[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

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

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

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

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'

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

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

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 EOF-map LABIN DANO=DANO PHI=PHWT W=FOM END EOF-map Thanks Abhinav Stanford Synchrotron Radiation

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,

[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?

Re: [ccp4bb] Identifying an unknown ligand

. 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

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

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

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