[ccp4bb] relative domain motion calculation...

Dear All, I am working with a protein containing tandem domains, connected with 3-4 residue linker. I want to calculate the relative motion/orientation of one domain with respect to the hinge region as well as with respect to the other domain. Both the domains have very less seq. identity (<20%). P

[ccp4bb] AW: [ccp4bb] Cleaved peptide density!

Dear Dipankar, as Bonsor mentioned, 2-3 weeks is something completely different from the few hours normally used for enzyme assays. A lot may happen during the long crystallization that does not happen in the assay. Also, your enzyme will still have the remainder of the catalytic machinery (oxy

Re: [ccp4bb] visualizing .mrc maps in coot and model building

Dear onetwo, Coot will open .mrc files. However, different programs often modify the header of the mrc file, which can cause problems. This recent paper gives more information about the standard format for mrc files and proposed extensions to it: http://www.ncbi.nlm.nih.gov/pubmed/25882513 T

Re: [ccp4bb] on the electron microscopy function of refmac5

Dear Smith, The easiest way to access the EM functions of REFMAC are to use the scripts provided here: http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/em_fitting/em_fitting.html. Best wishes, Alan On 21 Apr 2015, at 04:20, Smith Liu wrote: > Dear All, > > The CCP4 document says r

Re: [ccp4bb] relative domain motion calculation...

I am not sure about a web server, but if you use gesant to align one domain of the two structures, then fit the second domain of structure 1 to the second domain of the aligned structure 2; the polar angle Kappa will give you the amount of rotation between the second domains. Eleanor On 21 April

Re: [ccp4bb] relative domain motion calculation...

Hi Mintu You can use Chimera to calculate rotation angel. http://www.cgl.ucsf.edu/chimera/videodoc/AlignDomains/ Veerendra On 21/4/15 3:39 PM, "Mintu Chandra" wrote: >Dear All, >I am working with a protein containing tandem domains, connected with >3-4 residue linker. I want to calculate th

Re: [ccp4bb] advice on anomoulous data collection strategy---low resolution, radiation damage, high mosaicity

On Mon, 20 Apr 2015 23:15:17 +, Keller, Jacob wrote: >>I have processed test data sets (measured at the SLS) which have only a few >>non-zero pixels on each frame. Can be nicely integrated - but it was insulin. >What were the values of the non-zero pixels, I wonder? How many total count

Re: [ccp4bb] off topic: DLS instrument

Adam, We had a trial of the Avid nano W130i DLS system. I liked the small size and the disposable cuvettes. At present we have a Dynapro which is an old machine now but works well. Best wishes Clare From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tianyu Wang Sent: 17

[ccp4bb] PDBe workshop - Making the most of PDB and EMDB data

Dear All, The PDBe team will be running a satellite workshop at ECM29 this summer - http://ecm29.ecanews.org/programme/satellite-meetings/ Registration is through the usual ECM registration process. We look forward to seeing you there and answer your queries about PDB and EMDB. Best wishes,

Re: [ccp4bb] advice on anomoulous data collection strategy---low resolution, radiation damage, high mosaicity

>Burning/frying the crystal is never the right strategy, at least not if you >use a Pilatus detector. >Burning/frying is a strategy that results from the widespread misunderstanding >of using Rsym >as a criterion of data quality. I apologise if I didn't make myself clear. The point I tried to

Re: [ccp4bb] on NCS restraint

All: I strongly disagree with Reza's suggestion that one should abandon NCS at better than 2.5 Å resolution (or even Herman's suggestion at better than 2.0 Å resolution). Either of these may be true in any particular case, BUT one should do the experiment - Run parallel refinements from the s

Re: [ccp4bb] on NCS restraint

Hi all, We have carried out a large-scale test of the use of Refmac's NCS-restraints during model building with ARP/wARP. We have found advantageous to have such restraints turned on with data resolution extending to as high as 1.5 A. Vi

Re: [ccp4bb] on NCS restraint

Hi, I have to agree with Steven. I was too haste in my reply to the initial e-mail. As Steven put it, it is best to run multiple experiments at the same time and identify which produces the best result. On a follow up to Victor Lamin's reply, have the results been published? Best wishes, Reza

Re: [ccp4bb] on NCS restraint

Dear Reza, > have the results been published? Not all of them. The first implementation of NCS-restraints in ARP/wARP's model building at a resolution of 2.3 A and lower was published: Wiegels T, Lamzin VS. Use of noncrystallogra

Re: [ccp4bb] on NCS restraint

All: Oops, someone pointed out to me off line that I slipped-up earlier today when I wrote that LSSR is an abbreviation for "Local >Secondary< Structure Restraints". Rather it is an abbreviation for "Local Structure >Similarity< Restraints". I know better, but I guess my unconscious got the b

[ccp4bb] Phaser going into infinite loop in Ample

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 We are having a problem with AMPLE and hope someone can help. The protein is about 70 amino acids long and we suspect it forms a coiled-coil. Our previous attempts at molecular replacement have failed so we hoped that AMPLE, with its ability t

Re: [ccp4bb] relative domain motion calculation...

Dear Mintu, one possible option is the webserver DynDom. Kind regards, Matic On 21. 04. 2015 09:39, Mintu Chandra wrote: Dear All, I am working with a protein containing tandem domains, connected with 3-4 residue linker. I want to calculate the relative motion

Re: [ccp4bb] AW: [ccp4bb] Cleaved peptide density!

Once thing I don't fully understand: do you have a cleaved density or a cleaved peptide? If your peptide is sitting in a binding site, and that you can see only the part inside the pocket, with the rest supposably sitting in a 'more opened' part of the molecule, or else outside of the molecule,