Re: [ccp4bb] Refining alt. confs for only part of a ligand

2017-10-27 Thread Nick Pearce 
Conformer A atoms don’t “see” conformer B atoms so as far as the program is 
concerned the B conformer only has the last ring. 
You should set all confA atoms not in the last ring to blank conformers.

So: 
last ring - A +B conformers
rest of ligand - no conformer

Thanks,
Nick

—

Nick (Nicholas) Pearce
Post-doctoral Researcher
Lab of Piet Gros
Crystal & Structural Chemistry Group
Universiteit Utrecht

> On 27 Oct 2017, at 13:41, Derek Logan  wrote:
> 
> Hi,
> 
> This is a cross-post to ccp4bb and phenixbb. I'm trying to refine a largish 
> small molecule ligand. It has two conformations that differ only in the 
> orientation of a terminal aromatic ring, i.e. variation in the last torsion 
> angle. I previously refined it as two independent conformations for the whole 
> molecule, but that showed too much deviation between the conformations in the 
> region that is "identical", i.e. that can be modelled just as nicely with a 
> single conformation. With Occam's razor I split the molecule at the last 
> torsion angle. Conformation A is the whole molecule; conformation B is just 
> the last ring. Both have the same residue number, just different altloc 
> labels. However when I refine this using phenix.refine, the B conformation 
> refines as if it were not attached to the A conformation (see the attached 
> screen dump). I tried it using Refmac and the two conformations separated 
> even more. Clearly this didn't work as I was expecting. What am I doing 
> wrong? Is it even possible to do it this way?
> 
> /Derek
> 
>

Re: [ccp4bb] Unknown electron density

2017-10-26 Thread Nick Pearce 
I agree that the difference density isn’t “noise". However, just because it’s 
not noise doesn’t mean that it is modellable (with an atomic model) — the 
crystallographic density is an average over billions of molecules, and if its 
not obvious at 1.6Å what is bound, then it’s probably a superposition of states 
(or a highly disordered molecule with large B-factors, which in this case 
amounts to pretty much the same thing). When it’s a superposition of states in 
solvent regions, there are too many free parameters to build a reliable model: 
you don’t know how many alternate conformations to model, or how many species 
of molecules there are. It could be 1 conformer of PEG with 1 superposed 
conformer of water or 2 of PEG + 1 of water or 1 of PEG + 1 of something else + 
1 of water… or literally anything…

So unless you have some prior information as to what is bound, I would play it 
safe and model nothing — the conservative approach.

Thanks,
Nick

—

Nick (Nicholas) Pearce
Post-doctoral Researcher
Lab of Piet Gros
Crystal & Structural Chemistry Group
Universiteit Utrecht

> On 26 Oct 2017, at 18:00, Vijaykumar Pillalamarri <vijaypkuma...@gmail.com> 
> wrote:
> 
> Thanks Nick.
> 
> May be it is not that weak. The blue map contour level was set to 1.5. I have 
> attached another image in which the blue map is contoured to 1.0. I feel the 
> green density (contoured at 3.0) is not just some noise.
> 
> On 26 October 2017 at 20:38, Nick Pearce <n.m.pea...@uu.nl 
> <mailto:n.m.pea...@uu.nl>> wrote:
> Hi,
> 
> Given the weakness and shapelessness of the density I doubt it is "one 
> conformation of one thing", but rather a superposition of "one or more 
> conformations of one or more things”. If that is the case then there probably 
> isn’t enough information in the electron density or enough prior information 
> to restrain a modelling approach — i.e. you could build a model that fit the 
> density, but you could never determine if it was “correct”. I would probably 
> just leave that bit un-modelled.
> 
> Thanks,
> Nick
> 
> —
> 
> Nick (Nicholas) Pearce
> Post-doctoral Researcher
> Lab of Piet Gros
> Crystal & Structural Chemistry Group
> Universiteit Utrecht
> 
>> On 26 Oct 2017, at 16:53, Vijaykumar Pillalamarri <vijaypkuma...@gmail.com 
>> <mailto:vijaypkuma...@gmail.com>> wrote:
>> 
>> Dear Dr. Vaheh,
>> 
>> I tried fitting waters around Co but the positive density is still present 
>> even after refinement.
>> 
>> Thanks,
>> Vijaykumar
>> 
>> On 26 October 2017 at 20:19, Oganesyan, Vaheh <oganesy...@medimmune.com 
>> <mailto:oganesy...@medimmune.com>> wrote:
>> Water molecules completing Co coordination?
>> 
>>  
>> 
>> Regards,
>> 
>>  
>> 
>> Vaheh Oganesyan
>> 
>> www.medimmune.com <http://www.medimmune.com/>
>>  
>> 
>> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK 
>> <mailto:CCP4BB@JISCMAIL.AC.UK>] On Behalf Of Vijaykumar Pillalamarri
>> Sent: Thursday, October 26, 2017 10:24 AM
>> To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
>> Subject: [ccp4bb] Unknown electron density
>> 
>>  
>> 
>> Dear ccp4bb,
>> 
>>  
>> 
>> I am solving the structure of a 1.6 Angstrom data of a metallo protein. 
>> While everything else is straight forward, this density (see the picture) 
>> seems unfamiliar to me. I don't see any thing fits in the density. This 
>> density present just above Histidine-Cobalt. What ever I try to fit, the 
>> molecule clahes with histidine ( I mean the distance between His and 
>> molecule is <2 Angstrom). 
>> 
>>  
>> 
>> The crystallization condition is 0.1M Bistris, 19% PEG 3350 and 50% glycerol.
>> 
>>  
>> 
>> Any suggestions?
>> 
>>  
>> 
>> Thanks,
>> 
>> Vijaykumar Pillalamarri
>> 
>> UGC-SRF
>> 
>> C/O: Dr. Anthony Addlagatta
>> 
>> Principal Scientist
>> 
>> CSIR-IICT, Tarnaka
>> 
>> Hyderabad, India-57
>> 
>> Mobile: +918886922975
>> 
>> To the extent this electronic communication or any of its attachments 
>> contain information that is not in the public domain, such information is 
>> considered by MedImmune to be confidential and proprietary. This 
>> communication is expected to be read and/or used only by the individual(s) 
>> for whom it is intended. If you have received this electronic communication 
>> in error, please reply to the sender advising of the error in transmission 
>> and delete the original message and any accompanying documents from your 
>> system immediately, without copying, reviewing or otherwise using them for 
>> any purpose. Thank you for your cooperation.
>> 
>> 
>> 
>> -- 
>> Vijaykumar Pillalamarri
>> UGC-SRF
>> C/O: Dr. Anthony Addlagatta
>> Principal Scientist
>> CSIR-IICT, Tarnaka
>> Hyderabad, India-57
>> Mobile: +918886922975
> 
> 
> 
> 
> -- 
> Vijaykumar Pillalamarri
> UGC-SRF
> C/O: Dr. Anthony Addlagatta
> Principal Scientist
> CSIR-IICT, Tarnaka
> Hyderabad, India-57
> Mobile: +918886922975

Re: [ccp4bb] Unknown electron density

2017-10-26 Thread Nick Pearce 
Hi,

Given the weakness and shapelessness of the density I doubt it is "one 
conformation of one thing", but rather a superposition of "one or more 
conformations of one or more things”. If that is the case then there probably 
isn’t enough information in the electron density or enough prior information to 
restrain a modelling approach — i.e. you could build a model that fit the 
density, but you could never determine if it was “correct”. I would probably 
just leave that bit un-modelled.

Thanks,
Nick

—

Nick (Nicholas) Pearce
Post-doctoral Researcher
Lab of Piet Gros
Crystal & Structural Chemistry Group
Universiteit Utrecht

> On 26 Oct 2017, at 16:53, Vijaykumar Pillalamarri  
> wrote:
> 
> Dear Dr. Vaheh,
> 
> I tried fitting waters around Co but the positive density is still present 
> even after refinement.
> 
> Thanks,
> Vijaykumar
> 
> On 26 October 2017 at 20:19, Oganesyan, Vaheh  > wrote:
> Water molecules completing Co coordination?
> 
>  
> 
> Regards,
> 
>  
> 
> Vaheh Oganesyan
> 
> www.medimmune.com 
>  
> 
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK 
> ] On Behalf Of Vijaykumar Pillalamarri
> Sent: Thursday, October 26, 2017 10:24 AM
> To: CCP4BB@JISCMAIL.AC.UK 
> Subject: [ccp4bb] Unknown electron density
> 
>  
> 
> Dear ccp4bb,
> 
>  
> 
> I am solving the structure of a 1.6 Angstrom data of a metallo protein. While 
> everything else is straight forward, this density (see the picture) seems 
> unfamiliar to me. I don't see any thing fits in the density. This density 
> present just above Histidine-Cobalt. What ever I try to fit, the molecule 
> clahes with histidine ( I mean the distance between His and molecule is <2 
> Angstrom). 
> 
>  
> 
> The crystallization condition is 0.1M Bistris, 19% PEG 3350 and 50% glycerol.
> 
>  
> 
> Any suggestions?
> 
>  
> 
> Thanks,
> 
> Vijaykumar Pillalamarri
> 
> UGC-SRF
> 
> C/O: Dr. Anthony Addlagatta
> 
> Principal Scientist
> 
> CSIR-IICT, Tarnaka
> 
> Hyderabad, India-57
> 
> Mobile: +918886922975
> 
> To the extent this electronic communication or any of its attachments contain 
> information that is not in the public domain, such information is considered 
> by MedImmune to be confidential and proprietary. This communication is 
> expected to be read and/or used only by the individual(s) for whom it is 
> intended. If you have received this electronic communication in error, please 
> reply to the sender advising of the error in transmission and delete the 
> original message and any accompanying documents from your system immediately, 
> without copying, reviewing or otherwise using them for any purpose. Thank you 
> for your cooperation.
> 
> 
> 
> -- 
> Vijaykumar Pillalamarri
> UGC-SRF
> C/O: Dr. Anthony Addlagatta
> Principal Scientist
> CSIR-IICT, Tarnaka
> Hyderabad, India-57
> Mobile: +918886922975

[ccp4bb] Creating local/specific B-factor restraints in refmac

2017-02-02 Thread Nick Pearce 
Hi,

As far as I can tell from the refmac documentation, the only way to change 
B-factor restraints for nearby atoms is by changing the weighting globally, 
using, e.g.,

==
BFAC 1.0 1.5 2.0 3.0 4.5
==

Is there a way to implement a specific local b-factor restraint similarly to a 
distance restraint, i.e.

==
exte dist first chain A resi  308 alte A atom  N   second chain A resi  308 
alte D atom  N   value 0.0 sigma 0.02 type 1
==
becomes something like
==
exte bfac first chain A resi  308 alte A atom  N   second chain A resi  308 
alte D atom  N   value 0.0 sigma 10.0 type 1
==

such that the restraint can be imposed locally, between specific atoms?

Thanks,
Nick

—>
Nicholas Pearce
Post-doctoral Researcher
Universiteit Utrecht