Re: [ccp4bb] Searching similar local structural conformations

Dear Lei You can use ASSAM for this http://27.126.156.175/assam/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3394286/ In the past I've also used SPASM locally for this http://xray.bmc.uu.se/usf/spasm.html but I think you'll need to generate your own up to date database to search. Best wi

Re: [ccp4bb] Protein concentration for the initial crystallisation trials

Hi, Another way of estimating a starting protein concentration is to watch your concentration process – if your protein is in a spin concentrator (with an appropriate membrane cutoff size say ~ [MW protein]/3) and is losing volume really quickly then keep going. As soon as the concentration st

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Re: [ccp4bb] Searching similar local structural conformations

Lei, The DeGrado lab developed a tool that would do just what you seek to do and could function as a PyMOL plugin. I played with it a few years ago after I found an interesting cation-pi sandwhich in my structure. I e-mailed then with the author, hoping to link the tool to the entire current PDB i

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Re: [ccp4bb] Protein concentration for the initial crystallisation trials

Hi Armando, I echo Rodger’s advice at 10 mg/ml to start. Our high-throughput crystallization lab has a FAQ page that notes this https://hwi.buffalo.edu/high-throughput-crystallization-center/hts-faqs/ but we absolutely recommend looking at conditions where the precipitant concentration varies

Re: [ccp4bb] Protein concentration for the initial crystallisation trials

Dear Armando, in case you have enough material to spare, I would use a concentrator to create a saturated solution, i.e. concentrate until it precipitates. Measure the concentration of the saturated solution, i.e., supernatant without disturbing the solution with the precipitate. You can start

Re: [ccp4bb] Protein concentration for the initial crystallisation trials

I usually set a partial screen, maybe 24-48 conditions. If less than half the wells have precipitate, double protein concentration. If most have precipitate, maybe reduce protein or halve concentration of screen reagents. I usually start at 10 mg/mL or so. You can conveniently change protein conc.

[ccp4bb] Protein concentration for the initial crystallisation trials

Dear all, I was wondering how to guess the optimal protein concentration for the initial crystallisation trials. Is there any trick or assay other than the classic PCT from Hampton? Armando To unsubscribe from the CCP4BB

Re: [ccp4bb] Searching similar local structural conformations

?Hi Lei, Rosetta uses something very similar to this for designing proteins that bind to ligands/proteins. Perhaps look there. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031 From: CCP

[ccp4bb] Searching similar local structural conformations

Dear CCP4ers, We identify a potential ion binding site formed by four residues in a structure. I want to search if any other structures have a similar local residual geometry. Is there any programs to perform such a searching? For example, to search in Protein Data Bank using coordinates of the

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