Re: [ccp4bb] New Version of the Protein Geometry Database Now Available

to try out the search - it is a catalytic quartet of residues - a superset of the catalytic triad. Regards Tom Oldfield, PDBe. HEADERHYDROLASE (SERINE PROTEINASE) 22-JAN-85 5CHA 5CHA 3 COMPNDALPHA CHYMOTRYPSIN A (E.C.3.4.21.1) 5CHA 4 SOURCECOW

Re: [ccp4bb] Vector approximation of B-strands

. Is there a simpler way to do this, am I over thinking the problem? This was helpful http://en.wikipedia.org/wiki/User:Vossman/3D_Line_Regression http://en.wikipedia.org/wiki/User:Vossman/3D_Line_Regression but I'm still struggling Thanks, Grant -- Tom Oldfield , PhD Team Leader Head of PDBe Databases

Re: [ccp4bb] How to config CPU to run ccp4 with multi-processor

Hi If any use: I have commonly used the C/C++ and Java threaded code to create parallel processes. Python threading is badly implemented and best avoided, use sub-processes instead as these are forked. 1) CPU intensive code with no dependency scales close to N where N cores available, for

Re: [ccp4bb] Data mining interactions in the PDB

Katherine I am not exactly sure what sort of tool you would like to use, but there are a couple of options found here... http://www.ebi.ac.uk/pdbe-as/pdbetemplate/ The last option DB search http://www.ebi.ac.uk/pdbe-as/pdbesearch/ allows you upload a fragment of structure - a small number of

Re: [ccp4bb] protein dodecamer

page to check that this correct. You can also [Get] a list of entries as text or XML, or put the SQL into the query browser to fine tune this. Regards Tom Oldfield Check with PISA@EBI, it has database searches where you can fetch all dodecamers in the PDB Eugene On 20 Feb 2013, at 06:29

Re: [ccp4bb] relationship between resolution and B values

Tom Oldfield Dear all, Could you please teach me any method to present the relationship between resolution and B values of all the x-ray structures in Protein Data Bank. Can the PDB statistics in RCSB do it? Thank you very much! Q. Cai No virus found in this message. Checked by AVG

Re: [ccp4bb] 3D alignment of points (atoms)

Hi In you post you say you want to fit a small number of points. Note that the original algorithm of Kabsch has a number of maths pathalogical conditions where points have symmetry or lie in a plane/line - this is common for a small number of points (fitting residues or your example). The

Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers

Hi I would just like to note that a web-browser plug in is on the client machine - to view a PDB file in any viewer like this (ie Astex-viewer, jmol) requires that file to be physically downloaded onto the client computer - and put into the TEMP folder of that machine. As such, the act of

Re: [ccp4bb] JME editor in PRODRG

Shya There have been a number of issues of the releases of the JVM, particularly with browser IE9 - most resulting in security exceptions when accessing data files. You should be able to update your Java on your computer as these problems appear to have been finally resolved through the

Re: [ccp4bb] Out of topic: Plot Ligand-protein interactions

if this is suitable. Regards Tom Oldfield Dear all, I would like to know what program/software you usually use to plot the 2D interactions between ligand and protein. As far as I know, LigPlot is powerful but need some skills. Also a web-based program from PDB server is easy to use

Re: [ccp4bb] 64-bit CCP4

Some important reason for using 64bit is due to the following. The effective precision of a float (32bit) is about 5 dp The effective precision of a double/real*8 (64 bit) is about 10 dp The number of dp is only approximate since we are encoding this using binary. The max/min value of a

Re: [ccp4bb] PISA question

that this has effected your work. We are have identified and fixed the problem and are currently testing the change and should have the fix in production by the end of the week. Regards Tom Oldfield PDBe Dear CCP4bb, We are trying to get some detailed interface information from

Re: [ccp4bb] PDB data mining

Robert Immormino Does this service answer you question. It is limited to 10,000 return results for the statistical analysis so it is possible to ask general questions where the statistics are truncated. http://www.ebi.ac.uk/pdbe-as/pdbestatistics/PDBeStatisticsAtom.jsp Tom Oldfield Hi

Re: [ccp4bb] diverging Rcryst and Rfree

Rakesh Looking at the http://www.pdbe.org/statistics Structure Statistics Then for all structures a we see that Rdiff of 0.7 is not that uncommon with this about 1 sigma away from the mean value of 0.4 for all structutures and 0.45 for your resolution range For structures with Rdiff

Re: [ccp4bb] Method to calculate the axis of an alpha helix

Yuan SHANG 1) DIY The way that has been used is to calculate the inertia tensor matrix for helix (or any other secondary structure element). You can chose backbone atoms or just the CA atoms. Then calculate the eigen vectors and values from this and the largest eigen vector will be the best

Re: [ccp4bb] R-Rfree vs resolution

: Rdiff from the Experiment drop down and resolution for the second parameter drop down. [show Distribution] will then produce a dynamic rotatable graph that can be selected to determine subsets. Regards Tom Oldfield PDBe Dear all, I remember that there used to be a post about the R-Rfree

Re: [ccp4bb] Question about R/Rfree value difference

-wise to deposit the structure in the current state of refinement as there is clearly an issue. Regards Tom Oldfield Hi Sampath, this is how the distribution of Rwork, Rfree and Rfree-Rwork look like for 'all' PDB structures refined at around 2A resolution. The indicates where your structure

[ccp4bb] R-free/R and resolution analysis

Tom Oldfield Does anyone already have the PDB-wide R/Rfree gap versus resolution data (it does not seem that the PDB maintains one)? Ed. The friendly people in Uppsala has something here by the name Harry Plotter: http://xray.bmc.uu.se/gerard/supmat/eds/plotter.html This might be somewhat