Re: [ccp4bb] Comparison of Water Positions across PDBs

For detailed examination of this topic, see: Koellner, G., Kryger, G., Millard, C. B., Silman, I., Sussman, J. L. & Steiner, T. (2000). Active-site gorge and buried water molecules in crystal structures of acetylcholinesterase from Torpedo californica. Journal of Molecular Biology 296, 713-735.

[ccp4bb] Add C-terminal amide

Hello experts, I am currently working on a structure of a protein-peptide complex. The peptide was synthesized with a C-terminal amide group. What is the best way to add this in Coot and refine in Refmac? I did a search on the web but only found a protocol for CNS not for Coot/Refmac. Thanks f

Re: [ccp4bb] Comparison of Water Positions across PDBs

http://www.ccp4.ac.uk/html/watertidy.html On 10/29/2013 04:43 PM, Elise B wrote: Hello, I am working on a project with several (separate) structures of the same protein. I would like to be able to compare the solvent molecules between the structures, and it would be best if the waters that e

Re: [ccp4bb] Comparison of Water Positions across PDBs

Hi Elise, Not exactly what you are asking for, but lsqman will compare waters between structures with a cut-off. (However, it will not renumber the waters as you wanted) http://xray.bmc.uu.se/usf/lsqman_man.html#S71 If you want to look at waters related by NCS in a single PDB file with m

[ccp4bb] PhD studentship

Dear Colleagues, A three year Wellcome Trust funded PhD studentship has recently become available at the Wellcome Trust Centre for Cell Biology (www.wcb.ed.ac.uk). The successful candidate will join students in the second year of the Wellcome Trust Four Year PhD Programme in Cell Biology. Qual

Re: [ccp4bb] Comparison of Water Positions across PDBs

Hi Elise, How about taking the homologue structure with highest number of waters and use it to run molecular replacement on all other datasets? Then you could keep only the good waters (manually unfortunately) which will ensure they will all have the same numbers. Probably not the fastest

Re: [ccp4bb] Comparison of Water Positions across PDBs

Downloading structures of the same homologous family with blast. Then superimpose them on a reference structure. You may then try to look at over lapping water molecules On 30 Oct 2013 02:23, "Elise B" wrote: > Hello, > > I am working on a project with several (separate) structures of the same >

[ccp4bb] Comparison of Water Positions across PDBs

Hello, I am working on a project with several (separate) structures of the same protein. I would like to be able to compare the solvent molecules between the structures, and it would be best if the waters that exist in roughly the same position in each PDB share the same residue number. Basically,

Re: [ccp4bb] crystals with large solvent content -dehydratation

Hi Andre, Are you sure that the cryoprotectant has been optimized?..I am sure you must have already done it but just in case..sometimes the cryo protectant which makes the ice rings disappear is not the best one and playing around that concentration as well as different alternatives can have a hu

Re: [ccp4bb] crystals with large solvent content -dehydratation

Hi, you could try dehydration in microdialysis buttons - this allows for slow gradual increase in PEG over few days and full control of other parameters, including lowering salt concentration. It was the only dehydration method that worked well for our large membrane protein: http://www.ncbi.nlm

Re: [ccp4bb] Is it possible for a ligand cif file from the CCP4 library to contain errors ?

Can the fixes in the CCP4 dictionary be rolled out through the update system of CCP4? That way we can avoid (at least to some extent) that people keep working with erroneous restraint files. Some of these errors can really mess up your structure. Cheers, Robbie > -Original Message- > From

Re: [ccp4bb] bluetooth monitor

The best technology would be "Wigig," but I don't think it's on the market yet. Some wireless monitor connection solutions appear to be available using Intel WiDi and Miracast. Check your favourite vendor for availability and requirements. On 10/29/2013 01:05 PM, Brett, Thomas wrote: Hi al

Re: [ccp4bb] bluetooth monitor

The biggest I could find is a 7inches monitor for car media centers. I'm not sure it will be a great deal for a wall monitor. Gian On 10/29/13 6:10 PM, David Schuller wrote: IMHO Bluetooth is way too slow for a monitor connection. On 10/29/2013 01:05 PM, Brett, Thomas wrote: Hi all: I was won

Re: [ccp4bb] bluetooth monitor

IMHO Bluetooth is way too slow for a monitor connection. On 10/29/2013 01:05 PM, Brett, Thomas wrote: Hi all: I was wondering if anyone had economical suggestions on a bluetooth LED or LCD monitor. I would like to have a wall mounted monitor that one could easily connect laptops and imacs to f

[ccp4bb] bluetooth monitor

Hi all: I was wondering if anyone had economical suggestions on a bluetooth LED or LCD monitor. I would like to have a wall mounted monitor that one could easily connect laptops and imacs to for structure display, doing tutorials on building into maps, etc. thanks -tom Tom J. Brett, PhD Assis

[ccp4bb] Postdoctoral position in UC Irvine

UNIVERSITY OF CALIFORNIA, IRVINE DEPARTMENT OF PHYSIOLOGY & BIOPHYSICS POSTDOCTORAL SCHOLAR One postdoctoral position is available immediately in Dr. Rongsheng Jin’s laboratory at the Department of Physiology and Biophysics, UC Irvine, and will remain open until filled. The new postdoctoral sc

Re: [ccp4bb] Is it possible for a ligand cif file from the CCP4 library to contain errors ?

On 29/10/13 06:54, Jodie Johnston wrote: Thanks Everyone for your input I shall triple check my reasoning tomorrow and email Garib if I do think there is an issue. Make suer that you are using the latest dictionary (of course) http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/Dic

Re: [ccp4bb] crystals with large solvent content -dehydratation

Dear Andre, you could try with the protocol described in the following paper Acta Crystallogr D Biol Crystallogr. 2013 69,920-3. Using high-throughput in situ plate screening to evaluate the effect of dehydration on protein crystals. Douangamath A, Aller P, Lukacik P, Sanchez-Weatherby J, Morae

Re: [ccp4bb] crystals with large solvent content -dehydratation

I wonder if there is a big difference between dehydrating in a drop, where the amount of mother liquor is essentially unlimited, and dehydrating a mounted crystal in something like the FMS, where there is only a thin film of ML on the surface. In the latter case, once the surface fluid is gone,

Re: [ccp4bb] crystals with large solvent content -dehydratation

Dear Andre, We had a similar case where the crystals were bigger and diffraction was lousy. Our standard dehydration approaches were not very successful. I suggest reading this - Post-crystallization treatments for improving diffraction quality of protein crystals. Heras B

Re: [ccp4bb] crystals with large solvent content -dehydratation

Dear Andre, 66% solvent is on the high side but not a good reason for poor resolution. Other with similaa solvent content have achieved resolutions of 1.5 Ang. and even better. I would screen at a lower protein concentration. It will require more precipitant and you should end up with less w

Re: [ccp4bb] crystals with large solvent content -dehydratation

Hi Andre, a very effective method is the use of a humidity control device. It has the great advantage that you can characterize changes that occur and also move straight to data collection. There are several HC1 devices in Europe (developed here at the EMBL and available at Diamond, BESSY and

[ccp4bb] crystals with large solvent content -dehydratation

Dear all I'm trying to solve a beautiful large crystal that, unfortunately, doesn't go further than 5 A resolution. I believe that in this case, the lack of resolution is due the high solvent content (about 66%). Therefore, my next strategy should be the dehydratation. Yet, I never (sucessfully

Re: [ccp4bb] Data mining interactions in the PDB

If you are interested in finding other interactions that look like one particular one, rather than just classifying things (e.g., "is this cyan, sea-foam, turquoise or teal?"), then I'd recommend the substructure searching capabilities of the DrugSite server You can specify any arbitrary s

Re: [ccp4bb] Is it possible for a ligand cif file from the CCP4 library to contain errors ?

Thanks Everyone for your input I shall triple check my reasoning tomorrow and email Garib if I do think there is an issue. Thanks Jodie From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Eleanor Dodson [eleanor.dod...@york.ac.uk] Sent: Tuesd

Re: [ccp4bb] Is it possible for a ligand cif file from the CCP4 library to contain errors ?

There are errors in every branch of human endeavour I am sure! Please if you find something wrong. send your suggested correction to Garib & Paul, and once there is a fix notify us all via the BB. CCP4 has always depended heavily on the users noticing the bugs Thank you for your observation. Elean

Re: [ccp4bb] Is it possible for a ligand cif file from the CCP4 library to contain errors ?

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Jodie, except for the matter if there is 'right' and 'wrong' in science or rather 'good' and 'bad' models, Garib Murshudov maintains the cif-library and if you send him a compilation of possible fixes he would surely appreciate your input. Best,

[ccp4bb] Is it possible for a ligand cif file from the CCP4 library to contain errors ?

Hi I wanted to check is it possible that there could be errors in the library cif files associated with CCP4 and coot ? I have noticed a couple of potential errors in a ligand cif file from the CCP4 library. Perhaps it is my error - I shall need to triple check it again but, if it appears