Re: [ccp4bb] Ligand geometry obs. vs. ideal

I second Tim Gruene's suggestion of SHELXL; it's perfect for this. However, there is a steep learning curve, so I strongly urge you to pay close attention to the SHELXL (and SHELXPRO) manuals. On Wed, Sep 12, 2012 at 11:44 AM, Yuri Pompeu wrote: > Hi everyone, > I am trying to show that a ligand

Re: [ccp4bb] Ligand geometry obs. vs. ideal

Hi Yuri, If you have access to mogul you can get an understanding of what your geometry should be based on the small molecule database. Of course not everything is well represented so if your ligand is unusual this will flag up in lower statistical significance. Mogul will allow you to unders

Re: [ccp4bb] Ligand geometry obs. vs. ideal

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Yuri, at 1.18A resolution you can also refine using shelxl. It's basically your choice on a per-atom-basis what properties you wish to restrain and which to leave unrestrained. With L.S. refinement and given enough RAM it can print esds of your

Re: [ccp4bb] Ligand geometry obs. vs. ideal

In case it helps… After you've done unrestrained refinement, you can use prosmart to generate external self-restraints to the current conformation (using the -self_restrain keyword). This is flexible - you can specify residue ranges, and it works for protein, ligand, DNA/RNA, waters, etc. These

Re: [ccp4bb] Ligand geometry obs. vs. ideal

You can do unrestrained refinement in refmac, at your resolution it may be OK. If you want to keep protein restrained, you can either use harmonic restraints or come up with a special cif-file for your ligand with large esd targets. There is no direct way to tell refmac to exclude specific r

Re: [ccp4bb] ligand geometry evaluation

bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Ivan Shabalin [shabali...@inbox.ru] Sent: Friday, 25 May 2012 5:58 a.m. To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] ligand geometry evaluation Dear all, I found that thread in my search of what ideal values for metal Phenix is using. I tried

Re: [ccp4bb] ligand geometry evaluation

Well - I am not familiar with the PHENIX dictionary but you are right; if you restrain metal bond distances the structure will reflect the restraints but if you don't restrain the distances then the respective gradients for a light atom and a heavy one can produce some very odd and unrealistic resu

Re: [ccp4bb] ligand geometry evaluation

Dear all, I found that thread in my search of what ideal values for metal Phenix is using. I tried to use that command "phenix.pdb_interpretation model.pdb write_geo_files=true" for my pdb file, and I get all the values for most atoms, like: >>bond pdb=" CB LEU B 332 " segid="B " pdb="

Re: [ccp4bb] Ligand geometry

> d if you do so, be sure to tell us which versions of refmac and coot you are using I use Win Coot-0.7-pre-1 (version 4039), and Refmac5 from CCP4i. It seems you are using an 'old' CCP4 (you dont specify the version, 6.1.3?) with an old(er) dictionary. WinCoot currently uses its own (up t

Re: [ccp4bb] Ligand geometry

Dear Eleanor, Ros, On 29/04/12 11:32, Eleanor Dodson wrote: I think you will find the dictionaries for coot and refmac are different.. REFMAC default dictionary will $CLIBD/monomers/n/NAD.cif Who knows where coot finds its dictionaries ... Coot uses the environment variable COOT_REFMAC_LIB_D

Re: [ccp4bb] Ligand geometry

ligands becomes needlesly complicated. To the eye an oxygen is an oxigen, to a computer O1 is different from O2. Just stick to the definition given by the PDB (see Ligand Expo). It's there for a reason. Cheers, Robbie > Date: Sun, 29 Apr 2012 11:14:01 +0200 > From: hraaijmak...@xs4all

Re: [ccp4bb] Ligand geometry

I think you will find the dictionaries for coot and refmac are different.. REFMAC default dictionary will $CLIBD/monomers/n/NAD.cif Good knows where coot finds its dictionaries - Paul? 1) check the REFMAC restraints in that dictionary are sensible - spec, are the planes and chiral centres as

Re: [ccp4bb] Ligand geometry

Hmm, what are the perfect bonds, angles for NAD in your protein? remember that reactive groups can be in a "stressed" conformation, compared to ideal in vacuo conformations. As part of their functon. anyway, you'll have to check the restraints definition file (.cif). Bond lengths and angles are usu

Re: [ccp4bb] Ligand geometry

Hi Uma, How different are your NADs optimised in Refmac and Coot? Are you sure you are using the same geometric restraints? Coot has to know where Refmac's restraint files are. This info is passed through an environment setting on your computer (I don't know the name by hart. Anyone?). Are you

Re: [ccp4bb] ligand geometry evaluation

Wolfram, is there a program that, given ligand model coordinates and a ligand > library as input, will produce a list of deviations of bond angles and > distances from the library values? > yes, phenix.pdb_interpretation model.pdb write_geo_files=true does exactly this: reports model and ideal