Re: [ccp4bb] How to make a structure-based multiple sequence alignment on DALI server?

Hi, I would suggest the indonesia program... easy to use and very flexible. http://xray.bmc.uu.se/dennis/ Cheers Dave david wu wrote: > Hi all， > > I want to produce structure-based multiple sequence alignment of my protein > with five of its homologs on DALI server. However, when I tried th

Re: [ccp4bb] How to make a structure-based multiple sequence alignment on DALI server?

POSA at the Godzik lab does exactly what you are after, flexibly! http://fatcat.burnham.org/POSA/ Hi all=A3=AC I want to produce structure-based multiple sequence alignment of my =20= protein with five of its homologs on DALI server. However, when I =20 tried the "Database Search Form", on

Re: [ccp4bb] refmac5.3 vs refmac5.4

On Dec 5, 2007, at 14:05, Jianghai Zhu wrote: Hi all, I updated refmac5.3 to refmac5.4 and found out that the reported RMSDs are quite different from these two versions even the refining protocols are the same. refmac5.3 rmsBOND rmsANGLE rmsCHIRAL 0.006 0.694

[ccp4bb] ccp4 study weekend registration closes this Friday

Dear All the registration for the CCP4 study weekend closes on this Friday (7th) at 5pm GMT. Details for this/early next years event on "Low Resolution Structure Determination and Validation" are at http://www.cse.scitech.ac.uk/events/CCP4_2008/ so if you would like to join 400 souls in

[ccp4bb] coot: Show Symmetry

--- Hi All i want to display symmetry molecules in COOT, but regularly getting the following warning: There are no model molecules that can display symmetry (Cryst1 problem). How to troubleshoot this Cryst1 problem thanks in advance Vineet gaur --- This problem can also happen if the cryst card

[ccp4bb] SeMet peptide synthesis

Dear all, Does anyone know a reliable company that could perform a peptide synthesis including a SeMet residue? Thanks a lot in advance for your answers, Alfredo. Alfredo Torres-Larios, PhD Instituto de Fisiologia Celular, UNAM Mexico ---

Re: [ccp4bb] refmac5.3 vs refmac5.4

Weights are the same. 5.4 has a lot of small bug fixes and performance enhancement and some added stability things. And some new features I am planning to announce soon. Since I am responsible, my extremely biased view is that 5.4 is better. Garib On 5 Dec 2007, at 13:05, Jianghai Zhu wrote:

Re: [ccp4bb] refmac5.3 vs refmac5.4

> -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Anastassis Perrakis > Sent: 05 December 2007 13:45 > To: Jianghai Zhu > Cc: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] refmac5.3 vs refmac5.4 > > > On Dec 5, 2007, at 14:05, Jianghai Zhu wrote: >

[ccp4bb] PhD Position in Wuerzburg / Germany

A PhD position in structural biology is available in the group of Prof. Utz Fischer at the Institute of Biochemistry, Biocentre of the Julius Maximilans University, Wuerzburg/Germany. The successful applicant will work on the crystallographic structure determination of the Survival Motor Neuron (S

[ccp4bb] refmac5.3 vs refmac5.4

Hi all, I updated refmac5.3 to refmac5.4 and found out that the reported RMSDs are quite different from these two versions even the refining protocols are the same. refmac5.3 rmsBOND rmsANGLE rmsCHIRAL 0.006 0.694 0.046 refmac5.4 rmsBOND rmsANGLE rmsCHIRAL

Re: [ccp4bb] PEG MW vs. cryoprotectivity

In our recent experience, larger PEGs work similarly to smaller PEGs as far as vitrification goes. Additionally, transferring crystals to a solution of increased PEG concentration (as compared to mother liquor) can substantially reduce the amount of cryo needed for freezing and can be more gen

Re: [ccp4bb] How to make a structure-based multiple sequence alignment on DALI server?

Christoph Gille's program STRAP generates structure-based multiple sequence alignment, which can be combined with sequences for which no structure is available. http://www.charite.de/bioinf/strap/ Klaus -