Re: [ccp4bb] Positive densities map on selective residues on Coot

[Xiao Lei]

Hi Paul,

Thanks for the instructions! Works in my case.

On Mon, Mar 20, 2017 at 6:05 AM, Paul Emsley 
wrote:

> On 17/03/17 14:41, Xiao Lei wrote:
> >
> > In Coot, I could adjust the densities of map (2Fo-Fc in my case)
> > radius, but I'd like to show the density on selective residues, not
> > on the unselected part of structure, is there a way to do it?
>
> Yes.  Extensions -> Maps -> Mask Map by Atom Selection...
>
> After selecting your  model molecule, you will be asked about an Atom
> Selection
>
> use (for example)
>
> //A/20-30
>
> to mean residues 20 to 30 (inclusive) in the A chain.
>
> You will want to click the "Invert Masking" checkbutton.
>
> Masked maps often scroll "slowly" so increase (say to 0.5) the r.m.s.d.
> step in the Map Properties.
>
> Paul.
>
>

Re: [ccp4bb] Positive densities map on selective residues on Coot or Pymol

[Xiao Lei]

Hi Martin,

I followed your instructions and everything works. Thank you for your
illustration!

On Mon, Mar 20, 2017 at 3:52 AM, Martin Montgomery 
wrote:

> Hello,
>
> You need to tell pymol what to do with the map.
>
> Load your pdb file
> Load the map
>
> create an object with residues you wish to display the map around.  You
> can use the create command to do this or you can click on all the residues
> that you want to use in the main window then go to the object called (sele)
> in the right hand sidebar, click A and then copy to object.  This will
> create an object called obj01 with the selected residues.  You can rename
> this if you wish.
>
> Then you need to use the isomesh command to display the map.
>
>
> isomesh mapname, mapfilename.ccp4, 2.5, obj01, carve=2.0
>
> mapname is the name you want to appear in the right hand sidebar for the
> mesh (can be the same as the mapfilename if you wish)
>
> mapfilename would be D83Vchimmap1 (from your screen shot).
>
> 2.5 is the sigma setting and carve=2.0 means the mesh is created within
> 2.0 Å of the selected atoms.  Adjust these values to suit.
>
> You might want to go back to go back and check your FFT log and look at
> the grid settings.  It is a good idea to re run the FFT job but double the
> grid values from the original job.
>
> It is all covered here:
>
> https://pymolwiki.org/index.php/Display_CCP4_Maps
>
> Regards
>
> MGM
>
> Martin G Montgomery
> ATP Synthase Group
> Medical Research Council Mitochondrial Biology Unit
> University of Cambridge
> Wellcome Trust/MRC Building
> Cambridge Biomedical Campus
> Hills Road
> Cambridge
> Great Britain
> CB2 0XY
>
> www.mrc-mbu.cam.ac.uk
>
>
>
>
>
>
> On 18 Mar 2017, at 10:43, Eleanor Dodson 
> wrote:
>
> I think CCP4MG does this very selectively?
>
> Eleanor Dodson
>
> On 17 March 2017 at 17:03, Xiao Lei  wrote:
>
>> Dear All,
>>
>> Thanks for the information.
>> I tried the way suggested by pymol wiki, but pymol fail to display the
>> map.
>> This is what I did: Run Fft to generate simple mapin ccp4i, input mtz map
>> from refmac, set F1=FWT and PHIC=PHWT, Sigma=SigF, Weight=FOM.  Add the
>> file extension .map.ccp4 to the generated output map. After open by pymol,
>> only a unit cell sign is shown (I attach here), no map is displayed.. I
>> use Pymol 1.8.X in Win7.
>>
>> Any further input is appreciated.
>>
>>
>>
>> .
>>
>>
>>
>>
>> On Fri, Mar 17, 2017 at 7:41 AM, Xiao Lei  wrote:
>>
>>> Dear All,
>>>
>>> In Coot, I could adjust the densities of map (2Fo-Fc in my case) radius,
>>> but I'd like to show the density on selective residues, not on the
>>> unselected part of structure, is there a way to do it? I am using WinCoot
>>> 0.81.
>>>
>>> In addition, could Pymol do it?
>>>
>>> Thanks ahead!
>>>
>>
>>
>
>

[ccp4bb] Saving Coordinates of an Unnatural Amino Acid in Jligand

[John Bruning]

Hi All,
Apologies in advance for a potentially dumb question. 

I generated a cysteine adduct (DHZ) in JLigand. I can save the .cif and link 
file and I can get it to refine in Refmac just fine. 

For a different purpose, I need to save the coordinates of this unnatural amino 
acid, but when I go to Save Coordinates > it won't let me seem to do it. 

If I unlink my CYS and my molecule then I can Save Coordinates > CYS or LIG 
just fine. 

Thanks in advance for any help. 

Re: [ccp4bb] Positive densities map on selective residues on Coot

[Paul Emsley]

On 17/03/17 14:41, Xiao Lei wrote:



> In Coot, I could adjust the densities of map (2Fo-Fc in my case)
> radius, but I'd like to show the density on selective residues, not
> on the unselected part of structure, is there a way to do it?

Yes.  Extensions -> Maps -> Mask Map by Atom Selection...

After selecting your  model molecule, you will be asked about an Atom 
Selection


use (for example)

//A/20-30

to mean residues 20 to 30 (inclusive) in the A chain.

You will want to click the "Invert Masking" checkbutton.

Masked maps often scroll "slowly" so increase (say to 0.5) the r.m.s.d. 
step in the Map Properties.


Paul.

Re: [ccp4bb] Positive densities map on selective residues on Coot or Pymol

[Martin Montgomery]

Hello,

You need to tell pymol what to do with the map.

Load your pdb file
Load the map

create an object with residues you wish to display the map around.  You can use 
the create command to do this or you can click on all the residues that you 
want to use in the main window then go to the object called (sele) in the right 
hand sidebar, click A and then copy to object.  This will create an object 
called obj01 with the selected residues.  You can rename this if you wish.

Then you need to use the isomesh command to display the map.


isomesh mapname, mapfilename.ccp4, 2.5, obj01, carve=2.0

mapname is the name you want to appear in the right hand sidebar for the mesh 
(can be the same as the mapfilename if you wish)

mapfilename would be D83Vchimmap1 (from your screen shot).

2.5 is the sigma setting and carve=2.0 means the mesh is created within 2.0 Å 
of the selected atoms.  Adjust these values to suit.

You might want to go back to go back and check your FFT log and look at the 
grid settings.  It is a good idea to re run the FFT job but double the grid 
values from the original job.

It is all covered here:

https://pymolwiki.org/index.php/Display_CCP4_Maps 


Regards

MGM

Martin G Montgomery
ATP Synthase Group
Medical Research Council Mitochondrial Biology Unit
University of Cambridge
Wellcome Trust/MRC Building
Cambridge Biomedical Campus
Hills Road 
Cambridge
Great Britain
CB2 0XY

www.mrc-mbu.cam.ac.uk






> On 18 Mar 2017, at 10:43, Eleanor Dodson  wrote:
> 
> I think CCP4MG does this very selectively?
> 
> Eleanor Dodson
> 
> On 17 March 2017 at 17:03, Xiao Lei  > wrote:
> Dear All,
> 
> Thanks for the information.
> I tried the way suggested by pymol wiki, but pymol fail to display the map. 
> This is what I did: Run Fft to generate simple mapin ccp4i, input mtz map 
> from refmac, set F1=FWT and PHIC=PHWT, Sigma=SigF, Weight=FOM.  Add the file 
> extension .map.ccp4 to the generated output map. After open by pymol, only a 
> unit cell sign is shown (I attach here), no map is displayed.. I use Pymol 
> 1.8.X in Win7.
> 
> Any further input is appreciated.
> 
> 
> 
> .
> 
> 
> 
> 
> On Fri, Mar 17, 2017 at 7:41 AM, Xiao Lei  > wrote:
> Dear All,
> 
> In Coot, I could adjust the densities of map (2Fo-Fc in my case) radius, but 
> I'd like to show the density on selective residues, not on the unselected 
> part of structure, is there a way to do it? I am using WinCoot 0.81.
> 
> In addition, could Pymol do it? 
> 
> Thanks ahead!
> 
> 

[ccp4bb] Fwd: [ccp4bb] No improvement in R-factor after Refmac.

[Polisetty Satya Dev]

-- Forwarded message --
From: Polisetty Satya Dev 
Date: Mon, Mar 20, 2017 at 1:35 PM
Subject: Re: [ccp4bb] No improvement in R-factor after Refmac.
To: Sudipta Bhattacharyya 


Hi,
I had tried running xtriage but it does not show any sign of NCS. But
pointles is showing the following warning
* "one or more zones have data systematically missing from the input file
thus we cannot determine if reflections are truly systematically absent"*

Thank You,
Satya Dev

On Sun, Mar 19, 2017 at 5:22 AM, Sudipta Bhattacharyya <
sudiptabhattacharyya.iit...@gmail.com> wrote:

> Hi Satya Dev,
>
> You can feed the mtz output of SCALA to Phenix Xtriage and then see the
> presence of t-NCS and/or any other crystal pathologies. Another thing you
> can do is to merge and scale the data in P222 and then let the Phaser
> decide the best space group. Again, I am curious, when you ran pointless,
> did you check the absence conditions and the probability of assigning all
> the three screw axes?
>
> Good luck!
> Sudipta.
>
> On Sat, Mar 18, 2017 at 5:42 AM, Eleanor Dodson  > wrote:
>
>> You dont say whether there is Non cryst translation - that will be
>> reported at various stages - the pointless/aimless/ctruncate task gives it.
>>
>> But if it exists and the translation ihas a component of .5 along any
>> axis, that makes the SG estimate a bit uncertain - the absences could be
>> due to the NX translation.
>>
>> And even if the SG is correct - which likely after solving the MR with
>> the newest PHASER which tests carefully = then you will have zones with low
>> intensities, and those reflections always have a higher r factor of course.
>>
>> You could let Arp/Warp or Buccaneer rebuild starting from your existing
>> model? That is a verification that your solution is essentially right
>>
>> Eleanor
>>
>>
>>
>> On 18 March 2017 at 10:28, Isupov, Michail  wrote:
>>
>>> Hi,
>>>
>>> I have seen cases where in a correct space group
>>> 'R-work and R-free values 0.25 and 0.32 respectively'
>>> at 2 A resolution sound like not too bad values.
>>> In some of such cases when data from a different crystal
>>> in the same space group was available R-factors were much lower
>>> when the structure was refined against the new crystal data.
>>> I guess this phenomenon could be due to uneven freezing of the first
>>> crystal,
>>> or inconsistent degree of disorder between crystals.
>>>
>>> In other projects high R-factor values (e.g. FreeR around 33% at 2.1 A
>>> resolution)
>>>  are consistent through a range of crystals
>>> even when the refinement is in P1, although the map quality is good
>>> enough
>>> to see cofactors and to build  the missing parts of the structure (30%
>>> of residues).
>>> The disorder seems to be an intrinsic property of such crystal form.
>>>
>>> I do not know how to approach publishing these results since most
>>> referees will argue
>>> that such R-factors may be acceptable at 4A resolution but not close to
>>> 2 Angstrom.
>>>
>>> Best wishes,
>>>
>>> Misha Isupov
>>> 
>>> From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Randy
>>> Read [rj...@cam.ac.uk]
>>> Sent: Saturday, March 18, 2017 9:29 AM
>>> To: CCP4BB@JISCMAIL.AC.UK
>>> Subject: Re: [ccp4bb] No improvement in R-factor after Refmac.
>>>
>>> Hi,
>>>
>>> I was just going to make the same point!  The only thing to add is that,
>>> if there really is translational NCS (which is certainly possible with 4
>>> copies in the a.u.), then it’s essential both to account for it (which
>>> current versions of Phaser should do automatically, if you search for all 4
>>> copies in one job) and to try all possible space groups.  The situation
>>> Craig describes, in which it’s not immediately obvious whether your crystal
>>> has a crystallographic 2(1) and a pseudosymmetric non-crystallographic
>>> 2-fold or the reverse, is not uncommon.  However, we’ve found that the
>>> likelihood score accounting for the effect of tNCS is pretty good at
>>> discriminating the two possibilities.
>>>
>>> Best wishes,
>>>
>>> Randy Read
>>>
>>> -
>>> Randy J. Read
>>> Department of Haematology, University of Cambridge
>>> Cambridge Institute for Medical ResearchTel: +44 1223 336500
>>> Wellcome Trust/MRC Building Fax: +44 1223 336827
>>> Hills Road
>>> E-mail: rj...@cam.ac.uk
>>> Cambridge CB2 0XY, U.K.
>>> www-structmed.cimr.cam.ac.uk
>>>
>>> > On 18 Mar 2017, at 06:12, CRAIG A BINGMAN  wrote:
>>> >
>>> > You really need to approach such situations with caution.  Examination
>>> of the relatively small number of axial reflections probably show that
>>> there might be twofold screw axes in all three directions.  But a
>>> non-crystallographic microscopic translation of nearly 0.5 in the direction
>>> of a crystallographic axis will give the same pattern of strong