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

-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

[mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Yuri Pompeu Sent: 12 September 2012 19:45 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Ligand geometry obs. vs. ideal Hi everyone, I am trying to show that a ligand underwent catalysis during a soaking experiment. One of the things I would like to show

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 yuri.pom...@ufl.edu wrote: Hi everyone, I am trying to

[ccp4bb] Ligand geometry obs. vs. ideal

Hi everyone, I am trying to show that a ligand underwent catalysis during a soaking experiment. One of the things I would like to show is the geometry of the ligand, bond angles/lengths, dihedrals, etc... One of my models has a hi-res of 1.18A and the ligand density is really clear and

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

Re: [ccp4bb] ligand geometry evaluation

[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 to use that command phenix.pdb_interpretation model.pdb

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

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= CG LEU

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

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

Re: [ccp4bb] Ligand geometry

: [ccp4bb] Ligand geometry To: CCP4BB@JISCMAIL.AC.UK Dear All: I use Refmac5 to refine my model. After the run, I check the model quality by Coot. Here is the problem: In Coot, the ligand - NAD, has bad geometry as indicated by a big red bar. While the geometry of NAD fit nicely with the electron

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

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

] Ligand geometry To: CCP4BB@JISCMAIL.AC.UK 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

[ccp4bb] Ligand geometry

Dear All: I use Refmac5 to refine my model. After the run, I check the model quality by Coot. Here is the problem: In Coot, the ligand - NAD, has bad geometry as indicated by a big red bar. While the geometry of NAD fit nicely with the electron density. If I use refine tools (i.e. regularize

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