Re: [ccp4bb] CCP4-6.3.0 installtion

Thanks for the quick reply! Unfortunately I used the DMG package for the installation. Any suggestions about that? I return to my comment about the fresh installation on another machine, which worked perfect (with the update package). Should I delete the 6.3.0 installation and begin again from

Re: [ccp4bb] CCP4-6.3.0 installtion

Hi Yoni, You can have multiple versions of CCP4 installed on a system without causing problems (although usually only one is active). In general, it's sufficient to source the new ccp4.setup-(bash|csh) prior to compiling the new version (I'm assuming you're using a source version from the "m

[ccp4bb] CCP4-6.3.0 installtion

Hello all, I am trying, unsuccessfully, to upgrade my CCP4-6.1.3 with 6.3.0. The installation process works smoothly, but the programs (both CCP4 and arp/w) do not start. I think the problem is the previous version of CCP4 that was on this computer because of 3 reasons: 1. I have managed to ins

Re: [ccp4bb] unidentified density

Seems that this density is in a symmetry axis, if look is like that a mirror is crossing just in the middle of the density. If you really want to cover this density, I will try to fit with a small PEG molecule and some waters focusing yourself just on half of the density. R From: CCP4 bulletin

Re: [ccp4bb] unidentified density

Do you have matching 2Fo-Fc density? It is not obvious from the pictures. From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Sudhir Kumar Sent: Thursday, 18 October 2012 12:07 a.m. To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] unidentified density Dear all, I have been working o

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Re: [ccp4bb] Modelling Flexible Regions

These are excellent questions. There are probably no easy answers. The situation with flexible loops is that the peptide chain adapts multiple (>=3) conformations here and we traditional crystallographers are trying to fit one model into the density that is the result of multiple confirmations. Th

[ccp4bb] Structural Biology Faculty Position at Brown University

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Re: [ccp4bb] unidentified density

I think it's MPD. I have also observed in my crystals. Amit Luthra, Ph.D. Post-Doctoral Fellow The Radolf Laboratory Department of Medicine University of Connecticut Health Center [e] alut...@uchc.edu [p] 860/ 679 - 8390 From: CCP4 bu

Re: [ccp4bb] Modelling Flexible Regions

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Rhys Grinter, when you deposit a model, I think it is the consens to believe that you as its author have done your (reasonably) best to create that model given the data available, i.e. if you come to the conclusion that you cannot justify buildin

Re: [ccp4bb] unidentified density

I think it might be PEG. u should try to fit that. On Wed, Oct 17, 2012 at 7:13 AM, RHYS GRINTER < r.grinte...@research.gla.ac.uk> wrote: > Is this density on an 2 fold axis? > > From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Sudhir > Kuma

[ccp4bb] Stabilization of crystals and ligand exchange

Hi everyone, I am trying to get the structure of a protein-ligand complex were I need to exchange the ligand which it co-crystallises nicely with. Problem: either they crack, disolve, turn brown,... OR they still look very nice, well shaped but do not show a single reflection at the synchrotr

[ccp4bb] Modelling Flexible Regions

Hi All, This is a fairly basic question coming from a novice crystallographer, but I was wonder at what point it's reasonable to say 'I can't model that loop!'. I'm currently working on a couple of structures and there's density for where the a flexible loop on both structures goes, but there is

Re: [ccp4bb] cryo conditions

Thanks to all for the suggestions! We will try, this weekend at macCHESS, all those conditions for which we have reagents, and order the others now. > On Oct 16, 2012, at 9:01 PM, "Edward A. Berry" wrote: > >> Would someone suggest a cryoprotectant for index screen #59? It contains >> 0.02 M MgC

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Re: [ccp4bb] unidentified density

Is this density on an 2 fold axis? From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Sudhir Kumar [sudhir.1...@gmail.com] Sent: 17 October 2012 12:07 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] unidentified density Dear all, I have been workin

Re: [ccp4bb] cryo conditions

Dear Ed, Glycerol is a solubilizing agent. Unless something is done to conteract such effect the crystals will dissolve. Laura Vera from my lab made a presentation at ICCBM-14 on this subject. We have developed a set of balanced solutions, mixed solubilizers like glycerol and ethylene glyc