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 external restraints will attempt to maintain the original relative conformation throughout refinement. If you want any help doing this, feel free to email me off-board. Cheers, Rob On 12 Sep 2012, at 21:11, Edwin Pozharski wrote: 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 residue from restraints, at least to my knowledge. Cheers, Ed. On 09/12/2012 02:44 PM, Yuri Pompeu wrote: What is the best way to refine the ligand unrestrained and then generate measurements?
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 coordinates to its log file from which you can calculate all properties you mention - some of these might already be in the log-file itself. Cheers, Tim On 09/12/2012 08:44 PM, Yuri Pompeu wrote: 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 complete. What is the best way to refine the ligand unrestrained and then generate measurements? Also, the idea is to finally compare to ideal geometry. How should I generate these values (any softwares in mind)? ANy idea is welcome. Thanks a lot - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFQUak9UxlJ7aRr7hoRApdnAJ0SvhnucqonoCCrwaYMXaNeYlRPXACeJdyz qxDduM1vcxPCMYOmtkIOtkY= =Wt7O -END PGP SIGNATURE-
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 understand how far you are from ideal. Not really sure if this is what you might be after Joe P -- AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 2 Kingdom Street, London, W2 6BD. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking Compliance with our Code of Conduct and Policies. -Original Message- From: CCP4 bulletin board [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 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 complete. What is the best way to refine the ligand unrestrained and then generate measurements? Also, the idea is to finally compare to ideal geometry. How should I generate these values (any softwares in mind)? ANy idea is welcome. Thanks a lot
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 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 complete. What is the best way to refine the ligand unrestrained and then generate measurements? Also, the idea is to finally compare to ideal geometry. How should I generate these values (any softwares in mind)? ANy idea is welcome. Thanks a lot
[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 complete. What is the best way to refine the ligand unrestrained and then generate measurements? Also, the idea is to finally compare to ideal geometry. How should I generate these values (any softwares in mind)? ANy idea is welcome. Thanks a lot
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 residue from restraints, at least to my knowledge. Cheers, Ed. On 09/12/2012 02:44 PM, Yuri Pompeu wrote: What is the best way to refine the ligand unrestrained and then generate measurements?
