[ccp4bb] nonspecific interactions with GST beads

Hi all, I've recently switched over to using a GST system for purifying my proteins. Although I can get enough protein out of a few liters, I've always been finding that when I take some of the beads to run on a gel, I always get a decent amount of protein just stuck on there that won't elute o

Re: [ccp4bb] completeness in scala

On Tue, May 15, 2012, Toth, Eric wrote: > In sports, maximal effort is considered to be 110%, so you're actually > 9.9% short of getting everything you could out of that crystal at its > resolution limit. All things considered, that's not bad. In (U.S.) politics, the standard continues to be the

Re: [ccp4bb] completeness in scala

In sports, maximal effort is considered to be 110%, so you're actually 9.9% short of getting everything you could out of that crystal at its resolution limit. All things considered, that's not bad. _ Eric A. Toth, Ph.D. Assistant Professor Departme

[ccp4bb] completeness in scala

Just a curiosity - I have a dataset at 1.45A for which SCALA reports the highest resolution shell completeness at 100.1%. I am impressed :-) -- "Hurry up before we all come back to our senses!" Julian, King of Lemurs

Re: [ccp4bb] Strange Density

Hi Rhis, It may have been suggested already but still... X-ray fluorescence spectra can often tell you what elements you may be dealing with. Spectra won't tell anything about binding specifics, but any extra bit of information could help. Any descent synchrotron MX beamline, equipped for MAD/SA

[ccp4bb] how to ignore spot overlap in imosflm?

Dear all, Thanks for all of the suggestions, It helps me a lot as I am a newcomer to the structural world. Increasing the "Profile Tolerance" parametersas Dr Harry Powell has pointed out can increase the completeness by ten percent (from 50% to 60%). I will try other people's advice soon. A

Re: [ccp4bb] Strange Density

Your holo structure has a Ca++ and three water molecules that have not been built into your low resolution apo map. These atoms are not expected to be resolved at 3 A resolution, so I would expect them to appear as a large, misshapened, blob. Your screenshot only shows one contour level. It

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

One must remember that multiple sequences alignments are not just alignment of letters...they are amino acids with three dimensional (four if you count time) coordinates. The alignments can be very subjective and are best done in conjunction with a structural alignment of overlapping structures.

Re: [ccp4bb] How to refine CNS output file in refmac

Dear Vidisha The easiest way is to convert DNA names to standard pdb v3 names. You can do it using molprobity. The probelem is that GUA may have different meaning than G (RNA) or DG (DNA). regards Garib On 15 May 2012, at 16:37, tipu Lall wrote: > Dear CCP4 users, > > I am a beginner in thi

[ccp4bb] How to refine CNS output file in refmac

Dear CCP4 users, I am a beginner in this field. It would be kind of all of you if can help me how to move ahead with my problem. I have an output file from CNS of a binary complex (DNA-protein) and I am trying to refine it with refmac5 (restrain refinement) and job is failing with error messa

Re: [ccp4bb] Strange Density

On Tue, 2012-05-15 at 15:51 +0100, RHYS GRINTER wrote: > A colleague suggested that sulphate or phosphate could fit at these > distances, but these ions have not been added at any stage of the > crystallisation process. > I vaguely remember a report about 2-3 years ago at the ACA meeting of phos

Re: [ccp4bb] Strange Density

Try refining with: Na, Ca or Water at that position and compare the resulting maps. That should provide you with the information you need. It could be a weakly bound sodium, or calcium ion. It could be that calcium was not fully removed by EGTA treatment. Kelly ***

Re: [ccp4bb] Off topic about program for multiple protein sequence alignment

Dear Donghui, Your implied question seems to be "How do I know whether my MSA is good?" Errors in MSAs arise from two factors. First, due to computational limitations, heuristic methods are used for most MSA programs. As a result, one can never be certain that a progressive MSA method actually

[ccp4bb] Strange Density

Dear Community, As I'm a relatively new to protein crystallography this might turn out to be an obvious question, however. I'm working on the structure of a enzyme requiring Ca2+ for activity and with calcium coordinated in the active site by Asp and 2x backbone carbonyl groups, in a crystal s

Re: [ccp4bb] dm: Error in opening input map file.

Dear De-Feng Li, Thank you for your reply. Actually, I already used the script. The script and the log file are at the bottom of the email. Best wishes, Yu On Tue, May 15, 2012 at 3:18 AM, lidefeng wrote: > Dear Yu Feng, > > You could try it in script, but not in the CCP4i. The

Re: [ccp4bb] Off topic about program for multiple protein sequence alignment

mafft and muscle are both faster than clustalw and on average more accurate. You can also use different options for mafft to push for speed or accuracy depending on your needs and patience. Tcoffee has a flavour that includes structural information if available to assist alignment. Another flav

Re: [ccp4bb] Multiple structure alignment and citing CCP4bb

On Tue, 2012-05-15 at 07:27 +0100, Naveed A Nadvi wrote: > I was wondering if there is any software out there that can be used > for multiple structure superimposition and output some graphical plot > of residues based on their deviation from the reference molecule. And why exactly you cannot acco

[ccp4bb] Opportunities to develop new MX integration software

Dear All, Can I draw your attention to the following vacancies at Diamond Light Source for scientific programmers to work on the development of new integration software for MX. The work forms part of a European collaboration under the BioStruct-X (www.biostruct-x.org

Re: [ccp4bb] how to ignore spot overlap in imosflm?

Dear Xinghua, If you want to get the most out of your data, despite the fact that your data collection strategy was far from ideal, you may want to use EVAL15 (www.crystal.chem.uu.nl/distr/eval). It it pretty good in modelling the complete profile, including overlap, and therefore is good at d

Re: [ccp4bb] Off topic about program for multiple protein sequence alignment

Certainly different programs and different scoring matrices will give different answers. There is not necessarily a correct answer either, just different educated guesses. With high sequence identity, the answers should be fairly consistent. As you reduce the sequence identity (i.e. as it gets m

Re: [ccp4bb] Off topic about program for multiple protein sequence alignment

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Donghui, even within one program (clustalw) you would get different results by picking different weighting schemes (clustalx: Aligment->Alignment Parameter -> Multiple Alignment Parameter: BLOSUM, PAM, Gonnet...). As with any software I would as