Re: [ccp4bb] Jligand help
Thanks Ian.
Is it possible to force Jligand to keep only two hydrogens in this case?
I tried setting the N's charge to 0, but it reverts back to 1 after
regularization.
Thanks,
Abhinav
__
Abhinav Kumar, Ph.D.
The Joint Center for Structural Genomics
MS99, SLAC National Accelerator Laboratory
2575 Sand Hill Rd, Menlo Park, CA 94025
(650) 926-2992
On 08/07/2014 10:02 AM, Ian Tickle wrote:
Hi, I would say three: aliphatic amines such as the one you show are
weak bases so at neutral pH the protonated form predominates.
Aromatic amines are obviously trickier.
Cheers
-- Ian
On 7 August 2014 17:37, Abhinav Kumar <mailto:abhin...@slac.stanford.edu>> wrote:
Hi,
I am making a ligand in Jligand (figure attached) and have a
question about valency of nitrogen.
Jligand puts three hydrogens on nitrogen N1 when the ligand is
regularized.
Should there be two hydrogens or three?
--
Thanks,
Abhinav
______
Abhinav Kumar, Ph.D.
The Joint Center for Structural Genomics
MS99, SLAC National Accelerator Laboratory
2575 Sand Hill Rd, Menlo Park, CA 94025
(650) 926-2992
[ccp4bb] Jligand help
Hi, I am making a ligand in Jligand (figure attached) and have a question about valency of nitrogen. Jligand puts three hydrogens on nitrogen N1 when the ligand is regularized. Should there be two hydrogens or three? -- Thanks, Abhinav __ Abhinav Kumar, Ph.D. The Joint Center for Structural Genomics MS99, SLAC National Accelerator Laboratory 2575 Sand Hill Rd, Menlo Park, CA 94025 (650) 926-2992
Re: [ccp4bb] str solving problem
Hi Pramod, 1. You should try to identify the correct space group first. Did you integrate in p1 and run pointless? 2. A template with 31% identity is not a great model. The number of molecules in ASU will affect your chances of success. Hopefully it's not large. wrfac of 0.6 and Rfree of 0.5 suggest the solution may be incorrect. Did you try phaser? 3. Did you check for twinning? Thanks, Abhinav JCSG@SSRL, SLAC (650) 926-2992 On 06/17/2013 09:35 AM, Pramod Kumar wrote: Dear group I have a crystal data diffracted around 2.9 A*, during the data reduction HKL2000 not convincingly showed the space group (indexed in lower symmetry p1), while the mosflm given C-centered Orthorhombic, and again with little play around HKL2000 given CO, now the model for molecular replacement with closest identity of 31 given a contrast of 2, score 0.30 and wrfac 0.60. but "balbes" uses different models with lesser identity, no matter which way I am going the rFree keep on increasing during refinement in refmac, when I build the model in coot with deletion and addition of residue it starts with relatively low but gradually rises through almost all cycles although model fits to the density well and residue are building, coot validation parameters are also reasonable OK for geometry, rotamer, density fit,.. now my question * where should i first check for possible correction? * In molecular replacement what should be the red line for identity and related criteria? * if initial rFree starts around 50, how likely that its not the right way? * my rms bond angle is close to 1 while the bond length is 0.01 and chiral 0.1 concludes what is serious? *sincere apology for amateur query* if any... thanks in advance pramod -- Pramod Kumar. Graduate Student. Crystallography lab. Department Of Biotechnology. Indian Institute Of Technology Roorkee Uttranchal.247667 India +919359189657.
Re: [ccp4bb] Superpositions: Deviation by Residue
CCP4's superpose does this. It produces a table like this, but only for residues that are used in the alignment. .-..-. |Query| Dist.(A) | Target| |-++-| | + A:ARG 10 ||H+ A:GLN 223 | | + A:ARG 11 ||H+ A:ASN 224 | |H+ A:LYS 12 | <..6.19..> |H+ A:PRO 225 | |H+ A:LYS 13 | <--4.03--> |H+ A:ASN 226 | |H+ A:LYS 14 | <--3.73--> |H+ A:GLN 227 | |H+ A:GLN 15 | <..4.05..> |H- A:LEU 228 | |H+ A:LYS 16 | <..3.41..> |H- A:ILE 229 | |H+ A:GLU 17 | <..1.75..> |H. A:SER 230 | |H- A:ILE 18 | <++1.97++> |H- A:LEU 231 | Thanks, Abhinav JCSG@SSRL, SLAC Phone: (650) 926-2992 Fax: (650) 926-3292 On 11/28/2011 02:53 PM, Jacob Keller wrote: Let me refine my question (sorry for my lack of clarity): is there a program that will output the distances between the corresponding ca's of a superposition on a residue-by-residue basis, and not just a global RMSD value (doubtless these numbers are part of the superposition algorithm itself)? I want to plot these values as a function of residue number to show which parts of the structures deviate more or less from each other. Jacob
Re: [ccp4bb] QC Server (was Re: [ccp4bb] Another paper & structure retracted)
The server has always been available to everyone. Thanks, Abhinav JCSG@SSRL, SLAC Phone: (650) 926-2992 Fax: (650) 926-3292 On 08/12/2011 11:10 AM, Kevin Jin wrote: I seriously think this sever should be available to folks. It is very helpful for most students. Kevin
Re: [ccp4bb] Modified residue list
If you simply want a list of modified residues, here is one that I compiled a while ago. More details on each can be found at LigandExpo. '0CS' => 'ALA', '0NC' => 'ALA', 'AA3' => 'ALA', 'AA4' => 'ALA', 'ABA' => 'ALA', 'AHO' => 'ALA', 'AHP' => 'ALA', 'AIB' => 'ALA', 'ALC' => 'ALA', 'ALM' => 'ALA', 'ALN' => 'ALA', 'ALS' => 'ALA', 'APH' => 'ALA', 'AYA' => 'ALA', 'B2A' => 'ALA', 'B3A' => 'ALA', 'BAL' => 'ALA', 'BNN' => 'ALA', 'CAB' => 'ALA', 'CHG' => 'ALA', 'CLB' => 'ALA', 'CLD' => 'ALA', 'DAB' => 'ALA', 'DAL' => 'ALA', 'DBU' => 'ALA', 'DBZ' => 'ALA', 'DHA' => 'ALA', 'DNP' => 'ALA', 'DPP' => 'ALA', 'FLA' => 'ALA', 'HAC' => 'ALA', 'HMF' => 'ALA', 'HV5' => 'ALA', 'IAM' => 'ALA', 'KYN' => 'ALA', 'LAL' => 'ALA', 'MAA' => 'ALA', 'NAL' => 'ALA', 'NAM' => 'ALA', 'NCB' => 'ALA', 'ORN' => 'ALA', 'PAU' => 'ALA', 'PRR' => 'ALA', 'PYA' => 'ALA', 'SEC' => 'ALA', 'SEG' => 'ALA', 'TIH' => 'ALA', 'UMA' => 'ALA', 'CLV' => 'ALA,PHE,GLY', 'X9Q' => 'ALA,PHE,GLY', '175' => 'ALA,SER,GLY', 'CRW' => 'ALA,SER,GLY', 'CRX' => 'ALA,SER,GLY ', 'MDO' => 'ALA,SER,GLY', 'AYG' => 'ALA,TYR,GLY', '2MR' => 'ARG', 'AAR' => 'ARG', 'ACL' => 'ARG', 'AGM' => 'ARG', 'ALG' => 'ARG', 'ARM' => 'ARG', 'BOR' => 'ARG', 'CIR' => 'ARG', 'DAR' => 'ARG', 'DIR' => 'ARG', 'HAR' => 'ARG', 'HMR' => 'ARG', 'HRG' => 'ARG', 'MAI' => 'ARG', 'MGG' => 'ARG', 'NMM' => 'ARG', 'NNH' => 'ARG', 'OPR' => 'ARG', 'ORQ' => 'ARG', '0A5' => 'ASN', 'AFA' => 'ASN', 'AHB' => 'ASN', 'B3X' => 'ASN', 'DMH' => 'ASN', 'DSG' => 'ASN', 'MEN' => 'ASN', 'NYG' => 'ASN,TYR,GLY', '0A0' => 'ASP', '0AK' => 'ASP', '2AS' => 'ASP', '3MD' => 'ASP', 'ACB' => 'ASP', 'AEI' => 'ASP', 'AKL' => 'ASP', 'ASA' => 'ASP', 'ASB' => 'ASP', 'ASI' => 'ASP', 'ASK' => 'ASP', 'ASL' => 'ASP', 'ASQ' => 'ASP', 'B3D' => 'ASP', 'BFD' => 'ASP', 'BHD' => 'ASP', 'DAS' => 'ASP', 'DMK' => 'ASP', 'DOH' => 'ASP', 'DSP' => 'ASP', 'IAS' => 'ASP', 'LAA' => 'ASP', 'OHS' => 'ASP', 'OXX' => 'ASP', 'PAS' => 'ASP', 'PHD' => 'ASP', 'TAV' => 'ASP', 'SUI' => 'ASP,GLY', 'DYG' => 'ASP,TYR,GLY', 'XYG' => 'ASP,TYR,GLY', '0A8' => 'CYS', '5CS' => 'CYS', 'BBC' => 'CYS', 'BCS' => 'CYS', 'BCX' => 'CYS', 'BPE' => 'CYS', 'BTC' => 'CYS', 'BUC' => 'CYS', 'C3Y' => 'CYS', 'C5C' => 'CYS', 'C6C' => 'CYS', 'CAF' => 'CYS', 'CAS' => 'CYS', 'CCS' => 'CYS', 'CEA' => 'CYS', 'CME' => 'CYS', 'CMH' => 'CYS', 'CML' => 'CYS', 'CMT' => 'CYS', 'CS0' => 'CYS', 'CS1' => 'CYS', 'CS3' => 'CYS', 'CS4' => 'CYS', 'CSA' => 'CYS', 'CSB' => 'CYS', 'CSD' => 'CYS', 'CSE' => 'CYS', 'CSO' => 'CYS', 'CSP' => 'CYS', 'CSR' => 'CYS', 'CSS' => 'CYS', 'CSU' => 'CYS', 'CSW' => 'CYS', 'CSX' => 'CYS', 'CSZ' => 'CYS', 'CY0' => 'CYS', 'CY1' => 'CYS', 'CY3' => 'CYS', 'CY4' => 'CYS', 'CYA' => 'CYS', 'CYD' => 'CYS', 'CYF' => 'CYS', 'CYG' => 'CYS', 'CYM' => 'CYS', 'CYQ' => 'CYS', 'CYR' => 'CYS', 'CZ2' => 'CYS', 'CZZ' => 'CYS', 'DCY' => 'CYS', 'EFC' => 'CYS', 'FOE' => 'CYS', 'GT9' => 'CYS', 'HTI' => 'CYS', 'K1R' => 'CYS', 'M0H' => 'CYS', 'MCS' => 'CYS', 'NPH' => 'CYS', 'OCS' => 'CYS', 'OCY' => 'CYS', 'P1L' => 'CYS', 'PBB' => 'CYS', 'PEC' => 'CYS', 'PR3' => 'CYS', 'PYX' => 'CYS', 'R1A' => 'CYS', 'R1B' => 'CYS', 'R1F' => 'CYS', 'R7A' => 'CYS', 'RCY' => 'CYS', 'SAH' => 'CYS', 'SCH' => 'CYS', 'SCS' => 'CYS', 'SCY' => 'CYS', 'SHC' => 'CYS', 'SIB' => 'CYS', 'SMC' => 'CYS', 'SNC' => 'CYS', 'SOC' => 'CYS', 'TNB' => 'CYS', 'YCM' => 'CYS', 'GYC' => 'CYS,TYR,GLY', 'DGN' => 'GLN', 'GHG' => 'GLN', 'GLH' => 'GLN', 'MEQ' => 'GLN', 'MGN' => 'GLN', 'NLQ' => 'GLN', 'QLG' => 'GLN,LEU,GLY', 'CRQ' => 'GLN,TYR,GLY', '5HP' => 'GLU', 'AR4' => 'GLU', 'B3E' => 'GLU', 'CGA' => 'GLU', 'CGU' => 'GLU', 'CRU' => 'GLU', 'DGL' => 'GLU', 'GAU' => 'GLU', 'GGL' => 'GLU', 'GLQ' => 'GLU', 'GMA' => 'GLU', 'GSU' => 'GLU', 'ILG' => 'GLU', 'LME' => 'GLU', 'MEG' => 'GLU', 'NHL' => 'GLU', 'PCA' => 'GLU', '0AC' => 'GLY', 'CHP' => 'GLY', 'CR5' => 'GLY', 'CSI' => 'GLY', 'FGL' => 'GLY', 'GHP' => 'GLY', 'GLZ' => 'GLY', 'GSC' => 'GLY', 'IGL' => 'GLY', 'LPG' => 'GLY', 'LVG' => 'GLY', 'MEU' => 'GLY', 'MGY' => 'GLY', 'MPQ' => 'GLY', 'NMC' => 'GLY', 'PG9' => 'GLY', 'PGY' => 'GLY', 'SAR' => 'GLY', 'SHP' => 'GLY', 'TBG' => 'GLY', '4F3' => 'GLY,TYR,GLY', 'CR2' => 'GLY,TYR,GLY', 'CRO' => 'GLY,TYR,GLY', 'MFC' => 'GLY,TYR,GLY', '3AH' => 'HIS', 'DDE' => 'HIS', 'DHI' => 'HIS', 'HBN' => 'HIS', 'HIA' => 'HIS', 'HIC' => 'HIS', 'HIP' => 'HIS', 'HIQ' => 'HIS', 'HSO' => 'HIS', 'MHS' => 'HIS', 'NEM' => 'HIS', 'NEP' => 'HIS', 'NZH' => 'HIS', 'OHI' => 'HIS', 'PSH' => 'HIS', 'PVH' => 'HIS', 'CR8' => 'HIS,TYR,GLY', 'RC7' => 'HIS,TYR,GLY', 'B2I' => 'ILE', 'DIL' => 'ILE', 'IIL' => 'ILE', 'ILX' => 'ILE', 'IML' => 'ILE', '0AG' => 'LEU', '1LU' => 'LEU', '2LU' => 'LEU', '2ML' => 'LEU', 'BLE' => 'LEU', 'BTA' => 'LEU', 'BUG' => 'LEU', 'CL0' => 'LEU', 'CLE' => 'LEU', 'DLE' => 'LEU', 'DNE' => 'LEU', 'DNG' => 'LEU', 'DNM' => 'LEU', 'DON' => 'LEU', 'FLE' => 'LEU', 'HLU' => 'LEU', 'LED' => 'LEU', 'LEF' => 'LEU', 'MHL' => 'LEU', 'MLE' => 'LEU', 'MLL' => 'LEU', 'MNL' => 'LEU', 'NLE' => 'LEU', 'NLN' => 'LEU', 'NLO' => 'LEU', 'NL
Re: [ccp4bb] orthogonal limits of a protein
I have a program that would calculate the limits of the protein along it's axes of inertia (besides doing many other things). If you are interested, please let me know. Thanks Abhinav j...@ssrl Phone: (650) 926-2992 Fax: (650) 926-3292 Francois Berenger wrote: Hello, Is there a ccp4 tool to find automatically the smallest virtual orthogonal "box" that contain a given PDB ? Even if your favorite tool is not part of ccp4, I would be happy to know about it. ;) Thanks, Francois.
Re: [ccp4bb] real space correlation coefficients and coot? or a program from CCP4?
How about overlapmap in ccp4? Thanks Abhinav Stanford Synchrotron Radiation Lightsource Joint Center for Structural Genomics Mail Stop 99 Phone: (650) 926-2992 Fax: (650) 926-3292 Vellieux Frederic wrote: Dear all, I am writing because I have a question that concerns coot or ccp4 (don't know which one). I have 2 maps and one model. One of the map is an experimental map that has not seen one inch of a model, the second map is generated after refinement of a molecular replacement model. Same molecule, obviously. They both look good. I am trying to find out which of the 2 maps is the most informative. Hence I wish to compute a global (real space) correlation coefficient "a la Alwyn Jones". In fact 2 sets of numbers per map : an average real space correlation coefficient, and a residue-per-residue correlation coefficient. The average real space correlation coefficient I can easily compute if I have the residue-by-residue real space correlation coefficients by writing a small jiffy program. I'm sure that someone must have done this. I suppose I could use CNS, but it's a bit tedious with having to generate the mtf file... Hence I am looking for something simpler. I did not see anything in the Phenix GUI. Any way of doing what I want in coot? Or in ccp4i? Thanks, Fred.
Re: [ccp4bb] Anomalous map creating
This should do: cad hklin1 original.mtz hklin2 refined.mtz hklout Fp_phase.mtz << EOF_CAD LABIN FILE 1 E1=DANO LABIN FILE 2 E1=PHWT E2=FOM END EOF_CAD fft hklin Fp_phase.mtz mapout anom_diff.map
Re: [ccp4bb] structure alignment based on the ligand
Hi,I am attaching a program that will do what you want.After entering the file names (one fixed and the other moving), the program asks for anchor atom names, i.e. a few atoms in your ligand that you want to use as reference atoms for computing the alignment. If you do not give any atom names, all atoms of the ligand will be used as the anchor atoms.You can repeat this process to align all of your pdb files to one reference file.#!/usr/bin/perl
##
use warnings;
use strict;
##
#
# DESCRIPTION: LSQKAB
# AK 3/08
#
## Reference:
## A solution for the best rotation to relate two sets of vectors
## -- Wonfgang Kabsch, Acta Cryst. A32, 922, 1976
#
##
my ( @R, @RtR, @avector, @mu, @bvector, @U );
##
my $line = '-' x 70 . "\n";
print $line;
print " Enter reference pdb name: ";
#my $ref_pdb = "1mht.pdb";
my $ref_pdb = ;
chomp $ref_pdb;
print " Enter moving pdb name: ";
#my $mov_pdb = "1x1b.pdb";
my $mov_pdb = ;
chomp $mov_pdb;
print " Ligand residue chain and number must be same in both files.\n";
print " Enter residue chain and number: [Z 999] ";
#my $chain_num = "Z 999";
my $chain_num = ;
chomp $chain_num;
my ( $chain_mol, $num_mol ) = split " ", $chain_num;
print " Enter anchor atoms: (case sensitive) ";
#my $anchor_atoms = "N1 N3 N6 N7 N9 C2' C4' SD CG C";
my $anchor_atoms = ;
chomp $anchor_atoms;
unless ($anchor_atoms) {
print " ==> All atoms in the residue '$chain_num' will be used for LSQ.\n";
}
print $line;
print "Reference pdb:\t$ref_pdb\n";
print "Moving pdb:\t$mov_pdb\n";
print "Range:\t$chain_mol-$num_mol\n";
##
my %pdb_ref = ReadPDB($ref_pdb);
my %pdb_mov = ReadPDB($mov_pdb);
## Verify that the anchor atoms are present in both files in that residue.
Delete_missing_anchor_atoms();
print "Anchor atoms:\t$anchor_atoms\n";
print $line;
### find centroids
my @center_ref = Center( \%pdb_ref );
my @center_mov = Center( \%pdb_mov );
### shift molecule to origin
Move_to_origin( @center_ref, \%pdb_ref );
Move_to_origin( @center_mov, \%pdb_mov );
Construct_R(); ### r[ij] = sum_atoms(yi * xj)
Construct_RtR();### RtR = R-transpose * R
#Print_matrix(\...@r);
#Print_matrix(\...@rtr);
Eigen(@RtR);### Eigen values (mu) /Eigen vectors (a-vector) of RtR
#print "\nEigen values = @mu\n";
#Print_matrix(\...@avector);
Construct_bvector();### bvector = (R * a-vector)/sqrt(eigen value)
#Print_matrix(\...@bvector);
Construct_U(); ### U = Rotation matrix = b-vector * a-vector
Print_matrix( \...@u );
my @translation = Apply_trans( @center_ref, @center_mov, @U );
printf "%12.6f\t", $_ for @translation;
print "\n";
Rotate_moving_pdb();### transform the moving structure
##
sub Apply_trans {
my ( $cxr, $cyr, $czr, $cxm, $cym, $czm, @mat ) = @_;
my @in = ( $cxm, $cym, $czm );
my @out = ( $cxr, $cyr, $czr );
for ( my $i = 0 ; $i < 3 ; $i++ ) {
for ( my $j = 0 ; $j < 3 ; $j++ ) {
$out[$i] -= $mat[$i][$j] * $in[$j];
}
}
return @out;
}
###
sub Center {
my $coord = shift;
my ( $sumx, $sumy, $sumz );
my $n = 0;
foreach my $atom ( keys %{$coord} ) {
$sumx += $coord->{$atom}{x};
$sumy += $coord->{$atom}{y};
$sumz += $coord->{$atom}{z};
$n++;
}
$sumx /= $n;
$sumy /= $n;
$sumz /= $n;
return ( $sumx, $sumy, $sumz );
}
###
sub Construct_R {
my @x;
my @y;
my $n = 0;
foreach my $atom ( keys %pdb_ref ) {
$x[$n][0] = $pdb_mov{$atom}{x};
$x[$n][1] = $pdb_mov{$atom}{y};
$x[$n][2] = $pdb_mov{$atom}{z};
$y[$n][0] = $pdb_ref{$atom}{x};
$y[$n][1] = $pdb_ref{$atom}{y};
$y[$n][2] = $pdb_ref{$atom}{z};
$n++;
}
my $natoms = $n;
for ( my $i = 0 ; $i < 3 ; $i++ ) {
for ( my $j = 0 ; $j < 3 ; $j++ ) {
$R[$i][$j] = 0;
for ( my $n = 0 ; $n < $natoms ; $n++ ) {
$R[$i][$j] += $y[$n][$i] * $x[$n][$j];
}
}
}
}
##
sub Construct_bvector {
for ( my $i = 0 ; $i < 3 ; $i++ ) {
for ( my $j = 0 ; $j < 3 ; $j++ ) {
$bvector[$i][$j] = 0;
for ( my $k = 0 ; $k < 3 ; $k++ ) {
$bvector[$i][$j] += $R[$j][$k] * $avector[$i][$k];
}
$bvector[$i][$j] /= sqrt( $mu[$i] );
}
}
}
Re: [ccp4bb] Identifying an unknown ligand
Some more info about this structure: Crystallization conditions: Glycerol, 0.1700M NaOAc, 25.5000% PEG-4000, 0.1M TRIS pH 8.5 This does not sit on any crystalllographic symmetry axis. But it sits right between two monomers and the NCS 2-fold axis. The protein is chemotaxis protein CheX. Environment: Some main chain amide Ns around it, as well as phobic side chains. No peak in anomalous difference fourier map. Thanks Abhinav Stanford Synchrotron Radiation Laboratory Joint Center for Structural Genomics Mail Stop 99 Phone: (650) 926-2992 Fax: (650) 926-3292 Abhinav Kumar wrote: Hi, I am refining a structure and have a region of unmodeled density into which I am trying to fit a ligand. The identity of the ligand is not obvious, so I modeled a bunch of dummy atoms into the density. Could you please have a look at the map and pdb files and help me identify this ligand? Please see http://smb.slac.stanford.edu/~abhinavk/UNL/unl.html Thanks Abhinav Stanford Synchrotron Radiation Laboratory Joint Center for Structural Genomics Mail Stop 99 Phone: (650) 926-2992 Fax: (650) 926-3292
[ccp4bb] Identifying an unknown ligand
Hi, I am refining a structure and have a region of unmodeled density into which I am trying to fit a ligand. The identity of the ligand is not obvious, so I modeled a bunch of dummy atoms into the density. Could you please have a look at the map and pdb files and help me identify this ligand? Please see http://smb.slac.stanford.edu/~abhinavk/UNL/unl.html Thanks Abhinav Stanford Synchrotron Radiation Laboratory Joint Center for Structural Genomics Mail Stop 99 Phone: (650) 926-2992 Fax: (650) 926-3292
Re: [ccp4bb] tortion angle restraints in REFMAC
If you want to restrain the OH group to a plane, you need to include it in the plane definition, and not the torsion definition. Thanks Abhinav Stanford Synchrotron Radiation Laboratory Joint Center for Structural Genomics Mail Stop 99 Phone: (650) 926-2992 Fax: (650) 926-3292 Huiying Li wrote: I want to impose restraints during REFMAC refinement on the tortion angles that control the tilting of an OH group from a plane in a ligand bound to the protein. A few things that confused me: 1. In library cif file, should I just increase or decrease the tor.value_angle_esd if I want to loosen or tighten the restraits? 2. What is the meaning of the last column in torsion angle parameters: _chem_comp_tor.period, in cif file? In the PDB output file REFMAC also lists the RMS and WEIGHT for the torsion angles, period 1 through 4. 3. In REFMAC gui under Geometric parameters, there is only one user controlled weight for torsion. By changing the weight here, does it change the torsion weight for all 4 periods? Thanks in advance for the help. Huiying
Re: [ccp4bb] sequential renumbering of a messed up pdb file
I have a program that can fix it provided the residues with same number are not adjacent in the pdb file. Please let me know and I can send you the program. Thanks Abhinav Abhinav Kumar JCSG @ SSRL, MS 99 2575 Sand Hill Road Menlo Park, CA 945025-7015 Phone: 650 926 2992 Fax: 650 926 3292 On Jul 31, 2008, at 4:09 PM, William Scott wrote: Hi folks: I am hoping there is a simple answer I have overlooked to the following question. I have a pdb file in it that has multiple residues that have the same number and chain ID, and I want to force them to be renumbered sequentially. Is there a simple way to do so (eg, pdbset) or am I doomed to fixing it manually? Thanks. Bill Scott William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/
Re: [ccp4bb] odd waters
Check the anomalous difference map on these sites. Thanks Abhinav Abhinav Kumar JCSG @ SSRL, MS 99 2575 Sand Hill Road Menlo Park, CA 945025-7015 Phone: 650 926 2992 Fax: 650 926 3292 On May 27, 2008, at 6:38 PM, Bernhard Rupp wrote: Dear All, something one/some of you might have seen already and might know what it might be/how to analyse: Material: dimer of Se-Met, Ni-purified, NaCl and NaAc in purification history. I have 4 'waters', 2 each in the same monomer location in a dimer of 2.5A Se-Met structure. They are multiple coordinated - perhaps dist octahedron - and refine down to B=2.0 and show correspondingly strong density. Surrounding protein Bs range from 15 backbone to 37 Arg sidechain First idea of course metal ions. But the distances are odd - 3.1 to 3.7, unusually long for common metal coordination. If I use Na+/Mg++, the Bs still refine down to 4 to 6 K+ B's run up to ~25, Ni++ to 35-40, could be partial occ. Given the charge distribution I doubt Cl- makes sense - it sure looks like a nice place for cation. Not enough space for sul- and fos-fates. No experiments possible, have to deal with what's on hand. Images on web: http://www.ruppweb.org/images/snap.gif http://www.ruppweb.org/images/mystery_ion.gif How common are such large coordination distances in protein/metal coordination and are there any (in silico) analysis tools one could use? Thx, br - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 [EMAIL PROTECTED] [EMAIL PROTECTED] http://www.ruppweb.org/ - The hard part about playing chicken is to know when to flinch -
