Re: [ccp4bb] Disorder or poor phases?

On 4/10/2012 10:44 PM, Kay Diederichs wrote: Hi Dale, my experience is that high-B regions may become visible in maps only late in refinement. So my answer to the original poster would be - both global reciprocal-space (phase quality) and local real-space (high mobility) features contribute

Re: [ccp4bb] Disorder or poor phases?

Hello, Kay is absolutely right. Just to make this clear: We all know that in many cases, you start out with poor phases (i.e. a weak SIR/MIR/MAD or a borderline replacement model) and your density is modest. The prudent thing to do at this stage is, to build only things you trust and have a look

[ccp4bb] Deadline april 16th: 24/25 May 2012 IGBMC symposium on “Future Challenges in Integrative Structural Biology”

Dear all, last reminder for our symposium at the IGBMC on 24/25 of May on “Future Challenges in Integrative Structural Biology”: the deadline is extended to april 16th 2012, see http://fcisb2012.u-strasbg.fr for registration and abstract submission. In addition to the presentations

[ccp4bb] Ligand fitting into density

Dear Crystallographers, The protein I am working with is having SG P3121, Structure is solved at 2.5A. the protein was soaked with compound, compound density is also looking prominent except one six membered ring. There is no density at all for the particular ring, but other parts of the

Re: [ccp4bb] Ligand fitting into density

Dear Dipankar, I have had a case where I had soaked the same compound in Trypsin (2.2 Å) and in Factor Xa (2.0 Å). In Trypsin, one six-membered ring was completely invisible, despite good resolution and phases, whereas this ring was clearly visible in the Factor Xa structure. The electron

[ccp4bb] unsubscribe

Dear CCP4 bulletin board, since I am retired, I would like to unsubscribe. It was fun reading the problems others have and to help them out. Best wishes Wolfram Saenger. -- Prof. Dr. Wolfram Saenger Freie Universität Berlin Fachbereich Biologie, Chemie, Pharmazie Institut fuer Chemie und

Re: [ccp4bb] Disorder or poor phases?

I am not sure anyone looks at plain 2fo-fc maps anymore - it almost always (at least since the beginning of the 3rd millennium) implies 2mfo-Dfc ML maps. Detailed explanation of coefficients and their relation to ML sigma A are in R.Read papers, BMC, Bricogne, etc pp BR, On Tue, Apr 10, 2012 at

Re: [ccp4bb] Ligand fitting into density

Dipankar, Herman's message describes the most common case, by far. In addition to his excellent post there are 4 other possibilities which I can think of of why, in general, the e- density may be missing for part of a ligand: - the compound solution are never 100% pure. One impurity may be the

Re: [ccp4bb] Ligand fitting into density

Sometimes you can distinguish disorder from the other possibilities if you have enough structures with the same protein. We have several examples where part of the ligand is not visible in the maps, but there is clear distortion of the ligand binding pocket to accommodate the missing piece. for

[ccp4bb] A creative and challenging job in science communication - join PDBe as its Outreach Coordinator!

Are you an aspiring science communicator who has a wonderful way with words? The Protein Data Bank in Europe (PDBe; http://pdbe.org/) is looking for an enthusiastic 'jack of all trades', to coordinate its outreach activities. We are looking for someone who will raise the profile of PDBe through

Re: [ccp4bb] Ligand fitting into density

Sent from my LG phone Kendall Nettles knett...@scripps.edu wrote: Sometimes you can distinguish disorder from the other possibilities if you have enough structures with the same protein. We have several examples where part of the ligand is not visible in the maps, but there is clear

[ccp4bb] .CBF raw images in iMOSFLM- error

Hello everyone, I am trying to process ###.cbf raw images (BNL X25) using the iMOSFLM utility and I get the following error message: Distance has refined to an unreasonable value This causes the program to freeze and not open the rest of the frames. Also it is not picking up the X and Y beam

Re: [ccp4bb] Ligand fitting into density

Dipankar, What you describe occurs frequently and some times improves with refinement and other times does not. I suggest not adding ligands until the rest of the structure is well behaved - usually around 25-28% Rfree. This will tend to favor the highest quality electron density and will not

Re: [ccp4bb] .CBF raw images in iMOSFLM- error

Hi Yuri If you can put some of the images on our ftp site (instructions sent separately) we'll have a look. There was a problem a while ago when some Pilatus detectors changed from writing the distance in metres to writing it in millimetres, but no-one told us until iMosflm started

Re: [ccp4bb] unsubscribe

I think the community should thank you Wolfram for all you have contributed - I do hope this message catches you or someone passes it on! All the best for your retirement eleanor Dodson On 11 April 2012 11:21, Wolfram Saenger saen...@chemie.fu-berlin.de wrote: Dear CCP4 bulletin board,

[ccp4bb] Question about PyMol

Hi All, Sorry for the dumb question, but if there was a way to export coordinates from PyMol. Is yes, then how? Thanks Christine

Re: [ccp4bb] Question about PyMol

Yes. File - Save Molecule... James On Apr 11, 2012, at 1:17 PM, Harman, Christine wrote: Hi All, Sorry for the dumb question, but if there was a way to export coordinates from PyMol. Is yes, then how? Thanks Christine

Re: [ccp4bb] Question about PyMol

Thanks for the quick reply. Wow such an easy thing to do. I am feeling really dumb now...:) Christine From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of James Stroud Sent: Wednesday, April 11, 2012 3:20 PM To: CCP4BB@JISCMAIL.AC.UK Subject: