Re: [ccp4bb] Fd-3m with pdbset - test pdb file

Dear bulletin board, Tim asked me for the pdb file I used for testing (coot version 0.6), which I have attached here. It is a totally artifical pdb file with one random small ligand in it. Using a symmetry radius of 50 Angstrom, one can get an idea of the symmetry in 'F d -3 m'. If in Tim's case w

Re: [ccp4bb] Reverse Translatase

Hi Jacob- What an intriguing proposition. I can think of multiple reasons why such a system would not exist, but there is a mechanistic one which is most fundamental, having to do with the nature of the genetic code. Say that there is a cellular machine which would unfold a protein and

Re: [ccp4bb] Reverse Translatase

Jacob, The idea is enticing, but don't forget that there are multiple degenerate codons for a given amino acid. Once the protein is synthesized, the specific codon information is lost. I think that's a fundamental problem. Keep the ideas coming, Mike Thompson - Original Message -

[ccp4bb] Reverse Translatase

Dear Crystallographers, does anyone know of any conceptual reason why a reverse translatase enzyme (protein-->nucleic acid) could not exist? I can think of so many things for which such an enzyme would be helpful, both to cells and to scientists...! Unless there is something I am missing, it w

Re: [ccp4bb] Can CCP4 calculate the R factor based on the given Fo, Fc, and sigFo by a mtz file?

Thanks a lot! > Hailiang Zhang wrote: >> Hi, >> >> I want to calculate the R factor based on the given Fo, Fc, and sigFo by >> a >> mtz file. Can some CCP4 tools do this? Thanks! >> >> Best Regards, Hailiang >> > > Yes- rstats > > something like > > rstats hklin sfall.mtz hklout rescaled.mtz < LA

Re: [ccp4bb] Can CCP4 calculate the R factor based on the given Fo, Fc, and sigFo by a mtz file?

Hailiang Zhang wrote: Hi, I want to calculate the R factor based on the given Fo, Fc, and sigFo by a mtz file. Can some CCP4 tools do this? Thanks! Best Regards, Hailiang Yes- rstats something like rstats hklin sfall.mtz hklout rescaled.mtz <

[ccp4bb] Can CCP4 calculate the R factor based on the given Fo, Fc, and sigFo by a mtz file?

Hi, I want to calculate the R factor based on the given Fo, Fc, and sigFo by a mtz file. Can some CCP4 tools do this? Thanks! Best Regards, Hailiang

Re: [ccp4bb] Fd-3m with pdbset

I was going to say that we could adopt the convention that the default setting of a centrosymmetric space group is the one with the origin on an inversion centre, since this is assumed by all programs that I am aware of, thus making ':2' for 'second setting' unnecessary and keeping the name to 11

Re: [ccp4bb] Refmac bref MIXED failed

Hi Garib, I tried with refmac 5.6 and the same inputs; it worked fine. Thanks, Lionel 2010/9/6 Garib N Murshudov > Could you please try refmac 5.6. I think we have fixed this problem. It is > available from: > > www.ysbl.york.ac.uk/refmac/latest_refmac.html > > You need to take experimental ve

Re: [ccp4bb] Fd-3m with pdbset

It seems that it's the new addition of ':n' which has pushed it over the limit of the 11 char field. Has this been thought through? I can see that the ':n' qualifier is necessary to disambiguate alternate origins. Without the redundant formatting spaces 9 chars would be sufficient even for 'P 4

Re: [ccp4bb] Problem with NCS detection in Parrot

Hi Florian, I have found that, in some cases, playing with -ncs-mask-filter-radius can help parrot to successfully detect and apply ncs averaging. In one recent case, with 8 molecules where NCS was not found without this option, values from 14 to 30 angstroms worked (but gave maps of variable q

Re: [ccp4bb] Refmac bref MIXED failed

Hi, I'm not sure whether it's related to the error you're seeing but as far as I know, in order for refmac to do mixed B-refinement (that is Biso and Baniso) you have to set yourself by editing (!!) the incoming pdb such that whichever atoms you'd like to have Biso refined should have only Biso

Re: [ccp4bb] Refmac bref MIXED failed

Could you please try refmac 5.6. I think we have fixed this problem. It is available from: www.ysbl.york.ac.uk/refmac/latest_refmac.html You need to take experimental version (it is now fairly stable) Regards Garib On 6 Sep 2010, at 15:01, Lionel Costenaro wrote: > Hello, > > When I run Ref

Re: [ccp4bb] fail to install ccp4i task for arp warp

On 31 Aug 2010, at 14:56, Jochen Kuper wrote: > sorry to bother you with this but I just can't figure out what goes wrong ... > > I am running the latest version of snow leopard on a MBP unibody with the > 64bit kernel. > > I have an up to date fink installation for native 64bit. I've seen th

[ccp4bb] Refmac bref MIXED failed

Hello, When I run Refmac with the mixed iso/anisotripic B-value option (refi bref MIXED), refmac failed with the error message below. My pdb comes from previous refmac runs with anisotropic B values for all atoms (H generated but not written). I just removed from the pdb the ANISOU lines for all w

Re: [ccp4bb] Fd-3m with pdbset

> > There seem to be a few CCP4 Fortran files that have character spgnam*10 > > from the good old days ... > > What good old days were those? The Cryst1-format for PDB-files in the ccp4 > documentation says > 56-66Space group symbol, left justified (not used) > which is eleven characters. Were

Re: [ccp4bb] Fd-3m with pdbset

On Mon, Sep 06, 2010 at 02:45:49PM +0100, Martyn Winn wrote: > > Yes, I can reproduce this, and I think I have found the bug. > It is simply that PDBSET dimensions the spacegroup name to 10 > characters. Increasing that to 20 allows you to use either > > spac 'F d -3 m :1' > or > spac 227 > > Ho

Re: [ccp4bb] Fd-3m with pdbset

Dear Herman, thanks for the tip. Unfortunately it does not help with my version of coot (linux, 0.6.1). Coot eats up all my memory (8GB RAM + 4GB swap) until it is being terminated by the OS. Which version of coot are you using? Could you send me your PDB-file that works for you, please (you coul

Re: [ccp4bb] Fd-3m with pdbset

Yes, I can reproduce this, and I think I have found the bug. It is simply that PDBSET dimensions the spacegroup name to 10 characters. Increasing that to 20 allows you to use either spac 'F d -3 m :1' or spac 227 However, it still won't recognise 'F d -3 m' because this is not in the syminfo file

[ccp4bb] Post-doc vacancy in the Integral Membrane Protein group, SGC, Oxford

Dear All, The Integral Membrane Protein group at the SGC in Oxford is looking for a post-doctoral research scientist with experience in purification and crystallisation of membrane proteins. In the past year we have developed a pipeline for the production of human membrane proteins in the bacul

Re: [ccp4bb] Problem with NCS detection in Parrot

Florian Schmitzberger wrote: Dear All, I am encountering a problem when using Parrot (for combined density modification and non crystallographic symmetry (NCS) averaging) in ccp4 6.1.13, run via ccp4i. Parrot does not detect the (2-fold) NCS present among my heavy atom substructure with 20

Re: [ccp4bb] Fd-3m with pdbset

Hi Tim, The string 'Fd-3m:1' is recognized by pdbset, but still produces 'F d -3 m :'. I did a test with a single small ligand with coot and if you delete the ':' from the CRYST1 card to make 'F d -3 m' coot happily accepts it and seems to produce the correct symmetry mates. I hope that this way y

[ccp4bb] Fd-3m with pdbset

Hello, I tried to assign a cell with space group F d -3 m to a PDB file using pdbset. Since it did not recognize the string 'F d -3 m' (nor 'F d -3 m :1') , I used the space group number 227. This resulted in the space group string 'F d -3 m :' in the PDB-file instead of 'F d -3 m :1' as it is list