Re: [ccp4bb] LINKR vs LINK ? procedure for modeling coordinated Zn+2

Hari, Before starting your dummy refmac job to write out the appropriate cif file, you will need to use Coot adjust the positions of the Cys and other Zn-ligand side chains to appropriate positions (consisatent with your electron density maps, of course) to coordinate to Zn. Typical Zn-S bonds

[ccp4bb] refines Query for non covalent interactions

Thanks to all for responding.. Infact precisely i am looking for some server that can calculate hydrogen bonds, electrostatic interactions, and hydrophobic interactions present in various pdbs...simultaneously Cheers GM

Re: [ccp4bb] LINKR vs LINK ? procedure for modeling coordinated Zn+2

Hello Eleanor and Roger Rowlett and everyone, I am still having a tough time with coordinated metal refinements in refmac ( and coot ) I followed Rogers suggestion of creating a pseudo refmac run and then using the output cif definition for Cys -SG Zn as an input for further refinement. Even If I

Re: [ccp4bb] Dissolving Hydrophobic ligands for co-crystallization and assays

As a piece of trivia regarding low-MW-PEG-as-solvent: the original paper in which the active compound of hashish (THC) was discovered (Science or Nature 1970's), the active fraction was dissolved in PEG-300 (I believe that was the MW), and injected into monkeys. If I recall correctly, the monk

Re: [ccp4bb] Dissolving Hydrophobic ligands for co-crystallization and assays

Tuhin, I have had some success with low molecular weight PEG eg. PEG200. -bob On Thu, May 13, 2010 at 1:00 PM, Tuhin Bhowmick wrote: > Dear All, >  does anyone have any clever suggestion/s for handling the solubility problem >  of highly hydrophobic compound, during co-crystallization or inhibiti

[ccp4bb] Dissolving Hydrophobic ligands for co-crystallization and assays

Dear All, does anyone have any clever suggestion/s for handling the solubility problem of highly hydrophobic compound, during co-crystallization or inhibition assays? The ligands I am using are almost insoluble in aquous medium (precipitates out or becomes turbid at ~1 micro molar conc.). In DM

Re: [ccp4bb] LINKR vs LINK ? procedure for modeling coordinated Zn+2

Has anyone answered this? Eleanor hari jayaram wrote: Hi Am trying to build coordinated Zn+2 by CYS -SG atoms and have it refine properly in refmac5.5 I added ZN ions in Coot at the Fo-Fc peaks. Then I defined manually the coordination relations in a text editor using LINK records. the ions we

Re: [ccp4bb] How to generate lib file for new ligand?

Vinson LIANG wrote: Dear all, I have fit my ligand into its density with coot. Then, I add the ligand into the protein's pdb and try to do refine with refmac5. First, the error comes, error message Refmac_5.5.0109: New ligand has been encountered. Stopping now http://www.majorgr

Re: [ccp4bb] How to generate lib file for new ligand?

Hi, I encountered a similar problem, the way I solved it was to edit either the cif file or the pdb file to make the signifiers either the XX or the Bb the same. So that they are consistant over the two files. For example in the one I used one atom had a # afterwards in the pdb file but a * in

[ccp4bb] How to generate lib file for new ligand?

Dear all, I have fit my ligand into its density with coot. Then, I add the ligand into the protein's pdb and try to do refine with refmac5. First, the error comes,         error message  Refmac_5.5.0109:  New ligand has been encountered. Stopping now The next time, I input the .cif file genera

Re: [ccp4bb] noncovalent interactions

Depending on what exactly you are looking for, you may try PDBeMotif: http://www.ebi.ac.uk/pdbe-site/pdbemotif/ PISA: http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html Eugene On Wed, May 12, 2010 at 6:02 PM, gauri misra wrote: > Hi, > Which  free online servers are best for calculation of non