[ccp4bb] Problem with RCrane in coot-0.7

Hi, CCP4bbers: Did anybody here use the COOT plug-in RCrane? I download the COOT version 0.7 (coot-Linux-x86_64-centos-6-gtk2-python), and use the plug-in RCrane. However, after I optimized the rotamers, the RCrane window did not show any selectable rotamers (See the attached figure). BTW, I'm

Re: [ccp4bb] Problem with RCrane in coot-0.7

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Jiawei Wang, a collegue of mine has been working on a different plugin for coot and observed the same behaviour on our computer while e.g. Bernhard Lohkamp could not reproduce this behaviour. It appears to be an odd combination between the python

[ccp4bb] Anomalous atom or ligand?

Dear users, After detecting the anomalous peaks in a data, Is it necessary that there will be an anomalous atom in most of the peaks? In a particular case, a low ranking peak was assigned an anomalous atom because it was present in the native structure, while a peak with a rank higher than this o

Re: [ccp4bb] Problem with RCrane in coot-0.7

On 24/04/13 10:24, Jiawei Wang wrote: Hi, CCP4bbers: Did anybody here use the COOT plug-in RCrane? I download the COOT version 0.7 (coot-Linux-x86_64-centos-6-gtk2-python), and use the plug-in RCrane. However, after I optimized the rotamers, the RCrane window did not show any selectable rotam

Re: [ccp4bb] Modelling Software for beta turn design

Hi Wenzong, I would certainly try it also another way. Choose you beta turn sequence. Insert it between the sequences of both beta stands and submit the whole sequence (beta-turn-beta) to homology modeling. Try every beta turn sequence to select top results. You could download MolIde (http://d

[ccp4bb] common proteins that oligomerize?

I am looking for easily-available proteins that exist in equilibrium between two or more known oligomeric states in solution. BSA is a possibility, but I am concerned that the rate constant for association may be rather slow. Fast exchange would be better. Does anyone know of other possibiliti

Re: [ccp4bb] question about arginine sepharose 4B

Hi, You can make it :) There are a number of good ways to do so, but my favorite one is to order Cys-Arg dipeptide and then use iodoacetamide-agarose resin (very cheap) to load up the peptide. This method allows you to quantify the loading, if you care to know how much you immobilized and also it'

[ccp4bb] Postdoctoral positions in structure and function of membrane proteins at the NIH

Dear all, Will you please bring this to the attention of suitable candidates ? Postdoctoral positions in structure and function of membrane proteins at the NIH The research group of Dr. Anirban Banerjee at the National Institutes of Health (NIH) is seeking candidates for postdoctoral fellows t

[ccp4bb] Too high function value for reflection ... refmac

Dear users, While refining the structure, I get a message in the log file - Too high function value for reflection 408 0 103.7139 Too high function value for reflection2766 0 110.8577 Too high function value for reflection3439 0 127.2363

[ccp4bb] How to generate a complete viirus PDB

Dear all: I have one subunit PDB of one virus with a NCS record. Which program should I use to generate a complete virus PDB using the NCS? Thank you Hong Hsiang

Re: [ccp4bb] How to generate a complete viirus PDB

Hi Hong, you can usually download the 'biological assembly' from the PDBe, be warned that for viruses this is rather large, cheers, Matt. On 25/04/2013 08:19, Guan Hong Hsiang wrote: Dear all: I have one subunit PDB of one virus with a NCS record. Which program should I use to gener

Re: [ccp4bb] How to generate a complete viirus PDB

Hi Hong, I would recommend that you check out the services at the VIPERdb website http://viperdb.scripps.edu. It looks like the oligomer tool (http://viperdb.scripps.edu/oligomer_multi.php) might be useful for what you want to do. They have many of the virus structures from the PDB already proc