to do it myself? Thanks, Iris Iris Ben-Efraim, PhD Department of Biological Sciences Purdue University West Lafayette, IN 47906 e-mail: [EMAIL PROTECTED] Phone: 765-4946465 Fax: 765-4961189

Re: [ccp4bb] TLSANL: negative mean-sq displacements?

I'd also comment that the absolute values are quite large. Well, I have no knowledge what groups you've chosen, but for domain-sized groups, typical values are 1-10 deg**2. Values can be larger for smaller TLS groups. This is just a rule-of-thumb, but would make me suspicious whether the TLS refine

Re: [ccp4bb] References for 3D structures of covalent complexes

I found this question interesting, therefore I quickly searched the entire PDB V3 (http://wwpdb-remediation.rutgers.edu/) for LINK records linking two standard amino acid residues, excluding chain links and same-chain disulfides. Here are the results: http://cci.lbl.gov/~rwgk/tmp/protein_protei

[ccp4bb] Surface program

Hi, I just installed the newest version of ccp4i in windows. However, I can not find the program"surface" mentioned by some references around 2000-2002. Does this program no longer exist or renamed to something else? Thanks a lot.

Re: [ccp4bb] TLSANL: negative mean-sq displacements?

On Monday 26 February 2007 08:23, Richard Gillilan wrote: > Ok, Painter and Merritt describe this situation in their Acta Cryst > (2006) D62 439-450 article entitled "Optimal description of a protein > structure in terms of multiple groups undergoing TLS motion." At > least with regard to fit

Re: [ccp4bb] lsqkab and occupancy/B

Thanks to everyone for the suggestions. It appears that just adding a bfactor and occupancy flag is the way to go (eg - there's no way to make lsqkab less finicky). Since I'm just hacking this together and grep/sedding out the pairwise rmsds to pipe to another program, I'd prefer to use the eas

[ccp4bb] NCS Refinement

This is a general question concerning the application of NCS in the context of an electron microscopy density map. I would like to refine a crystallographically determined protein structure into an EM map of a biological structure with helical symmetry while retaining the interactions that

Re: [ccp4bb] lsqkab and occupancy/B

Jacob, lsqman from USF will be happy without B and Q, and you can pick the set of atoms that you want to align. I think that you can run it in script mode, as well. Kevin Jacob Corn wrote: Dear everyone, I'm attempting to do a large scripted pairwise alignment of theoretical models to calcu

Re: [ccp4bb] References for 3D structures of covalent complexes

Hi Lionel Definitely an engineered example for you: This is a paper describing (among other things) the 3D structure of a ligand-induced homodimer of E. coli DHFR (a functional monomer), via covalent linkage of the ligands themselves. Designing Protein Dimerizers: The Importance of Ligand Confo

[ccp4bb] lsqkab and occupancy/B

Dear everyone, I'm attempting to do a large scripted pairwise alignment of theoretical models to calculate rmsd over a pre-determined residue range, but the PDBs that I'm using have neither B-factor nor occupancy fields. Lsqkab is unhappy about this fact (see below), and I'm wondering if there's

Re: [ccp4bb] TLSANL: negative mean-sq displacements?

Ok, Painter and Merritt describe this situation in their Acta Cryst (2006) D62 439-450 article entitled "Optimal description of a protein structure in terms of multiple groups undergoing TLS motion." At least with regard to fitting L parameters from previously refined data, negative eigenva

[ccp4bb] References for 3D structures of covalent complexes

Dear all, I would be very interested and much grateful having references (bibliographic data, PDB entry code, web link...) on 3D structures of covalently linked (engineered or not) protein-protein complexes (e.g. heterodimers). Our own survey of the literature was not very "successful". Thank

[ccp4bb] Summary: [ccp4bb] Toyopearl GF column vs. Superdex

Hi all, Thanks to those who replied to my question. I thought others might be interested, so I'm giving the summary below. I think, we'll go for the Superdex, as we have more experience with it. 1) If the prices are similar then toyopearl may be a better choice as it has slightly bette

[ccp4bb] substitution on cyclohexyl rings

BS"D Hello All, One can find in many organic chemistry textbooks statements about how SN2 reactions on carbon atoms in cyclohexyl rings are not favoured because of hindrance from the axial substituents (even hydrogen). Unfortunately, I'm having trouble (say via google) finding some re

Re: [ccp4bb] dmmulti NCS mask

Hey all, this is wildly off-topic, but since we were even talking about NMR the other day, I was thinking why not EM? I'm trying to get negative stain images of a membrane protein. Problem is that the detergent (similar to triton) that best stabilizes the protein eats the carbon grid, even at c

[ccp4bb] NEW STRUCTURE BASED DRUG DISCOVERY COURSE - May & September 2007

NEW STRUCTURE BASED DRUG DISCOVERY COURSE - May & September 2007 A new course is being run at York to provide an introduction to the methods of structure-based drug discovery. Preliminary funding to start the course has been provided by the Modular Training for Industry initiative of the BBSRC wi

Re: [ccp4bb] dmmulti NCS mask

This is really a Q to Kevin Cowtan.. Is it important to have a "proper" mask for DMMULTI? I had always thought it was self correcting and as long as it was big enough then the program would update it? Eleanor Peter Adrian Meyer wrote: I would be very much afraid that the only way to get the

Re: [ccp4bb] Procheck vs Molprobity

Martin Hallberg wrote: I recently received a referee report that stated "The authors should describe the number of residues in the fully allowed, favored. The present statistic is misleading. Molprobity is far too loose (it even gives good values for structures that are wrong!) Procheck is m