Re: [ccp4bb] stoichiometry of complex and incubator

Hi , yes as *Konstantin* said if u have cysteine residue in ur any one of protein u can label that protein with Pyrene malemide or oregon malemide or other fluorescence dye then remove the dye by desalting column. titrate with second protein and do fluorescence anisotropy experiment

Re: [ccp4bb] stoichiometry of complex and incubator

hi Min, I think SPR(Surface plasmon resonance) should suit your situation. The Biacore instrument I worked on required 200 µL of 10-50 µG protein(ligate) for immobilisation and 150µL of various concentration of the other protein(ligand) in the range of 50-1000 µg/ml. (depending on your situation

[ccp4bb] mising atoms

hello, i have one problem regarding electrostatic field calculation . in a PDB with 2 A resolution many atoms of side chan if argenine and aspartate , lysine and glutamate are missing due to weak electron density . i want to calulate the field how should i go for it . if i ll build the side

Re: [ccp4bb] stoichiometry of complex and incubator

Dear Min, You can use microscale thermophoresis for this kind of tricky cases when you have limited amount of protein and ligands. There is enough literature on this topic. have a look in the following reference: Proc Natl Acad Sci U S A. 2006 Dec 26;103(52):19678-82 Hope this helps. Regards,

[ccp4bb] No reflections in resolution bin???

Dear CCP4BBers, Refmac is giving the error No reflections in resolution bin??? It seems there is no SigFP column. I wonder how to fix the problem. Thanks in advance. James

Re: [ccp4bb] mising atoms

On Thu, 2011-08-04 at 13:06 +0530, vandana kukshal wrote: in a PDB with 2 A resolution many atoms of side chan if argenine and aspartate , lysine and glutamate are missing due to weak electron density Aha! Take that, non-believers in the wisdom of the end user! :) Hope it does not revive

Re: [ccp4bb] No reflections in resolution bin???

On Thu, 2011-08-04 at 08:10 -0400, james09 pruza wrote: Refmac is giving the error No reflections in resolution bin??? It seems there is no SigFP column. I wonder how to fix the problem. This, of course, depends on the origin of the data. Most data processing software will include the

Re: [ccp4bb] No reflections in resolution bin???

james09 pruza wrote: Dear CCP4BBers, Refmac is giving the error No reflections in resolution bin??? It seems there is no SigFP column. I wonder how to fix the problem. Thanks in advance. James If the error is indeed due to a missing SigFP column, there are 2 ways to go about it I

Re: [ccp4bb] No reflections in resolution bin???

Dear James, You can get around this by having an artificial SIGFP. Two ways, you can assign an existing column to SIGFP i.e. LABIN FP=FP SIGFP=FP I am not sure if refmac will complain about this because MTZ data columns have a type 'F' for magnitudes and 'Q' for errors. Secondly you

[ccp4bb] Mixed Iso/Aniso in refmac5

Hello everyone, How does refmac5 pick atoms for B-factor refinement, particularly with the mixed option enabled? I dont see a place for entering a manual selection, eg resname FMN... Thank you

Re: [ccp4bb] stoichiometry of complex and incubator

Hi Min, Given the limited supply of your protein you could try the EDC-NHS zero-length crosslinking either in one-step or two-step protocol (Anal. Biochem. 185,131,1990). If your protein complex is like most protein complexes chances are there will be some electrostatic contacts at the

Re: [ccp4bb] Mixed Iso/Aniso in refmac5

On Thursday, 04 August 2011, Yuri Pompeu wrote: Hello everyone, How does refmac5 pick atoms for B-factor refinement, particularly with the mixed option enabled? In the MIX option, it simply keeps the atom treatment as it is given in the input file. Atoms with an ANISOU record are refined

[ccp4bb] gst-tag protein purify problem

hi guys, I have a DNA binding protein and expressed the DNA binding domain (150 aa) with his-sumo tag or gst tag at the n-terminal. I tried to purified it with Ni column or Gst column separately. But purity is lower than 50% after Ni or GST column. This protein only stable with 1M Nacl or higher.

Re: [ccp4bb] stoichiometry of complex and incubator

Dear all, Thank you all very much for your kind suggestions. Now we have some preliminary data of SPR. But we might try other new ideas suggested here. Best,Min Date: Thu, 4 Aug 2011 13:19:41 +0200 From: krishna@gmail.com Subject: Re: [ccp4bb] stoichiometry of complex and incubator To:

[ccp4bb] Symmetry Related molecules

Whats the best way to visualize all the symmetry related molecules, I know COOT will show them as backbone. I was looking for publication quality images...PyMol maybe? thank you for suggestions -- Yuri Pompeu

Re: [ccp4bb] Symmetry Related molecules

Hi Yuri, have a look at SuperSym plugin for pymol http://www.pymolwiki.org/index.php/SuperSym Best regards, Albert *Albert GUSKOV (Dr) *| Research Fellow | Division of Structural Computational Biology | Nanyang Technological University Proteos 7-01, Biopolis Drive 61, Singapore 138673 Tel: (65)

[ccp4bb] adding side-chains to a backbone model (without introducing clashes in the process)

Hello, Recently I was advised PULCHRA on phenixbb for such task (http://www.pirx.com/pulchra/index.shtml). I wonder if there is another tool in the CCP4 treasure chest for the same kind of task (preferably open source). Regards, F.