[ccp4bb] From the CNS1.2 trnaslation error

Hallow, Thank you for your kind attention. I am using CNS 1.2 to solve my structure with molecular replacement. As a novice CNS user, I was trying to follow the tutorial given at the CNS website. I have a tetramer. I have two queries. 1. There are two maps prepared from the self_rotaion.in

[ccp4bb] Reminder: Crystallographic Computing School registration deadline approaching

The registration deadline for the 2008 Crystallographic Computing School is in two weeks: *** July 25 *** The schedule of the program including abstracts from all speakers is available here: http://www.iucr.org/iucr-top/comm/ccom/kyoto2008/program.html This program puts a strong weight on fost

[ccp4bb] ArpWarp error

I'm running flexWarp on a MacBook Pro and on a Linux box. The program goes through several cycles and then gives the following errors when trying to improve an MR solution: If I start from the PDB file as is ERROR Exception class : 'IndexError' Message : '' BackTrace (limited to level 20) :

Re: [ccp4bb] pdbset bug - seqres record

Is this just a consequence of old/new conventions for the SEQRES records? If so, send a feature request to ccp4, asking for an option to be added to pdbset. Pete -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Ed Pozharski Sent: Thursday, July 10, 200

[ccp4bb] pdbset bug - seqres record

There is a bug in pdbset: when you output a sequence (using "SEQU PDB"), the residue names are shifted to the left by one position. Here is how it looks like: In PDB-file downloaded from the PDB: SEQRES 5 A 171 ALA THR CYS ... PDBSET output: SEQRES 5 A 171 ALA THR CYS ... I lo

Re: [ccp4bb] how to promote folding for an unfolded protein

Hi Jenny, check on non-reducing SDS PAGE whether your disulfide bond (I assume there is one) is correct, i.e. you have monomeric protein on SDS-PAGE. If there are disulfide linked oligomers, try expression in Origami strain at lower temperature, e.g. 25 deg C.Another possibility is to direct ex

Re: [ccp4bb] histidine modification

Hi, 1. the same image in jpg or png format occupies a mere 180 - 300 kB. It's nice to be considerate of other people's bandwidth especially since you're asking for help 2. how do you know it's a covalent modification? Anything on MS to confirm that? 3. this reminds me of http://www.jbc.org/cgi/c

Re: [ccp4bb] Hardware problem: "nVidia NV41 [Quadro FX 3450/4000 SDI]" on Redhat EL 5 (needed for stereo viewing)

On 16:05 Thu 10 Jul , Christian Rausch (Biol. Chemie) wrote: > We have tried the following installation scripts from Nvidia: > NVIDIA-Linux-x86-173.14.05-pkg1.run > NVIDIA-Linux-x86-173.14.09-pkg1.run > > And tried it with the following kernels: > vmlinuz-2.6.18-92.1.1.el5PAE > vmlinuz-2.6.18-

Re: [ccp4bb] Anion binding sites in proteins

I should like to point out here that almost ANY protein will pick up something from the crystallization solution (cations, anions). Unfortunately, in the majority of cases these partially occupied ions will not be seen or will be mistakenly interpreted as water molecules. One way to 'see' such thin

Re: [ccp4bb] how to promote folding for an unfolded protein

Jenny have a look at our REFOLD database: http://refold.med.monash.edu.au you can find several refolding protocols in there for immunoglobulin folds (you can blast your sequence against the refold database) cheers ashley -- Ashley Buckle Ph.D NHMRC Senior Research Fellow The Department of Bioc

Re: [ccp4bb] Anion binding sites in proteins

Hi Albert, Please refer to the following paper (and references therein) for a description of the four chloride located in the nucleosome structure.. 1: Davey CA, Sargent DF, Luger K, Maeder AW, Richmond TJ. Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a

[ccp4bb] Refmac scale questions

Hi, my refinement (Refmac_5.2.0019) in sp. grp. C2 with 2 TLS groups, bulk solvent, and overall anisotropic scaling gives the following output: - Overall : scale =1.143, B = 0.148 Babinet"s bulk solve

Re: [ccp4bb] Anion binding sites in proteins

There is a number of 'defined' anions known from structures of halorhodopsin and the cores of coiled-coil proteins often show them as well. -- Kornelius Zeth Max Planck Institute for Developmental Biology Dept. Protein Evolution Spemannstr. 35 72

Re: [ccp4bb] how to promote folding for an unfolded protein

Hi Jenny, there are probably as many 'folding enhancers' as there are crystallization additives. Arginine might only be the most popular, followed by things like proline and other amino acids. The mode of action of those can partly be explained by their mild chaotropic properties. For a difficult

Re: [ccp4bb] Anion binding sites in proteins

I have been interested in this topic as well, so could any responses that are not also addressed to the BB be sent to me as well? Thanks very much, Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Lab

[ccp4bb] how to promote folding for an unfolded protein

Dear CCP4 community, Sorry for this off-topic protein purification problem.I'm trying to purify an immunoglobulin-like beta sheet protein with a c-terminus HIS construct. The protein expressed both in the supernat and pellet ( majority ). I purified the supernat and after run gel filtration, it'

[ccp4bb] Anion binding sites in proteins

Dear all, can someone point me to something similar to Metal coordination sites in proteins (http://tanna.bch.ed.ac.uk), but describing anions (I'm mainly interested in chloride-binding sites)? Thank You, Albert -- Albert Guskov, Freie Universitaet Berlin Fachbereich Biologie, Chemie, Pharmazie In