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CCP4BB  December 2008

CCP4BB December 2008

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Subject:

Re: tortion angle restraints in REFMAC

From:

Ian Tickle <[log in to unmask]>

Reply-To:

Ian Tickle <[log in to unmask]>

Date:

Thu, 4 Dec 2008 20:52:27 -0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (200 lines)

Hi Huiyang

OK sorry for misunderstanding.  I think that kind of out-of-plane
restraint is usually enforced by means of a chiral restraint (even if
the group in question is not chiral).  You would need to calculate the
expected chiral volume of the C atom for the target position of the O
atom.

Cheers

-- Ian

> -----Original Message-----
> From: [log in to unmask] 
> [mailto:[log in to unmask]] On Behalf Of Huiying Li
> Sent: 04 December 2008 19:51
> To: [log in to unmask]
> Subject: Re: [ccp4bb] tortion angle restraints in REFMAC
> 
> Thank you all for suggestions and explanations. I did not 
> make it clear. The 
> tilt angle I wanted to restrain is the one from a C-OH bond 
> to a plane 
> (The C is in the plane). The O atom of OH group is not in the planar 
> restraint in the cif file. At 2.1A I can "see" the feature of 
> tilting of 
> this OH group from the initial density map when the ligand 
> was absent. 
> But the density seems not strong enough to convince REFMAC 
> that there is 
> a tilt there. I have used very low weight term of 0.05 in the 
> GUI to down 
> weight the X-ray term. Refinement still pushed OH into the 
> plane. I wonder 
> if there are other tricks that can impose the restraint for 
> this torsion 
> angle.
> 
> Best,
> Huiying
> 
> On Thu, 4 Dec 2008, Ian Tickle wrote:
> 
> > Hi Huiying
> > 
> > At 2.1A I would be very surprised if you see any density 
> for the H atom
> > in which case the refinement is not going to move it out of 
> the plane
> > whatever weight you give the torsion restraint.  To answer 
> your earlier
> > questions the period of a torsion restraint is the number of energy
> > minima in a complete rotation of the angle, so the OH bond 
> will have a
> > period of 2, and
> > yes the same overall weight is applied to all torsions 
> regardless of the
> > period, though individual torsions will also be weighted by 1/sd^2.
> > 
> > Cheers
> > 
> > -- Ian
> > 
> >> -----Original Message-----
> >> From: [log in to unmask]
> >> [mailto:[log in to unmask]] On Behalf Of Huiying Li
> >> Sent: 04 December 2008 16:35
> >> To: Abhinav Kumar
> >> Cc: [log in to unmask]
> >> Subject: Re: [ccp4bb] tortion angle restraints in REFMAC
> >> 
> >> Acturally, I want to find a way to keep the OH tilted out of the
> >> neightbouring plane by about 10 degrees. At 2.1A resolution
> >> the REFMAC
> >> refinement tends to refine it into the plane even though I
> >> have included
> >> torsion angle restraint in the library for the ligand. I
> >> thought I could
> >> play with the weight or the esd of the target value but
> >> having trouble to
> >> achieve it. In CNS, adjusting the force constant of the
> >> target value is a
> >> way to tighten or loosen the restrain. I would like to know how to
> >> "enforce" a geometry effectively in REFMAC.
> >> 
> >> Thanks for any comments.
> >> 
> >> Huiying
> >> 
> >> On Wed, 3 Dec 2008, Abhinav Kumar wrote:
> >> 
> >>> 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
> >>> 
> >> 
> >> --
> >> Huiying Li, Ph. D
> >> Department of Molecular Biology and Biochemistry
> >> Natural Sciences I, Rm 2443
> >> University of California at Irvine
> >> Irvine, CA 92697, USA
> >> Tel: 949-824-4322(or -1953);  Fax: 949-824-3280
> >> email: [log in to unmask]
> >> 
> >> 
> > 
> > 
> > Disclaimer
> > This communication is confidential and may contain 
> privileged information 
> > intended solely for the named addressee(s). It may not be 
> used or disclosed 
> > except for the purpose for which it has been sent. If you 
> are not the 
> > intended recipient you must not review, use, disclose, 
> copy, distribute or 
> > take any action in reliance upon it. If you have received 
> this communication 
> > in error, please notify Astex Therapeutics Ltd by emailing 
> > [log in to unmask] and destroy all copies of 
> the message and any 
> > attached documents.
> > Astex Therapeutics Ltd monitors, controls and protects all 
> its messaging 
> > traffic in compliance with its corporate email policy. The 
> Company accepts no 
> > liability or responsibility for any onward transmission or 
> use of emails and 
> > attachments having left the Astex Therapeutics domain.  
> Unless expressly 
> > stated, opinions in this message are those of the 
> individual sender and not 
> > of Astex Therapeutics Ltd. The recipient should check this 
> email and any 
> > attachments for the presence of computer viruses. Astex 
> Therapeutics Ltd 
> > accepts no liability for damage caused by any virus 
> transmitted by this 
> > email. E-mail is susceptible to data corruption, 
> interception, unauthorized 
> > amendment, and tampering, Astex Therapeutics Ltd only send 
> and receive 
> > e-mails on the basis that the Company is not liable for any 
> such alteration 
> > or any consequences thereof.
> > Astex Therapeutics Ltd., Registered in England at 436 
> Cambridge Science Park, 
> > Cambridge CB4 0QA under number 3751674
> >
> 
> -- 
> Huiying Li, Ph. D
> Department of Molecular Biology and Biochemistry
> Natural Sciences I, Rm 2443
> University of California at Irvine
> Irvine, CA 92697, USA
> Tel: 949-824-4322(or -1953);  Fax: 949-824-3280
> email: [log in to unmask]
> 
> 


Disclaimer
This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [log in to unmask] and destroy all copies of the message and any attached documents. 
Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain.  Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof.
Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674

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