[ccp4bb] degradation of protein durring freez thaw

Hello BB I apolozize an off topic query. I am working with small proetin-protein complex of 24kDa. I purify this N-terminal His-tagged complex through tylon resin in 20mM of Tris pH-8.0, 0.3M NaCl . After purification this protein complex are dialysed in 20mM tris pH=8.0.I am able to purify enou

[ccp4bb] Precipitation of protein-protein complex under most of the crystallization condition

Hello BB I am working with small protein-protein complex of Molecular weight 40kDa. This protein expresses well and soluble in 20mM Tris-Cl pH-8.0 and 50mM of KCl, could be concentrated upto 20mg per ml in this buffer. I have purifed this protein with Ni-NTA resin and they are free from any contam

[ccp4bb] Protein-DNA complex crystallisation

Hello all I am novice to this field and trying to crystallize a protein-protein complex verses DNA i.e a ternary complex of protein complex and DNA, which stochiometry is 2:!. I am wondering 1-what should be the DNA and protein ratio for the ternary complex like this typically for binary complex i

[ccp4bb] refmac runs, but no output files

Hi all I am using CCP4i, and running refmac for the refinement of the my data. I have ran this many times earlier successfully. Now as i run the refamc5 , it runs successfully and complete the job,but not writing any output file. At the end of the logfile, i get a sat

[ccp4bb] ccp4i unable to extract data from project Directory

Hi all I have successfully installed CCP-6.0.2 on Fedora core 6 by automated download page of the CCP4.But, as i tried to run the CCP4i, after defining the project directory , it is not able to extract thye file from the project directory and i get a massage of this kind " CCP4 encounterd an e

[ccp4bb] CCP4i unable to extract data from Project directory

Hi all I have successfully installed CCP-6.0.2 on Fedora core 6 by automated download page of the CCP4.But, as i tried to run the CCP4i, after defining the project directory , it is not able to extract thye file from the project directory and i get a massage of this kind " CCP4 encounterd an e

[ccp4bb] CCP4 GUI always show the job starts

Hi all I have recently installed the ccp4i on my linux system.Whenever. i run any program,GUI always list the job and show that this job is starting, never displays that particular job has finished. while, when i give look on the logfile of the particular job, then this has finished long back. w

Re: [ccp4bb] ccp4i unable to read mtz files

Hi Harry Yes, i have solved the problem. There was permission problem in the /tmp/thomas directory,that's causes this problem to me. Since,my account (login) in my computer had the root (administrative) permission and i was trying to run the program from my login after setenv as well as defining

[ccp4bb] program to create cartoon image from a PDB file which have only C-alpha coordinates

Hi all I am interested to make a cartoon image file from a old PDB. This PDB contains the coordinates of the only C-alpha atoms. Is there is any program to create cartoon image from this PDB? please, can any one suggest me? Thanks in advance With Best Regards Jhon Thomas

[ccp4bb] Problem in installation of the ccp4mg on the FC6

ist//bin/python: cannot execute binary file ./ccp4mg-1.0/bin/ccp4mg: line 285: /home/thomas/./ccp4mg-1.0/bin/..//pythondist//bin/python: cannot execute binary file Is any one have this kind of experience? please give the suggesstions. Thanks in advance Jhon thomas

[ccp4bb] refinemnet of the ligand in CNS

HEllo all i would like to refine a ligand along with the proetin molecule in CNS. When i google about this query i get all these informations to refine the ligands in cns. The critical box to fill in is the "protein coordinate file" (your pdb filename). Then save this file to your working directo

[ccp4bb] very low factor of coordiantes

Hi all I am refining an dataset of 2.9 A resolution. I am using TLS+restained refinemnet+ isotropic B factor and simple scaling. After reinement 10 cycle of refinemnt after geometry optimisation i found that b factor of the coordinates drastically goes down to 2.0 of att the atoms of the PDB. If i

[ccp4bb] surface area calcualtion

Hello all can any one suggest any server or tool which can calculate the burried surface area between the domains of the same monomer? PISA calculates the interfacial surace area between the monomer or oligomer. Can areamol calculate it? Thanks in advance Thomas

[ccp4bb] bad bond angle and bond length of a ligand

Hello all I am working with a 3.0 A dataset, which binds with cAMP. Though cAMP fit well in the density, validation tools (molprobity, procheck) suggest the bond angles and bond lengths of ligand of completely refined model is very bad. Can anyone suggest what could be the problem with model or re