Re: [ccp4bb] refmac auto matrix weight - 'reasonable' rmsds

Hi - A quick note - We (with Chris Ulens) have seen recently in one case that in a case MATRIX AUTO would give 'excessive' RMSD, close to 0.030. Checking the cell based on the projection of RMSDs to the cell axes, a utility kindly provided by WHATCHECK, it was suggested that the cell migh

Re: [ccp4bb] Tough ligand to bind?

Hi Nian, This isn't a solution but I remember seeing an excellent talk by Annie Hassell at the CCP4 study weekend a couple of years back. The paper from that talk may help you out. Acta Cryst. (2007). D63, 72-79 [ doi:10.1107/S0907444906047020 ] Crystallization of protein-ligand complexes A. M

Re: [ccp4bb] HETATM to ATOM change, and atom identifier change in REFMAC...

That is very very peculiar! as far as I know REFMAC doesnt really care whether you call something ATOM or HETATM . I suspect the problem is either in the cif file describing the co-factor - could the atom type fpr MO be set as N? or possibly in the PDB file - is the Atom name displaced to the

Re: [ccp4bb] HETATM to ATOM change, and atom identifier change in REFMAC...

the current makecif.tar.gz doesnt have all the known PDB Mo compounds it does have PCD.cif you could look at as a template try downloading from the pdb sites the dic for MSS MTQ MTV and see if one of these is your compound then use this as th starting point for the refmac dictionary all 4 ar

[ccp4bb] ccp4-dev

Is there an archive of ccp4-dev? I can't find one Phil

[ccp4bb] CCP4 Study Weekend 2008

The CCP4 Study Weekend (3rd - 5th January 2008), University of Leeds We cordially invite you to participate in this year's Study Weekend at the University of Leeds. The annual CCP4 Study Weekend is a chance to shake off the post-New Year torpor, and work hard and play hard with your fellow

[ccp4bb] Protein models in Blender

Hi all, I've had some spare time to teach myself blender, which seems to me to be a powerful model editing and animation tool. However, I've not found any python scripts or software to convert objects such as ribbons mesh made in ccp4mg or pymol into something that blender can use (I know its

Re: [ccp4bb] Protein models in Blender

Povray is just a renderer like the renderer in blender, only in the case of povray, the input file defines the model. I would think that if it is possible to generate a povray input file from molecule objects, it should be possible to generate a VRML file which blender can open. If I'm not mistaken

Re: [ccp4bb] Protein models in Blender

Hi, Thanks for the reply. With regards to Povray, I had mentioned that program as I had hoped that you could use a povray file generated in ccp4mg/povray/etc and then somehow read that into blender for futher editing (and make my life much easier - editing povray files to alter figures is a r

[ccp4bb] Predict potential sites for introducing cys to make a disulfide

Dear All: I vaguely remember a program that can predict sites for introducing a pair of Cys residues to make a disulfide. I had once used this before but now I had forgotten about it. Does any body know about this? My plan is introduce Cys residues into my structure that I can use for FRET anal

Re: [ccp4bb] Predict potential sites for introducing cys to make a disulfide

You're probably thinking of SSBOND, one of the programs Bart Hazes wrote a while back. You can find it here: http://eagle.mmid.med.ualberta.ca/forms/ssbond.html Cheers, Gerald At 04:03 PM 13/09/2007, Narayanan Ramasubbu wrote: Dear All: I vaguely remember a program that can predict sites fo

Re: [ccp4bb] Protein models in Blender

PyMOL can save both VRML2 (.wrl) and native PovRay versions of the current scene via the save command. Limited support for Maya .OBJ is present now as well (export bug fixed in current open-source code). VRML: save scene.wrl POVRAY: save scene.pov MAYA (triangles only, w/o coor) save