Re: [ccp4bb] metal electron density detection

If figured out by yourself, this web page would help; http://tanna.bch.ed.ac.uk/ METAL COORDINATION SITES IN PROTEINS tanna.bch.ed.ac.uk METAL COORDINATION SITES IN PROTEINS (last updated August 2011) This website assembles information about the geometry and constitu

Re: [ccp4bb] Pocket identification and substrate tunnelling

Dear Mohamed, There is a software called CAVER to calculate tunnels in the protein for a given pdb file. ( http://caver.cz/) It has also a PyMol plugin which you can find from its web site. Burak Sent from my iPhone On 20 Jan 2017, at 18:45, Mohamed Noor mailto:mohamed.n...@staffmail.ul.ie>>

Re: [ccp4bb] Asp-Asp pair facing each other at <3.0 A distance

In our acetone carboxylase structure, the active metal site contains a octahedral Mn coordinated with two His, one Asp, and one Glu residues. It looks very similar. https://www.nature.com/articles/s41598-017-06973-8 The protein may have a metal in the active site, is there any background infor

Re: [ccp4bb] cryo-em data conversion

You can convert it using EMAN2 by e2proc2d.py by typing e2proc2d.py *.tif @.mrc .star file can be generated in Relion. Also, you may subscribe the mailing list CCP-EM for EM-related questions. https://www.jiscmail.ac.uk/CCPEM. JISCMail - CCPEM List at WWW.JISCMAIL.AC.UK

Re: [ccp4bb] protein quasicrystals?

Have you tried microseeding of these sphere crystals? It may help to get better crystals. Burak From: CCP4 bulletin board on behalf of Yu Qiu Sent: 13 February 2018 15:09:43 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] protein quasicrystals? Hi, I have be

Re: [ccp4bb] coot: obtaining a clickable list of outiers in a Ramachandran plot

You can evaluate your structure in MolProbity, then it would give a list of Ramachandran outliers similar to the output of COOT. http://molprobity.biochem.duke.edu/index.php?MolProbSID=ktiuaj4c1v48mlgqq3inopfrf6&eventID=22 Regards, Burak From: CCP4 bulletin