Re: [ccp4bb] Off-pick: suggesiton of puck

[Jim Pflugrath]

Rigaku ACTOR robots can accept many different styles of pucks depending on the 
LN2 dewar baseplate that the particular ACTOR is equipped with.  Rigaku in 
China will sell ACTOR pucks, but if you are looking for ALS-style pucks or 
ESRF-style pucks or Unipucks or ???, then I am not sure where to get them.

Anyways, I have forwarded your query to my colleagues in China.

Jim


From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Frank 
[fanshil...@hotmail.com]
Sent: Monday, April 16, 2012 8:35 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Off-pick: suggesiton of puck

Hi guys:

Recently we need purchase some puck for Actor, unfortunately we can't find any 
agency in China.

I really appreciate that if anyone can give us some suggestion about that? such 
like brand, price, and necessary accessory?

Thanks for help

Best regards

Frank

Re: [ccp4bb] Off-topic-Cleavage with TEV protease

[Tim Fenn]

Also keep in mind that many of the purchased TEVs are formulated with
some reducing agent (e.g. AcTEV comes in a buffer with 5mM DTT, if I
recall correctly).  So unless the enzyme is buffer exchanged
beforehand, there will be some reducing agent introduced alongside it,
depending on the dilution.

HTH,
-Tim

On Mon, Apr 16, 2012 at 4:32 PM, Jason Forse  wrote:
> I've run into the same problem, and found David Waugh's FAQ to be a great 
> resource:
> http://mcl1.ncifcrf.gov/waugh_tech.html
> They use a 3mM buffer of 10:1 reduced:oxidized glutathione. I've tried that 
> and it cleaves my protein without reducing reducing the disulfide bridges.
>
> I'll second someone else's suggestion to add more TEV. That's worked for me 
> as well, as long as the TEV's relatively fresh and there isn't too much 
> reducing agent introduced along with it.
>
> Jason

[ccp4bb] Off-pick: suggesiton of puck

[Frank]

Hi guys:

Recently we need purchase some puck for Actor, unfortunately we can't find any 
agency in China.

I really appreciate that if anyone can give us some suggestion about that? such 
like brand, price, and necessary accessory?   

Thanks for help 

Best regards

Frank

Re: [ccp4bb] Off-topic-Cleavage with TEV protease

[Jason Forse]

I've run into the same problem, and found David Waugh's FAQ to be a great 
resource:
http://mcl1.ncifcrf.gov/waugh_tech.html
They use a 3mM buffer of 10:1 reduced:oxidized glutathione. I've tried that and 
it cleaves my protein without reducing reducing the disulfide bridges.

I'll second someone else's suggestion to add more TEV. That's worked for me as 
well, as long as the TEV's relatively fresh and there isn't too much reducing 
agent introduced along with it.

Jason

Re: [ccp4bb] bulk solvent treatment inside protein cavities

[Garib N Murshudov]

On 16 Apr 2012, at 17:14, Keitaro Yamashita wrote:

> Dear Garib,
> 
> I think it is better if refmac outputs final solvent mask when mskout 
> specified.
> If one just wanted to calculate the mask, NCYC 0 should be specified.
> 
> I hope my suggestion would be accepted, but I'm not in a hurry.

ok

> 
> 
>> FC_ALL is ML scaled FC+FMASK
>> 
>> Sometime it may be different from least-squares scaled FC+FMASK
> 
> For what purpose is FC_ALL_LS written?
> Can I check something by comparing FC_ALLto FC_ALL_LS?

There could be some differences, as I said FC_ALL maximum likelihood scaled 
(they are used for map calculation) and FC_ALL_LS least-squares scaled (it is 
used for Rfactor calculations)
> 
> I found somewhat large difference between FC_ALL_LS map and FC_ALL
> map in Se position.

Without data I could not say what might be going on.


> I used SAD function.
> What does it mean?
> 
> 
> Cheers,
> 
> Keitaro
> 
> 2012/4/17 Garib N Murshudov :
>> Dear Ketaro
>> 
>> At the moment mskout option is a signal that the program should stop.
>> Obviously I can add an option to continue. However if you have mskout option
>> it is likely that you want to check what is going on with the mask. If you
>> want to compare starting and final mask then you could run refmac with
>> mskout in the beginning and after refinement.
>> 
>> If you need it urgently then I can add continuation of refinement with
>> mskout option.
>> 
>> 
>> FC_ALL is ML scaled FC+FMASK
>> 
>> Sometime it may be different from least-squares scaled FC+FMASK
>> 
>> regards
>> Garib
>> 
>> On 16 Apr 2012, at 16:01, Keitaro Yamashita wrote:
>> 
>> Dear Garib,
>> 
>> Thank you very much for your quick reply.
>> 
>> I tried mskout option and the output looked almost the same as the map
>> generated by FC_ALL - FC.
>> 
>> By the way, when mskout option is specified, refmac stops before CGMAT
>> cycles.
>> Is there any way to do refinement with mskout option?
>> 
>> 
>> I have not tried but if you can use vector difference map then it should be:
>> 
>> FMASK = FC_ALL_LS - FC
>> 
>> 
>> What is FC_ALL in the new version?
>> 
>> 
>> Thanks,
>> 
>> Keitaro
>> 
>> 
>> 2012/4/16 Garib N Murshudov :
>> 
>> A follow up:
>> 
>> 
>> In the new version there is FC_ALL_LS, PHIC_ALL_LS
>> 
>> 
>> That should be FC_ALL_LS = FC + FMASK.
>> 
>> 
>> I have not tried but if you can use vector difference map then it should be:
>> 
>> FMASK = FC_ALL_LS - FC
>> 
>> 
>> But it is after scaling. If you write out mask map then it is just 0 1 map
>> 
>> (0 inside protein and 1 outside), except values are not 0 1 but 0 and some
>> 
>> constant
>> 
>> 
>> 
>> 
>> Regards
>> 
>> Garib
>> 
>> 
>> 
>> On 16 Apr 2012, at 15:09, Keitaro Yamashita wrote:
>> 
>> 
>> Dear Garib,
>> 
>> 
>> Is there REFMAC option to output solvent mask information (e.g. Fmask
>> 
>> and PHImask in mtz to check with Coot)?
>> 
>> 
>> I tried to generate it by subtracting (FC, PHIC) from (FC_ALL,PHIC_ALL).
>> 
>> But I'm not sure that FC_ALL = FC + FMASK is correct or not.
>> 
>> 
>> Keitaro
>> 
>> 
>> 
>> 2012/4/16 Garib N Murshudov :
>> 
>> 
>> Dear Allister
>> 
>> 
>> 
>> Could you please update refmac version. In the version you it seems that
>> 
>> 
>> bulk solvent mask calculation has some problems. New version (at the moment)
>> 
>> 
>> can be downloaded from this site:
>> 
>> 
>> 
>> http://www.ysbl.york.ac.uk/refmac/data/refmac_experimental/refmac5.7_linux.tar.gz
>> 
>> 
>> 
>> There is a mac version also.
>> 
>> 
>> 
>> 
>> regards
>> 
>> 
>> Garib
>> 
>> 
>> 
>> 
>> On 16 Apr 2012, at 11:37, Allister Crow wrote:
>> 
>> 
>> 
>> 
>> Board members,
>> 
>> 
>> 
>> I have a couple of questions regarding how to improve the solvent model as
>> 
>> 
>> applied to solvent-filled cavities inside proteins.
>> 
>> 
>> 
>> I am currently nearing the end of refinement of a protein structure at 2.8 A
>> 
>> 
>> resolution.  I recently switched Refmac versions, upon doing this I noticed
>> 
>> 
>> a modest improvement in R factors, but I also notice some new features in
>> 
>> 
>> the difference maps.  These features don't show up in the sigma-weighted
>> 
>> 
>> 2Fo-Fc maps and are unlikely to be 'ligands' of any form.  In fact, I
>> 
>> 
>> suspect that the appearance of these features (which are all located in
>> 
>> 
>> solvent channels within cavities inside the protein) are probably due to
>> 
>> 
>> some difference in how the bulk solvent contribution has been applied.
>> 
>> 
>> 
>> I've attached a picture of one such feature showing the difference between
>> 
>> 
>> Refmac 5.5 and 5.6.  (Both difference maps are contoured at 3 sigma- both
>> 
>> 
>> using the same model and refinement parameters).
>> 
>> 
>> 
>> My questions are therefore:
>> 
>> 
>> 
>> 1) has something substantial changed in the bulk solvent treatment between
>> 
>> 
>> Refmac versions 5.5 and 5.6?
>> 
>> 
>> 
>> 2) How can I go about changing the bulk solvent treatment to better account
>> 
>> 
>> for solvent contribution inside the prot

Re: [ccp4bb] software to generate protein topology diagram like those available at PDBsum webserver

[Parthasarathy Sampathkumar]

Dear All,

Guillaume Ponchel referred me to ProOrigami (which can be installed
locally) to generate protein topology diagrams:

http://munk.csse.unimelb.edu.au/pro-origami/


Thanks again.

Best wishes,
Partha


On Mon, Apr 16, 2012 at 12:12 AM, Parthasarathy Sampathkumar <
spart...@gmail.com> wrote:

> Dear All,
>
> Thanks to Herb, John, Simanshu, and Anu for link:
>
> http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/Generate.html
>
> to generate PDBsum like topology diagrams.
>
> Partha
> On Sun, Apr 15, 2012 at 8:08 PM, Parthasarathy Sampathkumar <
> spart...@gmail.com> wrote:
>
>> Dear All,
>>
>> I would like to generate a topology diagram similar to the ones available
>> for deposited entries at the PDBsum webpage (attached one such diagram here
>> for reference) for a new structure. Is this program is available for
>> download?
>>
>> I am aware of TopDraw. However, I am trying to analyze a ~850 a.a.
>> structure. So, some automation would be helpful.
>>
>> Thanks in advance for your help.
>>
>> Best wishes,
>> Partha
>>
>
>

Re: [ccp4bb] bulk solvent treatment inside protein cavities

[Keitaro Yamashita]

Dear Garib,

I think it is better if refmac outputs final solvent mask when mskout specified.
If one just wanted to calculate the mask, NCYC 0 should be specified.

I hope my suggestion would be accepted, but I'm not in a hurry.


> FC_ALL is ML scaled FC+FMASK
>
> Sometime it may be different from least-squares scaled FC+FMASK

For what purpose is FC_ALL_LS written?
Can I check something by comparing FC_ALLto FC_ALL_LS?

I found somewhat large difference between FC_ALL_LS map and FC_ALL
map in Se position.
I used SAD function.
What does it mean?


Cheers,

Keitaro

2012/4/17 Garib N Murshudov :
> Dear Ketaro
>
> At the moment mskout option is a signal that the program should stop.
> Obviously I can add an option to continue. However if you have mskout option
> it is likely that you want to check what is going on with the mask. If you
> want to compare starting and final mask then you could run refmac with
> mskout in the beginning and after refinement.
>
> If you need it urgently then I can add continuation of refinement with
> mskout option.
>
>
> FC_ALL is ML scaled FC+FMASK
>
> Sometime it may be different from least-squares scaled FC+FMASK
>
> regards
> Garib
>
> On 16 Apr 2012, at 16:01, Keitaro Yamashita wrote:
>
> Dear Garib,
>
> Thank you very much for your quick reply.
>
> I tried mskout option and the output looked almost the same as the map
> generated by FC_ALL - FC.
>
> By the way, when mskout option is specified, refmac stops before CGMAT
> cycles.
> Is there any way to do refinement with mskout option?
>
>
> I have not tried but if you can use vector difference map then it should be:
>
> FMASK = FC_ALL_LS - FC
>
>
> What is FC_ALL in the new version?
>
>
> Thanks,
>
> Keitaro
>
>
> 2012/4/16 Garib N Murshudov :
>
> A follow up:
>
>
> In the new version there is FC_ALL_LS, PHIC_ALL_LS
>
>
> That should be FC_ALL_LS = FC + FMASK.
>
>
> I have not tried but if you can use vector difference map then it should be:
>
> FMASK = FC_ALL_LS - FC
>
>
> But it is after scaling. If you write out mask map then it is just 0 1 map
>
> (0 inside protein and 1 outside), except values are not 0 1 but 0 and some
>
> constant
>
>
>
>
> Regards
>
> Garib
>
>
>
> On 16 Apr 2012, at 15:09, Keitaro Yamashita wrote:
>
>
> Dear Garib,
>
>
> Is there REFMAC option to output solvent mask information (e.g. Fmask
>
> and PHImask in mtz to check with Coot)?
>
>
> I tried to generate it by subtracting (FC, PHIC) from (FC_ALL,PHIC_ALL).
>
> But I'm not sure that FC_ALL = FC + FMASK is correct or not.
>
>
> Keitaro
>
>
>
> 2012/4/16 Garib N Murshudov :
>
>
> Dear Allister
>
>
>
> Could you please update refmac version. In the version you it seems that
>
>
> bulk solvent mask calculation has some problems. New version (at the moment)
>
>
> can be downloaded from this site:
>
>
>
> http://www.ysbl.york.ac.uk/refmac/data/refmac_experimental/refmac5.7_linux.tar.gz
>
>
>
> There is a mac version also.
>
>
>
>
> regards
>
>
> Garib
>
>
>
>
> On 16 Apr 2012, at 11:37, Allister Crow wrote:
>
>
>
>
> Board members,
>
>
>
> I have a couple of questions regarding how to improve the solvent model as
>
>
> applied to solvent-filled cavities inside proteins.
>
>
>
> I am currently nearing the end of refinement of a protein structure at 2.8 A
>
>
> resolution.  I recently switched Refmac versions, upon doing this I noticed
>
>
> a modest improvement in R factors, but I also notice some new features in
>
>
> the difference maps.  These features don't show up in the sigma-weighted
>
>
> 2Fo-Fc maps and are unlikely to be 'ligands' of any form.  In fact, I
>
>
> suspect that the appearance of these features (which are all located in
>
>
> solvent channels within cavities inside the protein) are probably due to
>
>
> some difference in how the bulk solvent contribution has been applied.
>
>
>
> I've attached a picture of one such feature showing the difference between
>
>
> Refmac 5.5 and 5.6.  (Both difference maps are contoured at 3 sigma- both
>
>
> using the same model and refinement parameters).
>
>
>
> My questions are therefore:
>
>
>
> 1) has something substantial changed in the bulk solvent treatment between
>
>
> Refmac versions 5.5 and 5.6?
>
>
>
> 2) How can I go about changing the bulk solvent treatment to better account
>
>
> for solvent contribution inside the protein cavities?
>
>
>
> Best wishes, and thanks in advance for all your help,
>
>
>
> - Allister Crow
>
>
>
>
> 
>
>
>
>
>
> Dr Garib N Murshudov
>
>
> Group Leader, MRC Laboratory of Molecular Biology
>
>
> Hills Road
>
>
> Cambridge
>
>
> CB2 0QH UK
>
>
> Email: ga...@mrc-lmb.cam.ac.uk
>
>
> Web http://www.mrc-lmb.cam.ac.uk
>
>
>
>
>
>
>
> Dr Garib N Murshudov
>
> Group Leader, MRC Laboratory of Molecular Biology
>
> Hills Road
>
> Cambridge
>
> CB2 0QH UK
>
> Email: ga...@mrc-lmb.cam.ac.uk
>
> Web http://www.mrc-lmb.cam.ac.uk
>
>
>
>
>
>
> Dr Garib N Murshudov
> Group Leader, MRC Laboratory of Molecular Biology
> Hills Road
> Cambridge
> CB2 0QH UK
> Email: ga...@mrc-

Re: [ccp4bb] bulk solvent treatment inside protein cavities

[Garib N Murshudov]

Dear Ketaro

At the moment mskout option is a signal that the program should stop. Obviously 
I can add an option to continue. However if you have mskout option it is likely 
that you want to check what is going on with the mask. If you want to compare 
starting and final mask then you could run refmac with mskout in the beginning 
and after refinement.

If you need it urgently then I can add continuation of refinement with mskout 
option.


FC_ALL is ML scaled FC+FMASK

Sometime it may be different from least-squares scaled FC+FMASK

regards
Garib

On 16 Apr 2012, at 16:01, Keitaro Yamashita wrote:

> Dear Garib,
> 
> Thank you very much for your quick reply.
> 
> I tried mskout option and the output looked almost the same as the map
> generated by FC_ALL - FC.
> 
> By the way, when mskout option is specified, refmac stops before CGMAT cycles.
> Is there any way to do refinement with mskout option?
> 
> 
>> I have not tried but if you can use vector difference map then it should be:
>> FMASK = FC_ALL_LS - FC
> 
> What is FC_ALL in the new version?
> 
> 
> Thanks,
> 
> Keitaro
> 
> 
> 2012/4/16 Garib N Murshudov :
>> A follow up:
>> 
>> In the new version there is FC_ALL_LS, PHIC_ALL_LS
>> 
>> That should be FC_ALL_LS = FC + FMASK.
>> 
>> I have not tried but if you can use vector difference map then it should be:
>> FMASK = FC_ALL_LS - FC
>> 
>> But it is after scaling. If you write out mask map then it is just 0 1 map
>> (0 inside protein and 1 outside), except values are not 0 1 but 0 and some
>> constant
>> 
>> 
>> 
>> Regards
>> Garib
>> 
>> 
>> On 16 Apr 2012, at 15:09, Keitaro Yamashita wrote:
>> 
>> Dear Garib,
>> 
>> Is there REFMAC option to output solvent mask information (e.g. Fmask
>> and PHImask in mtz to check with Coot)?
>> 
>> I tried to generate it by subtracting (FC, PHIC) from (FC_ALL,PHIC_ALL).
>> But I'm not sure that FC_ALL = FC + FMASK is correct or not.
>> 
>> Keitaro
>> 
>> 
>> 2012/4/16 Garib N Murshudov :
>> 
>> Dear Allister
>> 
>> 
>> Could you please update refmac version. In the version you it seems that
>> 
>> bulk solvent mask calculation has some problems. New version (at the moment)
>> 
>> can be downloaded from this site:
>> 
>> 
>> http://www.ysbl.york.ac.uk/refmac/data/refmac_experimental/refmac5.7_linux.tar.gz
>> 
>> 
>> There is a mac version also.
>> 
>> 
>> 
>> regards
>> 
>> Garib
>> 
>> 
>> 
>> On 16 Apr 2012, at 11:37, Allister Crow wrote:
>> 
>> 
>> 
>> Board members,
>> 
>> 
>> I have a couple of questions regarding how to improve the solvent model as
>> 
>> applied to solvent-filled cavities inside proteins.
>> 
>> 
>> I am currently nearing the end of refinement of a protein structure at 2.8 A
>> 
>> resolution.  I recently switched Refmac versions, upon doing this I noticed
>> 
>> a modest improvement in R factors, but I also notice some new features in
>> 
>> the difference maps.  These features don't show up in the sigma-weighted
>> 
>> 2Fo-Fc maps and are unlikely to be 'ligands' of any form.  In fact, I
>> 
>> suspect that the appearance of these features (which are all located in
>> 
>> solvent channels within cavities inside the protein) are probably due to
>> 
>> some difference in how the bulk solvent contribution has been applied.
>> 
>> 
>> I've attached a picture of one such feature showing the difference between
>> 
>> Refmac 5.5 and 5.6.  (Both difference maps are contoured at 3 sigma- both
>> 
>> using the same model and refinement parameters).
>> 
>> 
>> My questions are therefore:
>> 
>> 
>> 1) has something substantial changed in the bulk solvent treatment between
>> 
>> Refmac versions 5.5 and 5.6?
>> 
>> 
>> 2) How can I go about changing the bulk solvent treatment to better account
>> 
>> for solvent contribution inside the protein cavities?
>> 
>> 
>> Best wishes, and thanks in advance for all your help,
>> 
>> 
>> - Allister Crow
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> Dr Garib N Murshudov
>> 
>> Group Leader, MRC Laboratory of Molecular Biology
>> 
>> Hills Road
>> 
>> Cambridge
>> 
>> CB2 0QH UK
>> 
>> Email: ga...@mrc-lmb.cam.ac.uk
>> 
>> Web http://www.mrc-lmb.cam.ac.uk
>> 
>> 
>> 
>> 
>> 
>> 
>> Dr Garib N Murshudov
>> Group Leader, MRC Laboratory of Molecular Biology
>> Hills Road
>> Cambridge
>> CB2 0QH UK
>> Email: ga...@mrc-lmb.cam.ac.uk
>> Web http://www.mrc-lmb.cam.ac.uk
>> 
>> 
>> 
>> 

Dr Garib N Murshudov
Group Leader, MRC Laboratory of Molecular Biology
Hills Road 
Cambridge 
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk 
Web http://www.mrc-lmb.cam.ac.uk

Re: [ccp4bb] iMosflm version 1.0.6 & Mosflm version 7.0.8

[Phil Evans]

Aimless is a complete rewrite of Scala, but does essentially the same task. I 
haven't yet written it up properly, but there is a program document at

ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/aimless.html


A rough flow of the program is as follows:-

 Read file from eg POINTLESS, sort data if necessary (SORTMTZ no longer needed)

 Initial scale estimates from average intensities

 First round scaling with small selection of strong reflections, chosen on 
I/sigI

 First outlier rejection

 Optimise the combination of profile-fitted (for weak spots) or summation 
integration intensities (for strong spots) from MOSFLM

 First optimisation of sig(I) estimates

 Main scaling on relatively strong reflections, chosen on normalised intensity 
E^2  (eg 0.8 < E^2 < 5)

 Second outlier rejection

 Final optimisation of sig(I) estimates

 Final outlier rejection

 Final statistics

 Output of merged or unmerged data (MTZ or Scalepack format, or both)



Phil



On 16 Apr 2012, at 15:42, Jacob Keller wrote:

> Where can one find a discussion of the differences between Aimless and Scala?
> 
> JPK
> 
> On Mon, Apr 16, 2012 at 8:28 AM, Harry Powell  wrote:
> Dear all
> 
> We are pleased to announce the public release of new versions of iMosflm and 
> Mosflm. We have addressed many bugs and performance issues, and also tidied 
> things up in some of the tasks.
> 
> If you are using a previous version we strongly recommend that you upgrade.
> 
> In brief -
> 
>Improved processing for Pilatus images (both 6M and 2M)
>Faster processing for large datasets in iMosflm
>More reliability in indexing, refinement & integration
>Better feedback
>Easier multi-crystal strategy
> 
> Available from our website -
> 
>http://www.mrc-lmb.cam.ac.uk/harry/mosflm
> 
> ==
> 
> In more detail  (see 
> http://www.mrc-lmb.cam.ac.uk/harry/mosflm/ver708/Release_notes for more) -
> 
> Mosflm
> ==
> Non-Bragg spots (eg zingers and hot pixels) and ice spots are now
> automatically removed when forming the standard profiles.
> 
> Improvements in mosaicity estimation and refinement.
> 
> Improvements in standard deviation estimates.
> 
> Improved spot finding parameters for in-house diffraction images
> and for the very small spots that can be obtained from room
> temperature (in situ screening) crystals.
> 
> More robust integration of images with very small spot separation.
> 
> iMosflm
> ==
> The colour of the predicted reflections can be changed to improve
> visibility on weak diffraction images.
> 
> Improved selection of the correct indexing solution in cases of
> pseudosymmetry.
> 
> Scaling and merging now performed with AIMLESS rather than SCALA.
> Release Notes for iMosflm version 1.0.6
> 
> New features
> 
> 
> The speed of the interface has been much improved when processing a
> large number of images in the Integration pane. The largest speed-up
> came from not refreshing the profile displays afresh with every new
> image integrated.
> 
> A greatly improved multi-crystal strategy option is available that
> makes it much simpler to calculate a data collection strategy when
> multiple crystals or multiple segments from one crystal are required
> (see below, and also see the new iMosflm tutorial for details).
> 
> Bad spots identified during processing and whose numbers are plotted
> during integration can now be displayed in the Image display window.
> 
> New mosaicity estimation will produce successive plots up to 8 degrees
> if required.
> 
> Space group validation has been improved wherever a symbol can also be
> typed in editable, pull-down lists (Indexing and Strategy panes).
> 
> The multi-sector, pull-down sectors list used in the Integration pane
> has been adopted in the Indexing and Cell refinement panes.
> 
> Initial detector and crystal parameters are saved before refinement
> and checked that they have not refined to unreasonable values. Users
> may accept the warnings (& reset the parameters) or ignore them.
> 
> New items added to the Advanced integration tab of Processing options
> includes provision for outliers affected by ice rings.
> 
> The maximum number of images in an integration block has been
> increased from 20 to 200.
> 
> The FindHKL function has been placed within the Image display
> window's toolbar.
> 
> Smaller rotation increments have been added to the Rotation: setting
> in the Auto-complete menu in the Strategy pane.
> 
> The editable 'pie' widget displayed at the bottom of the Strategy pane
> for any sector can now be adjusted in single degree steps (previously
> only 5 degree changes were possible).
> 
> Individual images can now be deleted from the Images pane by selecting
> them (left-click) and then right-clicking on the selected image. This
> was previously only available for complete sectors.
> 
> Scala has been replaced by Aimless as the default scaling program used
> by the QuickScale command button. S

Re: [ccp4bb] bulk solvent treatment inside protein cavities

[Keitaro Yamashita]

Dear Garib,

Thank you very much for your quick reply.

I tried mskout option and the output looked almost the same as the map
generated by FC_ALL - FC.

By the way, when mskout option is specified, refmac stops before CGMAT cycles.
Is there any way to do refinement with mskout option?


> I have not tried but if you can use vector difference map then it should be:
> FMASK = FC_ALL_LS - FC

What is FC_ALL in the new version?


Thanks,

Keitaro


2012/4/16 Garib N Murshudov :
> A follow up:
>
> In the new version there is FC_ALL_LS, PHIC_ALL_LS
>
> That should be FC_ALL_LS = FC + FMASK.
>
> I have not tried but if you can use vector difference map then it should be:
> FMASK = FC_ALL_LS - FC
>
> But it is after scaling. If you write out mask map then it is just 0 1 map
> (0 inside protein and 1 outside), except values are not 0 1 but 0 and some
> constant
>
>
>
> Regards
> Garib
>
>
> On 16 Apr 2012, at 15:09, Keitaro Yamashita wrote:
>
> Dear Garib,
>
> Is there REFMAC option to output solvent mask information (e.g. Fmask
> and PHImask in mtz to check with Coot)?
>
> I tried to generate it by subtracting (FC, PHIC) from (FC_ALL,PHIC_ALL).
> But I'm not sure that FC_ALL = FC + FMASK is correct or not.
>
> Keitaro
>
>
> 2012/4/16 Garib N Murshudov :
>
> Dear Allister
>
>
> Could you please update refmac version. In the version you it seems that
>
> bulk solvent mask calculation has some problems. New version (at the moment)
>
> can be downloaded from this site:
>
>
> http://www.ysbl.york.ac.uk/refmac/data/refmac_experimental/refmac5.7_linux.tar.gz
>
>
> There is a mac version also.
>
>
>
> regards
>
> Garib
>
>
>
> On 16 Apr 2012, at 11:37, Allister Crow wrote:
>
>
>
> Board members,
>
>
> I have a couple of questions regarding how to improve the solvent model as
>
> applied to solvent-filled cavities inside proteins.
>
>
> I am currently nearing the end of refinement of a protein structure at 2.8 A
>
> resolution.  I recently switched Refmac versions, upon doing this I noticed
>
> a modest improvement in R factors, but I also notice some new features in
>
> the difference maps.  These features don't show up in the sigma-weighted
>
> 2Fo-Fc maps and are unlikely to be 'ligands' of any form.  In fact, I
>
> suspect that the appearance of these features (which are all located in
>
> solvent channels within cavities inside the protein) are probably due to
>
> some difference in how the bulk solvent contribution has been applied.
>
>
> I've attached a picture of one such feature showing the difference between
>
> Refmac 5.5 and 5.6.  (Both difference maps are contoured at 3 sigma- both
>
> using the same model and refinement parameters).
>
>
> My questions are therefore:
>
>
> 1) has something substantial changed in the bulk solvent treatment between
>
> Refmac versions 5.5 and 5.6?
>
>
> 2) How can I go about changing the bulk solvent treatment to better account
>
> for solvent contribution inside the protein cavities?
>
>
> Best wishes, and thanks in advance for all your help,
>
>
> - Allister Crow
>
>
>
> 
>
>
>
>
> Dr Garib N Murshudov
>
> Group Leader, MRC Laboratory of Molecular Biology
>
> Hills Road
>
> Cambridge
>
> CB2 0QH UK
>
> Email: ga...@mrc-lmb.cam.ac.uk
>
> Web http://www.mrc-lmb.cam.ac.uk
>
>
>
>
>
>
> Dr Garib N Murshudov
> Group Leader, MRC Laboratory of Molecular Biology
> Hills Road
> Cambridge
> CB2 0QH UK
> Email: ga...@mrc-lmb.cam.ac.uk
> Web http://www.mrc-lmb.cam.ac.uk
>
>
>
>

Re: [ccp4bb] bulk solvent treatment inside protein cavities

[Tallat Hussain Ghazi]

Hi there!
I think some of you have given my email for correspondence or CC, please I
do not have to do anything related to your conversation so please delete my
email address from your correspondence

I shall be grateful



 
THANKS & REGARDS!
 
Tallat Hussain Ghazi
IT Manager / Head of Web & Graphics Depts.
ITSS (Pvt) Ltd.
Email: tal...@itssols.com
Website: www.itssols.com
Mob: +92 (0)323 992
Tel: +92 (0)42 5694723-25
Fax: +92 (0)42 5694727




-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Keitaro Yamashita
Sent: Monday, April 16, 2012 7:09 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] bulk solvent treatment inside protein cavities

Dear Garib,

Is there REFMAC option to output solvent mask information (e.g. Fmask and
PHImask in mtz to check with Coot)?

I tried to generate it by subtracting (FC, PHIC) from (FC_ALL,PHIC_ALL).
But I'm not sure that FC_ALL = FC + FMASK is correct or not.

Keitaro


2012/4/16 Garib N Murshudov :
> Dear Allister
>
> Could you please update refmac version. In the version you it seems 
> that bulk solvent mask calculation has some problems. New version (at 
> the moment) can be downloaded from this site:
>
> http://www.ysbl.york.ac.uk/refmac/data/refmac_experimental/refmac5.7_l
> inux.tar.gz
>
> There is a mac version also.
>
>
> regards
> Garib
>
>
> On 16 Apr 2012, at 11:37, Allister Crow wrote:
>
>
> Board members,
>
> I have a couple of questions regarding how to improve the solvent 
> model as applied to solvent-filled cavities inside proteins.
>
> I am currently nearing the end of refinement of a protein structure at 
> 2.8 A resolution.  I recently switched Refmac versions, upon doing 
> this I noticed a modest improvement in R factors, but I also notice 
> some new features in the difference maps.  These features don't show 
> up in the sigma-weighted 2Fo-Fc maps and are unlikely to be 'ligands' 
> of any form.  In fact, I suspect that the appearance of these features 
> (which are all located in solvent channels within cavities inside the 
> protein) are probably due to some difference in how the bulk solvent
contribution has been applied.
>
> I've attached a picture of one such feature showing the difference 
> between Refmac 5.5 and 5.6.  (Both difference maps are contoured at 3 
> sigma- both using the same model and refinement parameters).
>
> My questions are therefore:
>
> 1) has something substantial changed in the bulk solvent treatment 
> between Refmac versions 5.5 and 5.6?
>
> 2) How can I go about changing the bulk solvent treatment to better 
> account for solvent contribution inside the protein cavities?
>
> Best wishes, and thanks in advance for all your help,
>
> - Allister Crow
>
>
> 
>
>
>
> Dr Garib N Murshudov
> Group Leader, MRC Laboratory of Molecular Biology Hills Road Cambridge
> CB2 0QH UK
> Email: ga...@mrc-lmb.cam.ac.uk
> Web http://www.mrc-lmb.cam.ac.uk
>
>
>
>

Re: [ccp4bb] iMosflm version 1.0.6 & Mosflm version 7.0.8

[Jacob Keller]

Where can one find a discussion of the differences between Aimless and
Scala?

JPK

On Mon, Apr 16, 2012 at 8:28 AM, Harry Powell wrote:

> Dear all
>
> We are pleased to announce the public release of new versions of iMosflm
> and Mosflm. We have addressed many bugs and performance issues, and also
> tidied things up in some of the tasks.
>
> If you are using a previous version we strongly recommend that you upgrade.
>
> In brief -
>
>Improved processing for Pilatus images (both 6M and 2M)
>Faster processing for large datasets in iMosflm
>More reliability in indexing, refinement & integration
>Better feedback
>Easier multi-crystal strategy
>
> Available from our website -
>
>http://www.mrc-lmb.cam.ac.uk/harry/mosflm
>
> ==
>
> In more detail  (see
> http://www.mrc-lmb.cam.ac.uk/harry/mosflm/ver708/Release_notes for more) -
>
> Mosflm
> ==
> Non-Bragg spots (eg zingers and hot pixels) and ice spots are now
> automatically removed when forming the standard profiles.
>
> Improvements in mosaicity estimation and refinement.
>
> Improvements in standard deviation estimates.
>
> Improved spot finding parameters for in-house diffraction images
> and for the very small spots that can be obtained from room
> temperature (in situ screening) crystals.
>
> More robust integration of images with very small spot separation.
>
> iMosflm
> ==
> The colour of the predicted reflections can be changed to improve
> visibility on weak diffraction images.
>
> Improved selection of the correct indexing solution in cases of
> pseudosymmetry.
>
> Scaling and merging now performed with AIMLESS rather than SCALA.
> Release Notes for iMosflm version 1.0.6
>
> New features
> 
>
> The speed of the interface has been much improved when processing a
> large number of images in the Integration pane. The largest speed-up
> came from not refreshing the profile displays afresh with every new
> image integrated.
>
> A greatly improved multi-crystal strategy option is available that
> makes it much simpler to calculate a data collection strategy when
> multiple crystals or multiple segments from one crystal are required
> (see below, and also see the new iMosflm tutorial for details).
>
> Bad spots identified during processing and whose numbers are plotted
> during integration can now be displayed in the Image display window.
>
> New mosaicity estimation will produce successive plots up to 8 degrees
> if required.
>
> Space group validation has been improved wherever a symbol can also be
> typed in editable, pull-down lists (Indexing and Strategy panes).
>
> The multi-sector, pull-down sectors list used in the Integration pane
> has been adopted in the Indexing and Cell refinement panes.
>
> Initial detector and crystal parameters are saved before refinement
> and checked that they have not refined to unreasonable values. Users
> may accept the warnings (& reset the parameters) or ignore them.
>
> New items added to the Advanced integration tab of Processing options
> includes provision for outliers affected by ice rings.
>
> The maximum number of images in an integration block has been
> increased from 20 to 200.
>
> The FindHKL function has been placed within the Image display
> window's toolbar.
>
> Smaller rotation increments have been added to the Rotation: setting
> in the Auto-complete menu in the Strategy pane.
>
> The editable 'pie' widget displayed at the bottom of the Strategy pane
> for any sector can now be adjusted in single degree steps (previously
> only 5 degree changes were possible).
>
> Individual images can now be deleted from the Images pane by selecting
> them (left-click) and then right-clicking on the selected image. This
> was previously only available for complete sectors.
>
> Scala has been replaced by Aimless as the default scaling program used
> by the QuickScale command button. Scala can be chosen from the
> "Processing options->Advanced integration" tab under the Pointless &
> Aimless/Scala switches.
>
> Files containing lists of spots can be read into iMosflm and displayed
> on the appropriate image. Files can be read from the main Session menu
> item 'Read spots file...' and from the 'Read spots file...' button
> (with an open file icon) next to the 'Index' button in the
> Autoindexing pane.
>
>
> Harry
> --
> Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills
> Road, Cambridge, CB2 0QH
>



-- 
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
***

Re: [ccp4bb] bulk solvent treatment inside protein cavities

[Garib N Murshudov]

A follow up:

In the new version there is FC_ALL_LS, PHIC_ALL_LS

That should be FC_ALL_LS = FC + FMASK. 

I have not tried but if you can use vector difference map then it should be: 
FMASK = FC_ALL_LS - FC

But it is after scaling. If you write out mask map then it is just 0 1 map (0 
inside protein and 1 outside), except values are not 0 1 but 0 and some constant



Regards
Garib


On 16 Apr 2012, at 15:09, Keitaro Yamashita wrote:

> Dear Garib,
> 
> Is there REFMAC option to output solvent mask information (e.g. Fmask
> and PHImask in mtz to check with Coot)?
> 
> I tried to generate it by subtracting (FC, PHIC) from (FC_ALL,PHIC_ALL).
> But I'm not sure that FC_ALL = FC + FMASK is correct or not.
> 
> Keitaro
> 
> 
> 2012/4/16 Garib N Murshudov :
>> Dear Allister
>> 
>> Could you please update refmac version. In the version you it seems that
>> bulk solvent mask calculation has some problems. New version (at the moment)
>> can be downloaded from this site:
>> 
>> http://www.ysbl.york.ac.uk/refmac/data/refmac_experimental/refmac5.7_linux.tar.gz
>> 
>> There is a mac version also.
>> 
>> 
>> regards
>> Garib
>> 
>> 
>> On 16 Apr 2012, at 11:37, Allister Crow wrote:
>> 
>> 
>> Board members,
>> 
>> I have a couple of questions regarding how to improve the solvent model as
>> applied to solvent-filled cavities inside proteins.
>> 
>> I am currently nearing the end of refinement of a protein structure at 2.8 A
>> resolution.  I recently switched Refmac versions, upon doing this I noticed
>> a modest improvement in R factors, but I also notice some new features in
>> the difference maps.  These features don't show up in the sigma-weighted
>> 2Fo-Fc maps and are unlikely to be 'ligands' of any form.  In fact, I
>> suspect that the appearance of these features (which are all located in
>> solvent channels within cavities inside the protein) are probably due to
>> some difference in how the bulk solvent contribution has been applied.
>> 
>> I've attached a picture of one such feature showing the difference between
>> Refmac 5.5 and 5.6.  (Both difference maps are contoured at 3 sigma- both
>> using the same model and refinement parameters).
>> 
>> My questions are therefore:
>> 
>> 1) has something substantial changed in the bulk solvent treatment between
>> Refmac versions 5.5 and 5.6?
>> 
>> 2) How can I go about changing the bulk solvent treatment to better account
>> for solvent contribution inside the protein cavities?
>> 
>> Best wishes, and thanks in advance for all your help,
>> 
>> - Allister Crow
>> 
>> 
>> 
>> 
>> 
>> 
>> Dr Garib N Murshudov
>> Group Leader, MRC Laboratory of Molecular Biology
>> Hills Road
>> Cambridge
>> CB2 0QH UK
>> Email: ga...@mrc-lmb.cam.ac.uk
>> Web http://www.mrc-lmb.cam.ac.uk
>> 
>> 
>> 
>> 

Dr Garib N Murshudov
Group Leader, MRC Laboratory of Molecular Biology
Hills Road 
Cambridge 
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk 
Web http://www.mrc-lmb.cam.ac.uk

Re: [ccp4bb] bulk solvent treatment inside protein cavities

[Garib N Murshudov]

Yes there is. If you use command line (it is not available on the ccp4i yet).

If you run with command lines

refmac5  mskout  < Dear Garib,
> 
> Is there REFMAC option to output solvent mask information (e.g. Fmask
> and PHImask in mtz to check with Coot)?
> 
> I tried to generate it by subtracting (FC, PHIC) from (FC_ALL,PHIC_ALL).
> But I'm not sure that FC_ALL = FC + FMASK is correct or not.
> 
> Keitaro
> 
> 
> 2012/4/16 Garib N Murshudov :
>> Dear Allister
>> 
>> Could you please update refmac version. In the version you it seems that
>> bulk solvent mask calculation has some problems. New version (at the moment)
>> can be downloaded from this site:
>> 
>> http://www.ysbl.york.ac.uk/refmac/data/refmac_experimental/refmac5.7_linux.tar.gz
>> 
>> There is a mac version also.
>> 
>> 
>> regards
>> Garib
>> 
>> 
>> On 16 Apr 2012, at 11:37, Allister Crow wrote:
>> 
>> 
>> Board members,
>> 
>> I have a couple of questions regarding how to improve the solvent model as
>> applied to solvent-filled cavities inside proteins.
>> 
>> I am currently nearing the end of refinement of a protein structure at 2.8 A
>> resolution.  I recently switched Refmac versions, upon doing this I noticed
>> a modest improvement in R factors, but I also notice some new features in
>> the difference maps.  These features don't show up in the sigma-weighted
>> 2Fo-Fc maps and are unlikely to be 'ligands' of any form.  In fact, I
>> suspect that the appearance of these features (which are all located in
>> solvent channels within cavities inside the protein) are probably due to
>> some difference in how the bulk solvent contribution has been applied.
>> 
>> I've attached a picture of one such feature showing the difference between
>> Refmac 5.5 and 5.6.  (Both difference maps are contoured at 3 sigma- both
>> using the same model and refinement parameters).
>> 
>> My questions are therefore:
>> 
>> 1) has something substantial changed in the bulk solvent treatment between
>> Refmac versions 5.5 and 5.6?
>> 
>> 2) How can I go about changing the bulk solvent treatment to better account
>> for solvent contribution inside the protein cavities?
>> 
>> Best wishes, and thanks in advance for all your help,
>> 
>> - Allister Crow
>> 
>> 
>> 
>> 
>> 
>> 
>> Dr Garib N Murshudov
>> Group Leader, MRC Laboratory of Molecular Biology
>> Hills Road
>> Cambridge
>> CB2 0QH UK
>> Email: ga...@mrc-lmb.cam.ac.uk
>> Web http://www.mrc-lmb.cam.ac.uk
>> 
>> 
>> 
>> 

Dr Garib N Murshudov
Group Leader, MRC Laboratory of Molecular Biology
Hills Road 
Cambridge 
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk 
Web http://www.mrc-lmb.cam.ac.uk

Re: [ccp4bb] bulk solvent treatment inside protein cavities

[Keitaro Yamashita]

Dear Garib,

Is there REFMAC option to output solvent mask information (e.g. Fmask
and PHImask in mtz to check with Coot)?

I tried to generate it by subtracting (FC, PHIC) from (FC_ALL,PHIC_ALL).
But I'm not sure that FC_ALL = FC + FMASK is correct or not.

Keitaro


2012/4/16 Garib N Murshudov :
> Dear Allister
>
> Could you please update refmac version. In the version you it seems that
> bulk solvent mask calculation has some problems. New version (at the moment)
> can be downloaded from this site:
>
> http://www.ysbl.york.ac.uk/refmac/data/refmac_experimental/refmac5.7_linux.tar.gz
>
> There is a mac version also.
>
>
> regards
> Garib
>
>
> On 16 Apr 2012, at 11:37, Allister Crow wrote:
>
>
> Board members,
>
> I have a couple of questions regarding how to improve the solvent model as
> applied to solvent-filled cavities inside proteins.
>
> I am currently nearing the end of refinement of a protein structure at 2.8 A
> resolution.  I recently switched Refmac versions, upon doing this I noticed
> a modest improvement in R factors, but I also notice some new features in
> the difference maps.  These features don't show up in the sigma-weighted
> 2Fo-Fc maps and are unlikely to be 'ligands' of any form.  In fact, I
> suspect that the appearance of these features (which are all located in
> solvent channels within cavities inside the protein) are probably due to
> some difference in how the bulk solvent contribution has been applied.
>
> I've attached a picture of one such feature showing the difference between
> Refmac 5.5 and 5.6.  (Both difference maps are contoured at 3 sigma- both
> using the same model and refinement parameters).
>
> My questions are therefore:
>
> 1) has something substantial changed in the bulk solvent treatment between
> Refmac versions 5.5 and 5.6?
>
> 2) How can I go about changing the bulk solvent treatment to better account
> for solvent contribution inside the protein cavities?
>
> Best wishes, and thanks in advance for all your help,
>
> - Allister Crow
>
>
> 
>
>
>
> Dr Garib N Murshudov
> Group Leader, MRC Laboratory of Molecular Biology
> Hills Road
> Cambridge
> CB2 0QH UK
> Email: ga...@mrc-lmb.cam.ac.uk
> Web http://www.mrc-lmb.cam.ac.uk
>
>
>
>

Re: [ccp4bb] Real Space Refine Zone for Ligand

[Paul Emsley]

On 16/04/12 03:52, Dipankar Manna wrote:


Dear Crystallographers,

After one round of refinement (restrained refinement) with ligand, I 
inport the .cif file through '->Import CIF Dictionary' into Coot. But 
when I am going for '->Real Space Refine Zone' for the ligand, its 
showing "Refinement set up failure. Failed to find restrained for: 
LIG". Please suggest.






If you are not using refmac-like restraints and not using pre-release 
Coot then this can happen :-( (my oversight).  The work-around is to 
stop, and on restarting, first read in your LIG dictionary then read in 
the rest of the files.


Fixed in 0.7-pre (and will be in 0.7+ of course).

Cheers,

Paul.

Re: [ccp4bb] Off-topic-Cleavage with TEV protease

[Florian Brückner]

I have used 5 mM beta-Mercaptoethanol, which is a weaker reducing agent than 
DTT, and that keeps TEV happy as well.

Cheers

Florian

Am 16.04.2012 um 09:31 schrieb Theresa Hsu:

> Dear all
> 
> I want to digest a tagged protein with TEV protease, it has disulfide 
> bridges. Is there any way of doing cleavage without DTT?
> 
> Thank you.
> 
> Theresa

-

Dr. Florian Brückner
Biomolecular Research Laboratory
OFLG/102
Paul Scherrer Institut
CH-5232 Villigen PSI
Switzerland

Tel.:   +41-(0)56-310-2332
Email:  florian.brueck...@psi.ch

[ccp4bb] iMosflm version 1.0.6 & Mosflm version 7.0.8

[Harry Powell]

Dear all

We are pleased to announce the public release of new versions of iMosflm and 
Mosflm. We have addressed many bugs and performance issues, and also tidied 
things up in some of the tasks.

If you are using a previous version we strongly recommend that you upgrade.

In brief - 

Improved processing for Pilatus images (both 6M and 2M) 
Faster processing for large datasets in iMosflm
More reliability in indexing, refinement & integration
Better feedback
Easier multi-crystal strategy

Available from our website - 

http://www.mrc-lmb.cam.ac.uk/harry/mosflm

==

In more detail  (see 
http://www.mrc-lmb.cam.ac.uk/harry/mosflm/ver708/Release_notes for more) - 

Mosflm
==
Non-Bragg spots (eg zingers and hot pixels) and ice spots are now 
automatically removed when forming the standard profiles.

Improvements in mosaicity estimation and refinement.

Improvements in standard deviation estimates.

Improved spot finding parameters for in-house diffraction images 
and for the very small spots that can be obtained from room 
temperature (in situ screening) crystals.

More robust integration of images with very small spot separation.

iMosflm
==
The colour of the predicted reflections can be changed to improve 
visibility on weak diffraction images.

Improved selection of the correct indexing solution in cases of 
pseudosymmetry.

Scaling and merging now performed with AIMLESS rather than SCALA.
Release Notes for iMosflm version 1.0.6

New features


The speed of the interface has been much improved when processing a
large number of images in the Integration pane. The largest speed-up
came from not refreshing the profile displays afresh with every new
image integrated.

A greatly improved multi-crystal strategy option is available that
makes it much simpler to calculate a data collection strategy when
multiple crystals or multiple segments from one crystal are required 
(see below, and also see the new iMosflm tutorial for details).

Bad spots identified during processing and whose numbers are plotted
during integration can now be displayed in the Image display window.

New mosaicity estimation will produce successive plots up to 8 degrees
if required.  

Space group validation has been improved wherever a symbol can also be
typed in editable, pull-down lists (Indexing and Strategy panes).

The multi-sector, pull-down sectors list used in the Integration pane
has been adopted in the Indexing and Cell refinement panes.

Initial detector and crystal parameters are saved before refinement
and checked that they have not refined to unreasonable values. Users
may accept the warnings (& reset the parameters) or ignore them.

New items added to the Advanced integration tab of Processing options
includes provision for outliers affected by ice rings.

The maximum number of images in an integration block has been
increased from 20 to 200.  

The FindHKL function has been placed within the Image display
window's toolbar.

Smaller rotation increments have been added to the Rotation: setting
in the Auto-complete menu in the Strategy pane.

The editable 'pie' widget displayed at the bottom of the Strategy pane
for any sector can now be adjusted in single degree steps (previously
only 5 degree changes were possible).  

Individual images can now be deleted from the Images pane by selecting
them (left-click) and then right-clicking on the selected image. This
was previously only available for complete sectors.

Scala has been replaced by Aimless as the default scaling program used
by the QuickScale command button. Scala can be chosen from the
"Processing options->Advanced integration" tab under the Pointless &
Aimless/Scala switches.

Files containing lists of spots can be read into iMosflm and displayed
on the appropriate image. Files can be read from the main Session menu
item 'Read spots file...' and from the 'Read spots file...' button
(with an open file icon) next to the 'Index' button in the
Autoindexing pane.


Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, 
Cambridge, CB2 0QH

Re: [ccp4bb] bulk solvent treatment inside protein cavities

[Eleanor Dodson]

Oh dear - this is the version of Refmac in the latest ccp4 release - can
this be updated on the web site as soon as possible ?
Eleanor

On 16 April 2012 12:02, Garib N Murshudov  wrote:

> Dear Allister
>
> Could you please update refmac version. In the version you it seems that
> bulk solvent mask calculation has some problems. New version (at the
> moment) can be downloaded from this site:
>
> http://www.ysbl.york.ac.uk/refmac/data/refmac_experimental/
> refmac5.7_linux.tar.gz
>
> There is a mac version also.
>
>
> regards
> Garib
>
>
> On 16 Apr 2012, at 11:37, Allister Crow wrote:
>
>
> Board members,
>
> I have a couple of questions regarding how to improve the solvent model as
> applied to solvent-filled cavities inside proteins.
>
> I am currently nearing the end of refinement of a protein structure at 2.8
> A resolution.  I recently switched Refmac versions, upon doing this I
> noticed a modest improvement in R factors, but I also notice some new
> features in the difference maps.  These features don't show up in the
> sigma-weighted 2Fo-Fc maps and are unlikely to be 'ligands' of any form.
>  In fact, I suspect that the appearance of these features (which are all
> located in solvent channels within cavities inside the protein) are
> probably due to some difference in how the bulk solvent contribution has
> been applied.
>
> I've attached a picture of one such feature showing the difference between
> Refmac 5.5 and 5.6.  (Both difference maps are contoured at 3 sigma- both
> using the same model and refinement parameters).
>
> My questions are therefore:
>
> 1) has something substantial changed in the bulk solvent treatment between
> Refmac versions 5.5 and 5.6?
>
> 2) How can I go about changing the bulk solvent treatment to better
> account for solvent contribution inside the protein cavities?
>
> Best wishes, and thanks in advance for all your help,
>
> - Allister Crow
>
>
> 
>
>
>
> Dr Garib N Murshudov
> Group Leader, MRC Laboratory of Molecular Biology
> Hills Road
> Cambridge
> CB2 0QH UK
> Email: ga...@mrc-lmb.cam.ac.uk 
> Web http://www.mrc-lmb.cam.ac.uk
>
>
>
>
>

Re: [ccp4bb] bulk solvent treatment inside protein cavities

[Garib N Murshudov]

Dear Allister

Could you please update refmac version. In the version you it seems that bulk 
solvent mask calculation has some problems. New version (at the moment) can be 
downloaded from this site:

http://www.ysbl.york.ac.uk/refmac/data/refmac_experimental/refmac5.7_linux.tar.gz

There is a mac version also.


regards
Garib


On 16 Apr 2012, at 11:37, Allister Crow wrote:

> 
> Board members,
> 
> I have a couple of questions regarding how to improve the solvent model as 
> applied to solvent-filled cavities inside proteins.
> 
> I am currently nearing the end of refinement of a protein structure at 2.8 A 
> resolution.  I recently switched Refmac versions, upon doing this I noticed a 
> modest improvement in R factors, but I also notice some new features in the 
> difference maps.  These features don't show up in the sigma-weighted 2Fo-Fc 
> maps and are unlikely to be 'ligands' of any form.  In fact, I suspect that 
> the appearance of these features (which are all located in solvent channels 
> within cavities inside the protein) are probably due to some difference in 
> how the bulk solvent contribution has been applied.
> 
> I've attached a picture of one such feature showing the difference between 
> Refmac 5.5 and 5.6.  (Both difference maps are contoured at 3 sigma- both 
> using the same model and refinement parameters).
> 
> My questions are therefore:
> 
> 1) has something substantial changed in the bulk solvent treatment between 
> Refmac versions 5.5 and 5.6?
> 
> 2) How can I go about changing the bulk solvent treatment to better account 
> for solvent contribution inside the protein cavities?
> 
> Best wishes, and thanks in advance for all your help,
> 
> - Allister Crow
> 
> 
> 
> 
> 

Dr Garib N Murshudov
Group Leader, MRC Laboratory of Molecular Biology
Hills Road 
Cambridge 
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk 
Web http://www.mrc-lmb.cam.ac.uk

[ccp4bb] sodium vs water near

[chandan kishore]

--- On Mon, 24/1/11, Eleanor Dodson  wrote:

From: Eleanor Dodson 
Subject: Re: [ccp4bb] Merging statistics and systematic absences
To: CCP4BB@JISCMAIL.AC.UK
Date: Monday, 24 Jan

Re: [ccp4bb] Off-topic-Cleavage with TEV protease

[Dima Klenchin]

I want to digest a tagged protein with TEV protease, it has disulfide 
bridges. Is there any way of doing cleavage without DTT?


Yes, no problem. TEV is slowly inactivated oxidation of the active site 
cysteine but that's about it. If you absolutely must have no reducer during 
cleavage, simply up the amount of the enzyme. But it's almost certain that 
most proteins with S-S bridges will be perfectly happy at low reducer 
concentration (0.2 mM TCEP, 1 mM DTT or something along these lines; 
particularly if there is more than one bridge - mass action is a powerful 
thing and, e.g., IgG has no problem at 10 mM DTT). So I wouldn't worry 
about it - just add enough TEV under conditions that make your protein happy.


Dima

Re: [ccp4bb] Off-topic-Cleavage with TEV protease

[Tim Gruene]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Theresa,

I was not aware you need DTT for TEV protease activity. People do
on-column digestion, and as far as I remember, a Ni-column would turn
really uglily brown of you used DTT on those columns.

Have you tried to leave out DTT and the cleavage did not work?

Cheers,
Tim

On 04/16/12 09:31, Theresa Hsu wrote:
> Dear all
> 
> I want to digest a tagged protein with TEV protease, it has
> disulfide bridges. Is there any way of doing cleavage without DTT?
> 
> Thank you.
> 
> Theresa
> 

- -- 
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

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[ccp4bb] Off-topic-Cleavage with TEV protease

[Theresa Hsu]

Dear all

I want to digest a tagged protein with TEV protease, it has disulfide bridges. 
Is there any way of doing cleavage without DTT?

Thank you.

Theresa

Re: [ccp4bb] Real Space Refine Zone for Ligand

[jens Preben Morth]

Hi Dipankar
you need to pit a unique identifier for each of your ligands,
eg
phenix.elbow --smiles=cyclopiazonic_acid.smi --id=CZA --output=cza --opt

best Preben

On 4/16/12 4:52 AM, Dipankar Manna wrote:


Dear Crystallographers,

After one round of refinement (restrained refinement) with ligand, I 
inport the .cif file through '->Import CIF Dictionary' into Coot. But 
when I am going for '->Real Space Refine Zone' for the ligand, its 
showing "Refinement set up failure. Failed to find restrained for: 
LIG". Please suggest.


Thanks and Regards,

Dipankar




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