Re: [ccp4bb] Criteria For Solvent Components

I do not think we "are there yet" especially when partial occupancies come into play. Then it is a real mess. We always collect "all available evidence" (databases, CSD, PDB seraches, anomalous, distances, geometry, fluorescence spectrum at beamline etc.) and then try to make the best guestimate ..

Re: [ccp4bb] SC example

Hello, Dear Tim, I have successfully executed the example. Since I did not know the correct output of the program, I did not find significant output as I expect. However, there is no error in the standard output. A warning message was displayed as "GRASP mode disabled: command ignored" I als

Re: [ccp4bb] SC example

Dear Tim, Thank you very much. I have checked on the location for example. I found the example script (sc.exam). Regards, Rojan -Original Message- From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de] Sent: Wednesday, June 15, 2011 10:27 AM To: Rojan Shrestha Cc: CCP4BB@JISCMAIL.AC.UK S

Re: [ccp4bb] SC example

Dear Rojan, Since you have CCP4 installed, you should have the example file in $CCP4/examples/unix/non-runnable/sc.exam. I attach the file for convenience. Tim On Wed, Jun 15, 2011 at 09:44:28AM +0900, Rojan Shrestha wrote: > Hello, > > > > I like to use surface complementary(sc) program of

Re: [ccp4bb] non-waters among structured solvent atoms

Hi Wolfram, This was an early study on the subject: http://www.ncbi.nlm.nih.gov/pubmed/8594192 The software is still accessible via the STAN server. Cheers, Robbie > Date: Tue, 14 Jun 2011 17:51:21 -0400 > From: wtem...@gmail.com > Subject: [ccp4bb] non-waters among structured solvent atoms

Re: [ccp4bb] non-waters among structured solvent atoms

A coordination distance table (metals, Cl) is in Marjorie Harding's papers 1. Harding M (2006) Small revisions to predicted distances around metal sites in proteins. Acta Crystallogr. D62(6), 678-682. 2. Harding M (2004) The architecture of metal coordination groups in proteins. Acta Crystallogr.

[ccp4bb] SC example

Hello, I like to use surface complementary(sc) program of CCP4. Since I am a new user, I would like to see the example. The example link of website is dead. Can somebody provide simple example of running SC from CCP4? Regards, Rojan

Re: [ccp4bb] non-waters among structured solvent atoms

How about halides? Anyone know of criteria for their binding sites? JPK ps Funny how my recent post was about almost exactly the same thing--serendipity, I guess? On Tue, Jun 14, 2011 at 5:07 PM, Nat Echols wrote: > On Tue, Jun 14, 2011 at 2:51 PM, wtempel wrote: >> >> Dear colleagues, >> foll

Re: [ccp4bb] "Small Angle X-ray Scattering (SAXS) Techniques for Macromolecules" Webinar

t - Original Message - From: "Angela Criswell" To: CCP4BB@JISCMAIL.AC.UK Sent: Monday, June 13, 2011 5:44:31 PM Subject: [ccp4bb] "Small Angle X-ray Scattering (SAXS) Techniques for Macromolecules" Webinar Dear colleagues, I would like to draw your attention to an upcoming free, educat

Re: [ccp4bb] 96-well block storage

Hi, The polypropylene mat good for repeated sealing and reusing 96-well blocks than tape/film, to minimize evaporation. Hampton sells it: http://hamptonresearch.com/product_detail.aspx?cid=10&sid=88&pid=567 To address the mold problem locally (for the crystallization setup/room), the biocide so

Re: [ccp4bb] 96-well block storage

> I'm surprised that a better re-sealing system has not been invented to > prevent evaporation from the blocks when they are stored. Companies that produce these screen want us to buy their screens as often as possible... We use transparent plastic seals from Hampton Research. The aluminum foi

Re: [ccp4bb] non-waters among structured solvent atoms

On Tue, Jun 14, 2011 at 2:51 PM, wtempel wrote: > Dear colleagues, > following a discussion in our lab, I have volunteered to dig out > articles from the literature about erroneous assignments of non-water > entities such as metal ions, halides in protein models. For example I > have the faint re

[ccp4bb] non-waters among structured solvent atoms

Dear colleagues, following a discussion in our lab, I have volunteered to dig out articles from the literature about erroneous assignments of non-water entities such as metal ions, halides in protein models. For example I have the faint recollection that data mining of the PDB for suspect "water" a

[ccp4bb] Criteria For Solvent Components

Dear Crystallographers, While I acknowledge that assigning solvent/ions/waters to blobs of density is prone to subjectivity, does anyone here know of any attempts to rigorously assign solvent blobs based on their characteristics, e.g., nearby residue types, height of peak, etc? I wrote previously

[ccp4bb] 96-well block storage

Hi all, Considering the popularity of 96-well deep well block format for purchasing and storing protein crystallization conditions, I'm surprised that a better re-sealing system has not been invented to prevent evaporation from the blocks when they are stored. We typically don't consume our bl

Re: [ccp4bb] Unit cell change - was Re: [ccp4bb] XDS question

You may well have a rhombohedral obverse/reverse twin. See Acta Cryst. B58 (2002) 477-481. George On Tue, Jun 14, 2011 at 03:07:40PM -0400, Edward A. Berry wrote: > I'm currently struggling with what I think is a variation on this theme, > would appreciate comments as to whether my thinking is re

[ccp4bb] proteases for limited proteolysis, catalog numbers

Dear all, I am about to purchase/prepare some proteases for protein limited proteolysis experiments. I would therefore greatly appreciate if you could offer any tips as to what "contemporary" products you are using with good confidence/pricing (US) for trypsin, chymotrypsin, elastase, carboxypeptid

[ccp4bb] Unit cell change - was Re: [ccp4bb] XDS question

I'm currently struggling with what I think is a variation on this theme, would appreciate comments as to whether my thinking is reasonable. The space group is basically rhombohedral, but along the lines of spots in the (hexagonal)L direction, with some crystals there are two weak spots between eac

Re: [ccp4bb] refmac problem with anisotropic Us

On 6/10/11 6:10 PM, Ed Pozharski wrote: On Fri, 2011-06-10 at 12:48 -0700, Ethan Merritt wrote: I don't think that combination makes any sense. Whatever anisotropic is being described by the TLS parameters can also be fully described by the individual anisotropic U^ij terms. So the TLS paramet

Re: [ccp4bb] XDS question

Dear Konstatin, First I would reiterate what Fred has said: you only know the space group once the structure has been solved and completely refined. Especially bad maps and unsuccesful molecular replacements may point to a wrong space group assignment. Second, what causes strong and weak reflecti

[ccp4bb] Postdoc position at the MRC-NIMR, London, UK

*Postdoc position at the MRC-National Institute for Medical Research, London, UK* **Applications are invited for a Postdoctoral position in the Division of Molecular Structure in the group of Katrin Rittinger. The position is aimed at the structural and mechanistic characterisation of proteins

Re: [ccp4bb] sortwater in ccp4

You would need to edit the source code and recompile Phil On 14 Jun 2011, at 14:00, Xin Huang wrote: > Hi, everyone. > > I am running into a problem with sortwater program in ccp4. There are 16 > protein molecules in the asymmetric unit of this crystal form and I want to > sortwater the wat

[ccp4bb] Program to analyze water mediated interactions?

Dear CCP4 community, I have few conserved water-mediated interactions in different antibody:antigen complexes and I want to get a list of those. It's hard to keep track by eye inspection. Is there a program that can perform such kind of job? PISA does a nice job on interfaces by ignores water.

[ccp4bb] sortwater in ccp4

Hi, everyone. I am running into a problem with sortwater program in ccp4. There are 16 protein molecules in the asymmetric unit of this crystal form and I want to sortwater the water molecules to the protein chains. Sortwater program has a max number of chains of 12 and max number of water

[ccp4bb] New episode of Quips - Quite Interesting PDB Structures

Hi all, A fresh installment of Quips (interactive stories about interesting entries from the PDB) is now available on the PDBe website. It is called "Getting a good rate of exchange - the mitochondrial ADP-ATP carrier" and can be found here: http://www.ebi.ac.uk/pdbe-apps/quips?story=ATPexchan

[ccp4bb] EMBO/EMBL Symposium: Structure and Dynamics of Protein Networks, 13 - 16 October 2011

Dear Colleagues, We are pleased to announce the *EMBO|EMBL Symposium*: *Structure and Dynamics of Protein Networks, 13 - 16 October 2011* Please visit the conference website: http://www.embo-embl-symposia.org . The symposium wi

Re: [ccp4bb] XDS question

Marco, indeed, as Fred says, the space group I422 may not be the correct one for the large cell. Use the model from the small cell for molecular replacement in the large cell. You may try I4(1)22, I4(1), I4 first, then lower symmetries: look into the International Tables what subgroups of I422