[ccp4bb] Modeling sugars with Coot and Phenix

Hello all, I have several questions regarding sugar modeling. These are questions for both Coot (0.9.4-pre/CCPEM) and Phenix (1.18.2-3874) usage (on a Mac) for modeling as correctly as possible several N-linked glycosylation (i.e. not ligand) sugars within a protein, and about the approach as it

[ccp4bb] powdery residue on pucks?

Hi All, We have been noticing lately that our crystal pucks return from different beamlines coated with the same powdery material. For the record, we typically undo our pucks, clean the assemblies and dry out the pucks within a day of receiving the shipping dewar, but notice the same thing

Re: [ccp4bb] Searching similar local structural conformations

Lei, The DeGrado lab developed a tool that would do just what you seek to do and could function as a PyMOL plugin. I played with it a few years ago after I found an interesting cation-pi sandwhich in my structure. I e-mailed then with the author, hoping to link the tool to the entire current PDB

[ccp4bb] Research technician position at La Jolla Institute for Immunology (California, USA)

The Ollmann Saphire laboratory at La Jolla Institute for Immunology (LJI) is seeking a technician to work as a part of our team. We are focused on infectious diseases and immune response in general, viral pathogens that cause hemorrhagic fever in particular. The lab has a solid core of structural

Re: [ccp4bb] A helix with leucine repeats

Could it be a member of a coiled coil at some point in its lifetime, as a part of its function in regulating position or activity of this receptor? Does the helix have sequence similarity to other coiled coils? see https://www.uniprot.org/help/coiled for a primer on the topic. Looks fun! Emily.

Re: [ccp4bb] cannot read h5 data file

Shijun, I have processed .h5 format data successfully that was collected at NSLS II AMX (this beamline has a Eiger 9M, not 16M, incidentally, but I don't think that this matters). I used XDSGUI without converting to .cbf format. To do so, and without knowing what the error messages are that you

Re: [ccp4bb] Differences in a homodimer protein

I assume that somehow the two subunits are distinguishable despite their forming a "homodimer." Otherwise I don't know how you would know that it is always the same subunit that contains the water molecule. If they are truly distinguishable, then, the first thing that's come to mind is the

Re: [ccp4bb] doubt regarding MR search model

Hello Randy, I'm chiming in about the last sentence in your reply: > Finally, I would suspect that getting a significantly lower LLG for two > copies of a dimer means that the dimer in your structure is slightly > different from the dimer in the model. > Will you please be more specific about

Re: [ccp4bb] just out of totally idle curiosity ...

I had previously considered to relocate, at least temporarily. But now a part of me wants to stay and fight for what we (as scientists) have managed to achieve. On Nov 9, 2016 12:45 AM, "Tom Peat" wrote: > I don't know about Europe, but it is very tight Down Under... > > >

Re: [ccp4bb] PyMOL v. Coot map 'level'

to be noisier (perhaps). I suppose that if you want comparable levels from the same map/mtz file then you should use absolute levels, not rmsd. ***What does PyMOL's 1.0 mean in electrons/A^3?*** Regards, Paul. Regards, Emily. On 01 Jun 2015, at 11:37, Emilia C. Arturo (Emily) ec...@drexel.edu

Re: [ccp4bb] PyMOL v. Coot map 'level'

the structure factors with phenix. Thanks All. Emily. Dale Tronrud On 5/29/2015 1:15 PM, Emilia C. Arturo (Emily) wrote: Hello. I am struggling with an old question--old because I've found several discussions and wiki bits on this topic, e.g. on the PyMOL mailing list (http

[ccp4bb] PyMOL v. Coot map 'level'

Hello. I am struggling with an old question--old because I've found several discussions and wiki bits on this topic, e.g. on the PyMOL mailing list ( http://sourceforge.net/p/pymol/mailman/message/26496806/ and http://www.pymolwiki.org/index.php/Display_CCP4_Maps), but the suggestions about how to

Re: [ccp4bb] Role of protein dimerization

Dear All, I have a question that is a little bit related to the previous discussion about crystallisation of a minority fraction monomers. I wonder if there is a review of some sort (or anything in principle) that would discuss role of dimerization (or more broadly oligomerization) in

Re: [ccp4bb] Offtopic: Software to closely visualize interacting partnets in protein complex

As I'm sure you've also found, it's not simple to find one [easily accessible] program that examines and reports every type of interaction that might be of interest to you. So I'm sending in a reference to another web-based tool that I've found complementary to PISA and the others mentioned here.

Re: [ccp4bb] protein quantification with carbohydrates

Tianyu, My suggestion is to determine the molar absorption coefficient empirically using the Edelhoch method ( http://www.rpgroup.caltech.edu/courses/PBL/bootcamp_June07/pdf/articles/Edelhoch1967.pdf). This involves measuring the absorbance at 280nm of your native and your unfolded protein (a

Re: [ccp4bb] Skin on drops

Artem, In addition to other answers, one of the more esoteric (but surprisingly effective) ways to destroy the protein 'skin' on drops is to add a tiny bit of Trypsin solution. Will you go a bit further and say what exactly you mean by a tiny bit of Trypsin solution? :-) What is the

[ccp4bb] clarification Re: Density fit analysis in Coot, and FEM

of analysis? ...or are the fits really that different (and maybe green versus red is not as big as the visual cue would have me assume)? Emily. On Thu, Feb 19, 2015 at 11:00 AM, Emilia C. Arturo (Emily) ec...@drexel.edu wrote: Hello all. I'd like to understand what it is I'm looking at when I use

[ccp4bb] Density fit analysis in Coot, and FEM

Hello all. I'd like to understand what it is I'm looking at when I use Coot's density fit analysis tool. I recognize that there was a post related to this topic on the Coot bb a while ago --the discussion was on how to interpret the red-ness or green-ness of the density fit plot (

Re: [ccp4bb] Crystallization problem

On Mon, Jan 26, 2015 at 8:22 PM, Monica Mittal monica.mitta...@gmail.com wrote: Hi everyone, I need an advice on some strange thing happening to one of the protein i am working on. I used to purify it and set up trays and get some needle shaped crystals and trying seeding and other

Re: [ccp4bb] Coot: How to connect N-terminal to neighbouring C-terminal

If the residues are consecutively numbered (Calculate Renumber residues), and are assigned the same chain ID (Calculate Change Chain ID), Coot might surprise you and link them on its own. On Wed, Jan 14, 2015 at 9:39 AM, Zhijie Li zhijie...@utoronto.ca wrote: Have you done it? 1) Click

Re: [ccp4bb] Demonstration for 2nd graders?

When my daughter was in Kindergarten, her class took a trip to our facility, and I showed them some of my crystal trays (What do you see here? Do you see anything? Clear drops ..., they effectively said). Then I showed them through the microscope several crystals, and I was pleasantly surprised

Re: [ccp4bb] asymmetric homotrimer in the asu

Hay, Indeed, we also incline to think of it as a monomer in solution, It is in fact possible that different solution conditions favor different oligomeric assemblies. For example, perhaps your protein, which in one set of solution conditions prefers the monomer, prefers some other assembly