Re: [ccp4bb] PDB structure validation

Try JCSG QC server: http://smb.slac.stanford.edu/jcsg/QC/ All our structures go through this server before submitted to the PDB and we rarely get any issues back from PDB. Thanks, Abhinav Abhinav Kumar, Ph.D. Joint Center for Structural Genomics SSRL, SLAC Nation

Re: [ccp4bb] Gnuplot: how to plot with resolution values as labels on x-axis?

Hi Kay, This may be helpful, assuming your data file has resolution in column 3. set xtics rotate by -30 plot 'file' u 1:2:xticlabels(3) Make sure you have a recent version of gnuplot. Thanks, Abhinav JCSG@SSRL, SLAC (650) 926-2992 On Jun 24, 2013, at 7:54 AM, Kay Diederichs wrote: Dear G

[ccp4bb]

Hi Nisha, Are your B-values residuals after TLS refinement or do they include TLS contribution? Residuals are typically low. Your mainchain/sidechain B value problem: did you try resetting B to a fixed value for all atoms and refining? Another point: if your I/sigI (outer shell) is 4.2, then wh

Re: [ccp4bb] A script is needed to renumber image

This script will not work. Try this: #! /bin/csh -f set i = 1081 while ( $i <=1440 ) set n = `echo $i | awk '{print $i-720}'` echo mv CD267A_3_pk_1_$i.img CD267A_3_pk_1_$n.img @ i++ end Thanks Abhinav j...@ssrl, SLAC Phone: (650) 926-2992 Fax: (650) 926-3292 On Dec 9, 2010, at 5:51

Re: [ccp4bb] Preventing close contact between protein and ligand

I have had a similar experience. I was trying to model a bunch of waters to simulate an unknown ligand (UNL) in an unmodeled density. The waters were all in different alternate conformations of the same residue number. When the occupancies of these waters were set to 0.5, the vdw repulsion b

Re: [ccp4bb] program to draw 2D image of a peptide

I have a perl script to do this. It creates a pymol script and runs pymol to generate the view you are looking for. Thanks Abhinav Stanford Synchrotron Radiation Laboratory Joint Center for Structural Genomics Mail Stop 99 Phone: (650) 926-2992 Fax: (650) 926-3292 -Original Messa

Re: [ccp4bb] "Dry" structures

Hi, Here is a result (attached) of analyzing over 2000 Structural Genomics structures. At ~2 A resolution, you would roughly expect 1 water for every two residues. Thanks Abhinav Stanford Synchrotron Radiation Laboratory Joint Center for Structural Genomics Mail Stop 99 Phone: (650) 926-2

Re: [ccp4bb] refmac5 refinement with PEG400

nav Stanford Synchrotron Radiation Laboratory Joint Center for Structural Genomics Mail Stop 99 Phone: (650) 926-2992 Fax: (650) 926-3292 -Original Message- From: Craig McElroy [mailto:[EMAIL PROTECTED] Sent: Wednesday, August 08, 2007 1:27 PM To: Kumar, Abhinav Cc: CCP4BB@JISCMAIL.AC

Re: [ccp4bb] refmac5 refinement with PEG400

Trying using "Make check none" in the script file. Thanks Abhinav Stanford Synchrotron Radiation Laboratory Joint Center for Structural Genomics Mail Stop 99 Phone: (650) 926-2992 Fax: (650) 926-3292 -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Beha

Re: [ccp4bb] software to calculate VDW interactions between small molecule and protein

I have a perl script to do this job. The pdb file should contain your ligand. Simplest way to run it is "lig_contact file.pdb" If the script does not find the ligand, you can switch to command line options. The script prepares a pymol input file and fires it up to display the interactions. Afte

Re: [ccp4bb] Real Space Correlation coefficients

Overlapmap will calculate residue-by-residue CC. Thanks Abhinav -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Charles W. Carter Jr. Sent: Tuesday, February 20, 2007 11:04 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Real Space Correlation coef

Re: [ccp4bb] mtz to hkl conversion

Hi Vineet, The following script should output the required CNS data file: mtz2various hklin Fobs.mtz HKLOUT Fobs.xpl << EOL LABIN FP=FP SIGFP=SIGFP FREE=FreeR_flag HLA=HLA HLB=HLB HLC=HLC HLD=HLD OUTPUT XPLOR END EOL Thanks Abhinav From: CCP4

Re: Writing out common waters from multiple files

Raji, Here is a perl script to do it. The cut-off distance to flag two waters identical is set to 0.3. You can change it as you wish. Also, water residues are named HOH. Thanks Abhinav -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Raji Eday