Re: [ccp4bb] SCA

There is a server at the Yale site, but if you want to play around more with the parameters, you can download the whole package and run it locally without too much trouble. There are some options which are not available through the server. The documentation is not great, however. The Gerstein p

Re: [ccp4bb] ccp4bb unsubscribe

On Jan 17, 2010, at 9:35 PM, Sonya Sivaraj wrote: > This message and any attachments may contain proprietary or confidential > information. If you are not the intended recipient or you received the > message in error, you must not use, copy or distribute the message. Please > notify the sender

[ccp4bb] Postdoctoral Position at Vanderbilt University

Postdoctoral and Staff Positions: Structural Biology and Biochemistry of Membrane Proteins The lab of Chuck Sanders at Vanderbilt University has openings for PhD-level staff and/or postdoctoral fellows to conduct studies of disease-related membrane protein structure, folding, and function. Prot

Re: [ccp4bb] incorrect linkage definitions ?

That would be a partial solution to the alpha-L-fucose problem, except for the fact that currently, the monomer library description for alpha-L-fucose is a beta! So, unless one is extremely vigilant, they will get beta fucoses, which I believe do not exist in N-linked sugars. Currently, anoth

Re: [ccp4bb] SCA

yes, other people can comment probably but i think entropy based estimates are better (as i remember less dependent on sample set size). and indeed yale has a server. which may or may not do what you want. secondly its not proper to distributed ohter people's software w/o their permission (actu

Re: [ccp4bb] incorrect linkage definitions ?

On Monday 18 January 2010, Engin Ozkan wrote: > Hi everybody, > > I have a question regarding glycosidic bonds. This relates to refmac, > phenix and cns, so I thought the best forum to pose this was here. > > We have these very nifty link descriptions, such as BETA1-4, ALPHA1-6, > etc. that com

[ccp4bb] incorrect linkage definitions ?

Hi everybody, I have a question regarding glycosidic bonds. This relates to refmac, phenix and cns, so I thought the best forum to pose this was here. We have these very nifty link descriptions, such as BETA1-4, ALPHA1-6, etc. that come with refmac and phenix. These essentially describe a ch

Re: [ccp4bb] Molecular Replacement

Dear Muhammed, In case you have used phaser for MR you could try to either decrease sequence identity or increase the rmsd of the search model (both ways are equivalent). This allows also to account for flexibility/movements in your target protein like Tim explained. Cheers, christian Muhammed

Re: [ccp4bb] parameters defining crystallographic model quality

Hi, for example, these qualities below will tell me something about your model: 1. Rfree, Rwork overall and shown in resolution shells; 2. Geometry statistics: - overall rmsd's bonds, angles, ...; - Molprobity statistics/scores; - histograms of deviations from ideal bonds, angels, ...;

[ccp4bb] DPI

Dear ccp4bbers, Can anyone suggests the acceptable range of DPI value as an coordinated error and except sfcheck, what other programs calculate it? Thanks in advance. James...

[ccp4bb] Postdoctoral position at the European Institute of Oncology, Milan

Post-doctoral research position at the European Institute of Oncology Milan, Italy A postdoctoral research position in structural biology is available in Marina Mapelli's group at the IFOM-IEO Campus, Milano. The group interests focuses on the structural and functional aspects of protein comp

Re: [ccp4bb] Molecular Replacement

Dear Muhammed, that's not uncommon. Your protein might undergo domain movements or contain flexible parts. if your structure contains any loops / floppy regions (with high B-values), you can exclude them from the search model. If it is composed of domains, chop it into pieces and search wit

Re: [ccp4bb] Stereo TF - VGA to 3-pin VESA Stereo Adapter

On Mon, Jan 18, 2010 at 7:33 AM, mesters wrote: > Hi, > > the following information might be of use for the ones that do not have a > 3-pin mini connector and are working under linux > > http://www.int03.co.uk/crema/hardware/stereo/ Didn't really see anything linux specific on that website bu

Re: [ccp4bb] SCA

Hi Azadeh, I looked into this and other related methods extensively once, and came out with the understanding that SCA is not really the best of this type of analysis (you can read some of the papers out there which analyze the several methods). I found that the java package from Mark Gerstein'

[ccp4bb] Molecular Replacement

Dear All; We have solved a crystal structrure of protein at 1.8 A. I have now another crystal of the same protein in aother unit cell,for the new crystal type resolution is 3.6 A but when I use our structure as a seach model It does't give any solution. Any suggestion would be highly appreciated.

[ccp4bb] arp/warp: missing 'wilsonb'

Hello, we have been trying to run arp warp 7.1.0 from ccp4-6.1.2 starting from experimental phases. As we hit the run or 'run& view comm script' button, a window appears saying "Can't read 'wilsonb': no such variable" followed by a polite apology and nothing else happens ever after. What might

Re: [ccp4bb] verifying a molecular replacement solution (test case where the true structure is known)

Looks like you have already gotten several good suggestions, but I also wrote a jiffy program for doing this that does not require the two PDB files to have the same atom names: http://bl831.als.lbl.gov/~jamesh/pickup/origins.com Which you run like this: origins.com right_origin.pdb wrong_orig

Re: [ccp4bb] parameters defining crystallographic model quality

I'd head to Gerard Kleywegt's "Practical Model Validation" web course post-haste: http://xray.bmc.uu.se/embo2001/modval/ Eric On Mon, Jan 18, 2010 at 11:00 AM, james09 pruza wrote: > Dear all, > > What are the standard methods for the crystallographic mo

[ccp4bb] parameters defining crystallographic model quality

Dear all, What are the standard methods for the crystallographic model judgment? What parameters should be included in the final refinement statistics in relation to the model error? What is Cruinkshank DPI and how can it be calculated and what information it gives about the quality of the model?

Re: [ccp4bb] Stereo TF - VGA to 3-pin VESA Stereo Adapter

Hi, the following information might be of use for the ones that do not have a 3-pin mini connector and are working under linux http://www.int03.co.uk/crema/hardware/stereo/ - J. - Sabuj Pattanayek wrote: Hi, I thought FX3700 would work. Good to hear confirmation from you. It wou

Re: [ccp4bb] 3D fitting

PISA will do that - an EBI service or available less prettily from ccp4i Eleanot Miri Hirshberg wrote: Sun., Jan. 17th 2010 EBI Greetings, I am looking for a 3D structure superposition program which takes two structures and superpose them based only on the coordinates X,Y,Z regardless of of re

Re: [ccp4bb] Reindexing P21.. the process?

Francis E Reyes wrote: Hi all I have data integrated and scaled to P21 via denzo/scalepack. I'm concerned about the workflow to obtain the alternate indexing arrangement (h,k,l) -> (h,-k,-h-l). I was thinking .sca ( not specifying NO MERGE) -> .mtz -> reindex but the documentation for reind

Re: [ccp4bb] verifying a molecular replacement solution (test case where the true structure is known)

> Alternative origins are documented in: > http://www.ccp4.ac.uk/dist/html/alternate_origins.html Note that this list makes no distinction between alternate origins and symmetry-equivalent origins. In principle, for any space group, any completely arbitrary alternate origin is permissible, all yo

[ccp4bb] SCA

Dear all, Does anyone have the current (or old) version of SCA? (SCA: statistical coupling analysis) It should be as a toolbox of Matlab software. Thank you in advance, Azadeh

Re: [ccp4bb] verifying a molecular replacement solution (test case where the true structure is known)

reforigin http://www.ccp4.ac.uk/dist/html/reforigin.html Does exactly what you want, but requires that the 2 PDB files have the same atoms - the CAONLY option can help with missing atoms, but it still won't work unless you have mutated your search model to the target sequence. solution_check A uti

Re: [ccp4bb] 3D fitting

In ccp4i select "Coordinate utilities/Superpose" And then on the first menu select "Superpose using secondary structure matching". It will automatically superpose based on fold rather than atom alignment. (This is the same software as used at the EBI for what used to be called MSDfold). Mi