[ccp4bb] Fw: [ccp4bb] structural homology

etc) and if you have gaps put them at the end or beginning of helices or strands. With evolution, strands are usually stay strands and helices stay helical, but may lengthen or shorten. Modeler is the the most advanced program but not the most intuitive. Both are free to academics. Dr. Pau

[ccp4bb] dumb software question

, etc measurements with links to the pdb? Thanks in advance. Paul Dr. Paul Kraft Structural Biologist cell 586-596-2770 email: haresea...@yahoo.com

[ccp4bb] multiple sequence alignments..should be done structurally if possible

 alpha helices, strands almost always strands, and the connecting chain lengths may vary. Be patient :-) Dr. Paul Kraft Structural Biologist cell 586-596-2770 email: haresea...@yahoo.com

[ccp4bb] Na acetate buffer, purification of a high pI protein...wash H6 collumn with 1+M NaCl

I have purified dozens of very high pI viral proteins, and I can't stress enough the requirement to wash your protein with at least 1M NaCl after binding it to the histidine collumn. DNA fragments often require a 2M NaCl wash. High pI proteins are very soluble. Dr. Paul Kraft Struc

[ccp4bb] before doing an elisa or buying a dye for affinity measurement....

PCR rxn to generate a W mutant would be easy too. Dye detection methods  can be problematic at times, and elisa's have there own problems... Dr. Paul Kraft Structural Biologist cell 586-596-2770 email: haresea...@yahoo.com email: kraft_proteome_resea...@yahoo.com This communication an

[ccp4bb] linux upgrade preferences for CCP4

hello, I'm considering upgrading my linux software from CENTOS5 to perhaps Fedora or UBUNTO. Does anyone have an opinion about the best linux version to upgrade to for not only CCP4 but also for general robustness and for the best standard apps..Thanks Paul Dr. Paul Kraft Structural Biol

Re: [ccp4bb] gst-tag protein purify problem

Forgot to add, a 150aa dna binding protein should only need a minimal hexahistidine tagthese proteins are typically very soluble and express well. Adding a GST or sumo tag is overkill. Dr. Paul Kraft Structural Biologist cell 586-596-2770 email: haresea...@yahoo.com email

Re: [ccp4bb] gst-tag protein purify problem

for source the source gene). Paul ps one thing I forgot, you mention it is a DNA binding protein, solublizing in 2M NaCl is much better than 1M NaCl, you could just be losing it...the protein that is :-)   Dr. Paul Kraft Structural Biologist cell 586-596-2770 email: haresea...@yahoo.com email

Re: [ccp4bb] Off Topic: How to delete loops from a protein/homology modeling

model with loops spliced in and energy minimized. There are many other more or less complicated programs, but it's a good one to start with. Paul Dr. Paul Kraft Structural Biologist cell 586-596-2770 email: haresea...@yahoo.com email: kraft_proteome_resea...@yahoo.com This communication and

Re: [ccp4bb] protein aggregation

Try taking the detergents out of your solublization buffer (that is if you know it's not a membrane protein) and only extract the buffer soluble portion. If you have a tag try switching the tag to a different terminus. Dr. Paul Kraft Structural Biologist cell 586-596-2770 email: ha

[ccp4bb] homology modeling

ogram that can be substituted for CHARM (will GROMOS from SWISS PROT work?).   Also is their any open source homology modeling program that includes solvent interactions in the minimization (it seems they all require $$, at least the good one's). Thanks in advance. Paul Dr. Paul Kraft

Re: [ccp4bb] purification of a strange protein

Paul Dr. Paul Kraft Structural Biologist cell 586-596-2770 email: haresea...@yahoo.com The information constituting this transmission is privileged and confidential. If you are not the intended recipient, please notify me immediately. --- On Tue, 6/8/10, Oliver Li wrote: From: Oliver Li Su

[ccp4bb] Fw: Re: [ccp4bb] Structural importance of ordered water?

waters in crystal structures vs NMR structures? Paul Kraft --- On Tue, 6/17/08, Sanishvili, Ruslan <[EMAIL PROTECTED]> wrote: From: Sanishvili, Ruslan <[EMAIL PROTECTED]> Subject: Re: [ccp4bb] Structural importance of ordered water? To: CCP4BB@JISCMAIL.AC.UK Date: Tuesday, June 17, 2008,

[ccp4bb] libstdc++.so.5: cannot open shared object file: No such file or directory

ll on the /examples/ and got the error "libstdc++.so.5: cannot open shared object file: No such file or directory" for pretty much all of the progrrams. I know this is a library problem I've seen before but can't remember how to fix it. Your help would be appreciated. Thank

[ccp4bb] libstdc++.so.5: cannot open shared object file: No such file or directory

annot open shared object file: No such file or directory" for pretty much all of the progrrams. I know this is a library problem I've seen before but can't remember how to fix it. Your help would be appreciated. Thanks, Paul Dr. Paul Kraft Structural Biology Research Associa

[ccp4bb] ipmosflm centos4.4 mouse enlarge doesn't work

have crappy data and the first indexing puts the spots slightly off and you need to "adjust" them. Any ideas besides switching to an older version of either centos or CCP4? Best Regards, Paul Dr. Paul Kraft Structural Biology Research Associate Dept. Biochemistry and Molecular Biology L

[ccp4bb] Fwd: Re: [ccp4bb] (bigger) fragment identification of limited proteolysis w/ mass-spec

Certainly you can seperate these fragments by SDS-PAGE, cut the bands out, redo the proteolysis and throw them into the MS again... Note: forwarded message attached. - Now that's room service! Choose from over 150,000 hotels in 45,000 destinations on Yahoo!