Re: [ccp4bb] fit-protein in coot

Fink shouldn't touch anything else. If in doubt, sudo mv /sw /sw.keep and you have effectively hidden it. Did you use my ubuntu coot debian, or os x stand-alone? I may have made a mistake packaging these. I never tried the fit protein script (since none of my recent enzymes contained amino ac

[ccp4bb] fit-protein in coot

Dear all, I have installed the latest version of Coot on my Ubuntu computer, but surprisingly I couldn't run the script (fit-protein /imol/). Coot didn't execute that script. I returned back to the previous version installed on my iMac, but I had also the same problem, although this was working

Re: [ccp4bb] How to determine ligand binding from diffraction pat tern?

Aha Dr. Palm Tough to generalize this, but if the ligand is weak or the site only partially occupied you need to refine almost to completion. Since you seem to be doing something akin to fragment screening I can only pass on my experience. I had plenty of cases where the Rfree was ~35 after a

Re: [ccp4bb] scala and cell dimensions

Thanks a lot, Graeme, using scala from ccp4 6.0.1 indeed did the trick (osx binaries). The data were processed with mosflm in fact. Cheers Jan Winter, G (Graeme) wrote: Hi Jan, This data is from XDS I'm guessing. Try Scala from CCP4 6.0.1 - this is a problem only with 602 I think. Cheers, Gr

Re: [ccp4bb] How to determine ligand binding from diffraction pattern?

I'm a fairly inexperienced crystallographer, but I have worked on a few cases very recently (from separate protein systems) in which the ligand was not "clear" in the electron density until quite a long way through refinement: in the latest case, it wasn't possible to be too confident of the ligand

Re: [ccp4bb] How to determine ligand binding from diffraction pattern?

I would like to expand on the question and answer below and compare your experiences: Looking for ligands in many different soaks / cocrystals of your protein of interest, you still should do molecular replacement and a bit of refinement. I agree with Steve, but how much refinement is necessary

[ccp4bb] scala and cell dimensions

Hi mosflm experts, last week's problem with mosflm solved, another one appearing. Scala fails with the error message below. These are ~10AA data. Scala finishes in p422, however dies in p222... Any ideas? Cheers Jan ~ scala.log Run(s):1 * Wavelength and cell extracted fro

Re: [ccp4bb] Movie for Powerpoint in windows -Summary

Hi All, Few days ago I posted a question of how to create an .avi movie file that can be played in WindowsMediaPlayer and inserted into powerpoint from a series of .png produced in Pymol? So many different suggestions. However, the most straight forward one came from (Joyce Gordon, Pe

[ccp4bb] Lectureship in Structural Biology

Lectureship in Structural Biology We are expanding our research in Structural Biology and seek to appoint a Lecturer (or possibly a Senior Lecturer or Reader). The School of Biological and Chemical Sciences at Queen Mary is a research-led School with excellent facilities for both X-ray c

Re: [ccp4bb] MR with electron density model

What have you tried so far for obtaining an MR solution? You have many options of software, search models, and parameters to use in the MR search. Software: Phaser and EPMR should be on your list to try. These two programs can crack most problems efficiently, Models: The highest homology models a

[ccp4bb] post-doc position opening

A post-doc position at oklahoma state university is available immediately in the field of protein crystallography. If interested, please send CV and contacts of three references directly to: [EMAIL PROTECTED] Thanks. Junpeng

Re: [ccp4bb] crystal problems

Detwinning without a known structure, and such a high twin factor must be very unreliable . If you have only IT1 and IT2, the detwin algorithm gives I1 = (TF*It1 + (1-TF)*IT2) / (1-2*TF) (Maybe signs wrong there!) Since (1-2*TF) is almost 0, this is pretty inaccurate.. But if you have

[ccp4bb] crystal problems

Dear All, I had written earlier about my twinned crystal that was giving me problems..thanks to all who responded, it was very helpful. I have another couple questions about the same crystal that is confusing us. The twinned crystals space group is P3. Twinning was found using the Yeate

[ccp4bb] specialization?

I was interested in corresponding with any research group that specializes in devising new protocols for protein crystallization. Are there any that just focus on this aspect of crystallography? Prof. Laura Juszczak Dept. of Chemistry Brooklyn College The Graduate Center The City Unive

Re: [ccp4bb] crystal shipping at room temperature

Dear Junhua, Try this simple experiment...put a MiTeGen loop up without crystal or solution and take am image. (...and then tell us what it looks like) Kris Kris F. Tesh, Ph D Director, Macromolecular Products Rigaku Americas Corporation 9009 New Trails Drive The Woodlands, TX 7738

Re: [ccp4bb] How to determine ligand binding from diffraction pattern?

Having done this a few hundred times, I would strongly suggest that you just collect the data and solve the structure. Since you already have the apo structure solved, then it really isn't that much work to do an MR solution on the complex. Be aware that quite frequently there is enough non-isomo

Re: [ccp4bb] How to determine ligand binding from diffraction pattern?

Hi Joe In principle, a FOM-weighted difference Fourier using the known phases of the apo structure is in essence a comparison of the diffraction patterns, however in practice it relies on the apo & ligand-bound crystals being highly isomorphous. The problem is that changes in the diffraction due

Re: [ccp4bb] Disordered active sites

Nian Huang wrote: Hi, all, I met some crystal structures with disordered active sites. Soaking common ligands can not make it become ordered. I am wondering what people generally do in such situation. Thanks, Nian Huang Swear?! This is quite common - the usual tricks may work - Sulphate ,

Re: [ccp4bb] crystal shipping at room temperature

Dear Junhua, This does indeed sound like a description of a fiber diffraction pattern. For example, as you probably already know, A-form DNA fibres give large bands close to 3.4 Angstroms at the top and at the bottom of the images. The exact positions of the bands are specific to the type of fibr

Re: [ccp4bb] A babyish question on coot

Hi Yanming, I am glad that at least one other person has encountered this problem so I do not feel too guilty for having asked Paul to do something about it. Anyway, the MAN was kind enough to add a masking function under the Extensions Menu. It is something called 'Mask map bla bla..'. (I am n

Re: [ccp4bb] How to determine ligand binding from diffraction pattern?

Dear Joe, Reflections that correspond to the reflection conditions of your space group symmetry (e.g. h=2n, h+k=2n, l=2n for C4) and are the reciprocal space equivalent of the ligand binding pocket in real space should be considered for comparison. But make sure you collect corresponding refle

Re: [ccp4bb] A babyish question on coot

Hi, After JED's email I tried immediately: case: a metal site which has very strong density and a HIS co-ordinating with the ion. After I click 'Real space refine zone' and then the residue HIS, the HIS will move to the density which belongs to the ion(clash with the ion) no matter how low t

Re: [ccp4bb] A babyish question on coot

It is actually a question of 'adult-crystallographer' addressing a 'baby-coot' ;-) I also have that problem - and moreover I had it when programming real space refine in ARP/wARP ages ago. An elegant solution now is the one implemented by Serge Cohen in my group, to use a map that has the d

Re: [ccp4bb] A babyish question on coot

Unreasonable geometry can be avoided by setting the refinement weight to a lower value -- either using Extensions->Set Matrix (Refinement Weight) or in your .coot file: (set-matrix ) There's also a coot-bb, btw. JED -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTE