Re: [ccp4bb] Staining Crystals with comassie

2013-10-16 Thread Danilo Belviso

Dear All,

izit dye is a solution containing methylene blue that you could prepare 
in your lab. I usually prepare a solution of 0.05%w/v of dye in water 
and then I add a volume of dye solution equals to 10% of the volume of 
the drop containing the crystal to test. I prefer to add the dye 
solution in small portions (if the volume permits) every 2-3h in order 
to limit the shock due to the new solution on the crystal. You should 
remember that this test is not definitive: the dye is a cationic dye, 
that needs of anion counter part to bind the protein. Therefore, the dye 
is not able to colour all protein crystals: in addition, colouration is 
affect by pH of the crystallization condition, since low pH could 
increase the positive charge on the protein reducing its ability to bind 
the dye.


You could try also glutaraldehyde as alternative. In order to perform 
this test, you should put the crystal into a low ionic strength buffered 
solution containing up to 2% glutaraldehyde. In this condition, 
formation of Schiff bases with the lysines and N-term residues occurs 
and the crystal become a yellow gel, while salt crystals dissolve and 
should not be coloured.


To perform comassie crystal staining you should prepare a solution of 
1% comassie in 40% MeOH and 10% Glacial Acetic Acid and add this 
solution as in methylene blue test. However, I rarely use this test 
because the use of MeOH and Glacial Acetic Acid causes the crystal 
dissolution.


Only a final tip: obviously these tests enable you to distinguish 
between protein and salt, however they do not differentiate between 
protein in the crystal and protein in solution. For these reason, in 
some cases could be difficult to see the crystal colouration due to the 
low contrast with the colouration of the solution. Hence, I prefer to 
put the crystals to test in a new solution with the same formulation of 
the drop where the crystals have grown but without protein and perform 
here the dye test that I have chosen. In this way, you can easily see 
the colouration of the crystal without background effect.


I hope I've helped you.

Danilo





On Tue, 15 Oct 2013 13:29:20 +0530, Swastik Phulera 
swastik.phul...@gmail.com wrote:

Dear All,
I am looking for a method to quickly differentiate between salt and
protein crystals. I have been told  thats its a popular alternative
to the commercially available izit dye. I would appreciate if some 
one

would share their comassie crystal staining protocol.

Swastik


Re: [ccp4bb] Staining Crystals with comassie

2013-10-16 Thread Danilo Belviso

Dear Swastik,

izit dye is a solution containing methylene blue that you could prepare 
in your lab. I usually prepare a solution of 0.05%w/v of dye in water 
and then I add a volume of dye solution equals to 10% of the volume of 
the drop containing the crystal to test. I prefer to add the dye 
solution in small portions (if the volume permits) every 2-3h in order 
to limit the shock due to the new solution on the crystal. You should 
remember that this test is not definitive: the dye is a cationic dye, 
that needs of anion counter part to bind the protein. Therefore, the dye 
is not able to colour all protein crystals: in addition, colouration is 
affect by pH of the crystallization condition, since low pH could 
increase the positive charge on the protein reducing its ability to bind 
the dye.


You could try also glutaraldehyde as alternative. In order to perform 
this test, you should put the crystal into a low ionic strength buffered 
solution containing up to 2% glutaraldehyde. In this condition, 
formation of Schiff bases with the lysines and N-term residues occurs 
and the crystal become a yellow gel, while salt crystals dissolve and 
should not be coloured.


To perform comassie crystal staining you should prepare a solution of 
1% comassie in 40% MeOH and 10% Glacial Acetic Acid and add this 
solution as in methylene blue test. However, I rarely use this test 
because the use of MeOH and Glacial Acetic Acid causes the crystal 
dissolution.


Only a final tip: obviously these tests enable you to distinguish 
between protein and salt, however they do not differentiate between 
protein in the crystal and protein in solution. For these reason, in 
some cases could be difficult to see the crystal colouration due to the 
low contrast with the colouration of the solution. Hence, I prefer to 
put the crystals to test in a new solution with the same formulation of 
the drop where the crystals have grown but without protein and perform 
here the dye test that I have chosen. In this way, you can easily see 
the colouration of the crystal without background effect.


I hope I've helped you.

Danilo





On Tue, 15 Oct 2013 13:29:20 +0530, Swastik Phulera 
swastik.phul...@gmail.com wrote:

Dear All,
I am looking for a method to quickly differentiate between salt and
protein crystals. I have been told  thats its a popular alternative
to the commercially available izit dye. I would appreciate if some 
one

would share their comassie crystal staining protocol.

Swastik


Re: [ccp4bb] A case of perfect pseudomerehedral twinning?

2013-10-16 Thread Randy Read
Hi,

It's not uncommon for pseudosymmetry to be found together with twinning, and 
the presence of pseudosymmetry perturbs the statistics used to test for 
twinning.   In that circumstance, as Phil suggests, a really good way to see 
what is going on is to take the lower symmetry solution and see if it really 
obeys higher symmetry, but you can do that either with coordinates or 
calculated structure factors.

Your NCS matrix specifies a 2-fold rotation around an axis that is about 1 
degree off the x axis.  Whether that 1 degree matters or not depends on how 
precisely the molecules are placed in the MR solution.  If 30.8649 is precisely 
half of the a-cell edge, then this corresponds to a 2(1) screw axis, but 
whether or not that is crystallographic depends on whether the origin of that 
axis is in the right place relative to the 2(1) you're assuming is correct.  
Working all that out from coordinates can be a bit of a challenge, which will 
really have you hitting the books!

The other way we've approached this kind of problem is to take the Fcalcs from 
an MR model (usually solved in P1 if possible to avoid making any assumptions 
about which symmetry operators are correct) and then use either pointless or 
xtriage to see if those Fcalcs obey higher symmetry.  Another good approach is 
to use the zanuda program in the CCP4 suite, which is designed to answer 
questions about pseudosymmetry and other related problems.

Good luck!

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 RoadE-mail: 
rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.   
www-structmed.cimr.cam.ac.uk

On 15 Oct 2013, at 22:31, Yarrow Madrona amadr...@uci.edu wrote:

 Thank you Dale,
 
 I will hit-the-books to better the rotation matrices. I am concluding
 from all of this that the space group is indeed P212121. So I still wonder
 why I have some outliers in the intensity stats for the two additional
 screw axis and why R and Rfree both drop by 5% when I apply a twin law to
 refinement in P21.
 
 Thanks for your help.
 
 -Yarrow
 
 
   Since Phil is no doubt in bed, I'll answer the easier part.  Your
 second matrix is nearly the equivalent position (x,-y,-z).  This
 is a two-fold rotation about the x axis.  You also have a translation
 of about 31 A along x so if your A cell edge is about 62 A you have
 a 2_1 screw.
 
 Dale Tronrud
 
 On 10/15/2013 12:29 PM, Yarrow Madrona wrote:
 Hi Phil,
 
 Thanks for your help.
 
 I ran a Find-NCS routine in the phenix package. It came up with what I
 pasted below:
 I am assuming the the first rotation matrix is just the identity. I need
 to read more to understand rotation matrices but I think the second one
 should have only a single -1 to account for a possible perfect 2(1)
 screw
 axis between the two subunits in the P21 asymetric unit. I am not sure
 why
 there are two -1 values. I may be way off in my interpretation in which
 case I will go read some more. I will also try what you suggested.
 Thanks.
 
 -Yarrow
 
 NCS operator using PDB
 
 #1 new_operator
 rota_matrix1.0.0.
 rota_matrix0.1.0.
 rota_matrix0.0.1.
 tran_orth 0.0.0.
 
 center_orth   17.72011.4604   71.4860
 RMSD = 0
 (Is this the identity?)
 
 #2 new_operator
 
 rota_matrix0.9994   -0.02590.0250
 rota_matrix   -0.0260   -0.99970.0018
 rota_matrix0.0249   -0.0025   -0.9997
 tran_orth   -30.8649  -11.9694  166.9271
 Hello Yarrow,
 
 Since you have a refined molecular replacement solution I recommend
 using that rather than global intensity statistics.
 
 Obviously if you solve in P21 and it's really P212121 you should have
 twice the number of molecules in the asymmetric unit and one half of
 the
 P21 asymmetric unit should be identical to the other half.
 
 Since you've got decent resolution I think you can determine the real
 situation for yourself: one approach would be to test to see if you can
 symmetrize the P21 asymmetric unit so that the two halves are
 identical.
  You could do this via stiff NCS restraints (cartesian would be better
 than dihedral).  After all the relative XYZs and even B-factors would
 be
 more or less identical if you've rescaled a P212121 crystal form in
 P21.
  If something violates the NCS than it can't really be P212121.
 
 Alternatively you can look for clear/obvious symmetry breaking between
 the two halves: different side-chain rotamers for surface side-chains
 for example.  If you've got an ordered, systematic, difference in
 electron density between the two halves of the asymmetric unit in P21
 then that's a basis for describing it as P21 rather than P212121.
 However if the two halves look nearly identical, down to equivalent
 

[ccp4bb] Deadline 20th October: Open Group Leader position at Grenoble Outstation of EMBL

2013-10-16 Thread Stephen Cusack

Deadline of 20th October is approaching !

Dear All,
The Grenoble Outstation of the European Molecular Biology Laboratory
is seeking to recruit a Group Leader in Structural Biology of Complexes.
   The appointed Group Leader will be an ambitious structural biologist
with an original multidisciplinary research programme oriented towards
structure-function relationships of macromolecular complexes in
eukaryotic systems. Particular, but not exclusive, areas of interest are
host-pathogen interactions, RNA biology or computational
biology/modelling. He/she will benefit from the world-class environment
of the EMBL Grenoble Outstation within the Partnership for Structural
Biology (www.psb-grenoble.eu) which gives access to integrated
state-of-the-art structural biology technologies, including ESRF
synchrotron X-ray beamlines for MX and SAXS, cryo-EM/tomography and NMR
as well as protein expression screening, insect cell, biophysics,
confocal microscopy and high-throughput crystallization platforms.

Applicants should have a Ph.D. and at least 3 years post-doctoral
experience and a strong record of achievement in structural, molecular
or cell biology.

Further information about research at EMBL Grenoble can be found on
http://www.embl.fr/index.php

Further information about the position can be found on
http://www.embl.fr/aboutus/jobs/searchjobs/index.php?loc=4list=1

Stephen Cusack


Re: [ccp4bb] Staining Crystals with comassie

2013-10-16 Thread Zhijie Li

Hi Danilo and all,

A little trick for the glutaraldehyde staining: you can hang a 1-2uL drop 
of 25% glutaraldehyde (or the most concentrated stock solution you can find) 
besides your crystal drop in the vapour diffusion chamber. The 
glutaraldehyde will get into the crystal drop via vapour diffusion. The 
color will normally show within 2hrs and become very intense overnight. It 
is also a gentle way of crosslinking the crystals 
(http://scripts.iucr.org/cgi-bin/paper?wb0066, and 
http://hamptonresearch.com/tip_detail.aspx?id=74, ).
Care should be taken when handling aldehyde concentrates: do not breathe 
it, and do not let the vapour get in touch with your eyes. Waste can be 
inactivated by concentrated glycine solution.


BTW, the acetic acid in the coommasie blue solution seems unnecessary in a 
crystal staining solution. The solution recipe seems to be taken from a gel 
staining solution. When staining polyacrylamide gels, the acid (oringinally 
HCl) is supposed to denature the proteins so that they do not diffuse in the 
gel. The MeOH is for solubilizing the commonly used coommassie R250. 
(Another thing: I strongly suggest to substitute the MeOH in PAGE staining 
and de-staining solutions with EtOH. EtOH works perfectly fine, without 
MeOH's poisonous effect on human. Our staining solution contains 20% EtOH 
and 20%HAc.)
For staining crystals, we do not need to add the acetic acid. Also 
coommassie G250 is more soluble in water than the R250 by having methyl 
groups instead of ethyl groups. 0.5% coommassie G250 can be readily made in 
DMSO or 95% EtOH. Then this stock solution can be diluted with water or the 
mother liquor 10x-100x for the staining. Many crystals can tolerate up to 
10% DMSO.


Zhijie



-Original Message- 
From: Danilo Belviso

Sent: Wednesday, October 16, 2013 3:53 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Staining Crystals with comassie

Dear All,

izit dye is a solution containing methylene blue that you could prepare
in your lab. I usually prepare a solution of 0.05%w/v of dye in water
and then I add a volume of dye solution equals to 10% of the volume of
the drop containing the crystal to test. I prefer to add the dye
solution in small portions (if the volume permits) every 2-3h in order
to limit the shock due to the new solution on the crystal. You should
remember that this test is not definitive: the dye is a cationic dye,
that needs of anion counter part to bind the protein. Therefore, the dye
is not able to colour all protein crystals: in addition, colouration is
affect by pH of the crystallization condition, since low pH could
increase the positive charge on the protein reducing its ability to bind
the dye.

You could try also glutaraldehyde as alternative. In order to perform
this test, you should put the crystal into a low ionic strength buffered
solution containing up to 2% glutaraldehyde. In this condition,
formation of Schiff bases with the lysines and N-term residues occurs
and the crystal become a yellow gel, while salt crystals dissolve and
should not be coloured.

To perform comassie crystal staining you should prepare a solution of
1% comassie in 40% MeOH and 10% Glacial Acetic Acid and add this
solution as in methylene blue test. However, I rarely use this test
because the use of MeOH and Glacial Acetic Acid causes the crystal
dissolution.

Only a final tip: obviously these tests enable you to distinguish
between protein and salt, however they do not differentiate between
protein in the crystal and protein in solution. For these reason, in
some cases could be difficult to see the crystal colouration due to the
low contrast with the colouration of the solution. Hence, I prefer to
put the crystals to test in a new solution with the same formulation of
the drop where the crystals have grown but without protein and perform
here the dye test that I have chosen. In this way, you can easily see
the colouration of the crystal without background effect.

I hope I've helped you.

Danilo





On Tue, 15 Oct 2013 13:29:20 +0530, Swastik Phulera
swastik.phul...@gmail.com wrote:

Dear All,
I am looking for a method to quickly differentiate between salt and
protein crystals. I have been told  thats its a popular alternative
to the commercially available izit dye. I would appreciate if some one
would share their comassie crystal staining protocol.

Swastik 


Re: [ccp4bb] Staining Crystals with comassie

2013-10-16 Thread R. M. Garavito

There are many caveats to using glutaraldehyde on crystals, either for fixing 
crystals or for staining them. 

First, I would not hang a 1-2uL drop of 25% glutaraldehyde in the vapour 
diffusion chamber, but add enough glutaraldehyde into the reservoir to make it 
0.5-1.0 % (a 1:25 or 1:50 dilution;  a 1% solution is 100 mM).  Not only will 
it be just as effective, the reservoir becomes the control: if the reservoir 
turns yellow, you have free amines in the system (Tris, ammonium, etc.).  

Second, the yellow color, which is due to Schiff's base formation, is harder to 
see in warm light (color temperature, not the temperature of the stage) when 
you are looking at small or thin crystals.  Use cool, white lights (like LEDs). 

Finally, keeps some buffer around that is suitable for solubilizing the 
protein.  If you are not sure about the color change, just add 10 uL of buffer 
to the crystals and watch if they dissolve.  If they don't when treated with 
glutaraldehyde, they are protein crystals.

As Zhijie said, be careful with handling glutaraldehyde.  It is highly volatile 
and dangerous.  If you smell it (and the sweet smell will be obvious), it is 
fixing you.  Keep a waste bottle half-full with 1 M ammonium sulfate, not 
glycine (too expensive), then just dump any glutaraldehyde waste into it.

Cheers,

Michael


R. Michael Garavito, Ph.D.
Professor of Biochemistry  Molecular Biology
603 Wilson Rd., Rm. 513   
Michigan State University  
East Lansing, MI 48824-1319
Office:  (517) 355-9724 Lab:  (517) 353-9125
FAX:  (517) 353-9334Email:  rmgarav...@gmail.com





On Oct 16, 2013, at 6:45 AM, Zhijie Li wrote:

 Hi Danilo and all,
 
 A little trick for the glutaraldehyde staining: you can hang a 1-2uL drop 
 of 25% glutaraldehyde (or the most concentrated stock solution you can find) 
 besides your crystal drop in the vapour diffusion chamber. The glutaraldehyde 
 will get into the crystal drop via vapour diffusion. The color will normally 
 show within 2hrs and become very intense overnight. It is also a gentle way 
 of crosslinking the crystals (http://scripts.iucr.org/cgi-bin/paper?wb0066, 
 and http://hamptonresearch.com/tip_detail.aspx?id=74, ).
 Care should be taken when handling aldehyde concentrates: do not breathe 
 it, and do not let the vapour get in touch with your eyes. Waste can be 
 inactivated by concentrated glycine solution.
 
 BTW, the acetic acid in the coommasie blue solution seems unnecessary in a 
 crystal staining solution. The solution recipe seems to be taken from a gel 
 staining solution. When staining polyacrylamide gels, the acid (oringinally 
 HCl) is supposed to denature the proteins so that they do not diffuse in the 
 gel. The MeOH is for solubilizing the commonly used coommassie R250. (Another 
 thing: I strongly suggest to substitute the MeOH in PAGE staining and 
 de-staining solutions with EtOH. EtOH works perfectly fine, without MeOH's 
 poisonous effect on human. Our staining solution contains 20% EtOH and 
 20%HAc.)
 For staining crystals, we do not need to add the acetic acid. Also coommassie 
 G250 is more soluble in water than the R250 by having methyl groups instead 
 of ethyl groups. 0.5% coommassie G250 can be readily made in DMSO or 95% 
 EtOH. Then this stock solution can be diluted with water or the mother liquor 
 10x-100x for the staining. Many crystals can tolerate up to 10% DMSO.
 
 Zhijie
 
 
 
 -Original Message- From: Danilo Belviso
 Sent: Wednesday, October 16, 2013 3:53 AM
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: Re: [ccp4bb] Staining Crystals with comassie
 
 Dear All,
 
 izit dye is a solution containing methylene blue that you could prepare
 in your lab. I usually prepare a solution of 0.05%w/v of dye in water
 and then I add a volume of dye solution equals to 10% of the volume of
 the drop containing the crystal to test. I prefer to add the dye
 solution in small portions (if the volume permits) every 2-3h in order
 to limit the shock due to the new solution on the crystal. You should
 remember that this test is not definitive: the dye is a cationic dye,
 that needs of anion counter part to bind the protein. Therefore, the dye
 is not able to colour all protein crystals: in addition, colouration is
 affect by pH of the crystallization condition, since low pH could
 increase the positive charge on the protein reducing its ability to bind
 the dye.
 
 You could try also glutaraldehyde as alternative. In order to perform
 this test, you should put the crystal into a low ionic strength buffered
 solution containing up to 2% glutaraldehyde. In this condition,
 formation of Schiff bases with the lysines and N-term residues occurs
 and the crystal become a yellow gel, while salt crystals dissolve and
 should not be coloured.
 
 To perform comassie crystal staining you should prepare a solution 

[ccp4bb] CCP4 Release 6.4.0 follow-up

2013-10-16 Thread Eugene Krissinel
Dear CCP4 users,

It has been reported to us shortly after 6.4.0 release last week, that the 
software was dysfunctional for some users. The reason was found to be the clash 
between Qt framework distributed with CCP4 6.4.0 and the one installed locally. 
This problem is now fixed, and new CCP4 distribution packages are available 
from our web-site:

http://www.ccp4.ac.uk/download/

In order to identify whether your CCP4 setup is affected by the bug, please 
check if any of the symptoms below applies:

- ccp4i shows permanently Network off? in low-right corner
- greyed, dysfunctional Manage Updates button in ccp4i
- even if Manage Updates button is functional, CCP4 updater does not start
- QtRView result viewer does not start
- other Qt-based applications, such as qtpisa and viewhkl, do not start or do 
not work properly

If you find your setup affected by the bug, or have any doubts, we advise you 
to re-install 6.4.0 now.

CCP4 setups with working updater will be synchronised with today's changes 
through the corresponding update soon. 

CCP4 Core Group apologises for any inconvenience and would like to encourage 
all users to report any problems with CCP4 software that they have encountered.

Sincerely yours,

Eugene Krissinel


-- 
Scanned by iCritical.



Re: [ccp4bb] A case of perfect pseudomerehedral twinning?

2013-10-16 Thread Yarrow Madrona
Thanks Randy,

The a cell edge is 56.118, so not exactly half of 30.86. I am currently
refining using NCS cartesian restraints as Phil suggested. Then I will
visually inspect the model as well as compare b-factors. Thanks for your
suggestions, I will look into them.

-Yarrow

 Hi,

 It's not uncommon for pseudosymmetry to be found together with twinning,
 and the presence of pseudosymmetry perturbs the statistics used to test
 for twinning.   In that circumstance, as Phil suggests, a really good way
 to see what is going on is to take the lower symmetry solution and see if
 it really obeys higher symmetry, but you can do that either with
 coordinates or calculated structure factors.

 Your NCS matrix specifies a 2-fold rotation around an axis that is about 1
 degree off the x axis.  Whether that 1 degree matters or not depends on
 how precisely the molecules are placed in the MR solution.  If 30.8649 is
 precisely half of the a-cell edge, then this corresponds to a 2(1) screw
 axis, but whether or not that is crystallographic depends on whether the
 origin of that axis is in the right place relative to the 2(1) you're
 assuming is correct.  Working all that out from coordinates can be a bit
 of a challenge, which will really have you hitting the books!

 The other way we've approached this kind of problem is to take the Fcalcs
 from an MR model (usually solved in P1 if possible to avoid making any
 assumptions about which symmetry operators are correct) and then use
 either pointless or xtriage to see if those Fcalcs obey higher symmetry.
 Another good approach is to use the zanuda program in the CCP4 suite,
 which is designed to answer questions about pseudosymmetry and other
 related problems.

 Good luck!

 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 15 Oct 2013, at 22:31, Yarrow Madrona amadr...@uci.edu wrote:

 Thank you Dale,

 I will hit-the-books to better the rotation matrices. I am concluding
 from all of this that the space group is indeed P212121. So I still
 wonder
 why I have some outliers in the intensity stats for the two additional
 screw axis and why R and Rfree both drop by 5% when I apply a twin law
 to
 refinement in P21.

 Thanks for your help.

 -Yarrow


   Since Phil is no doubt in bed, I'll answer the easier part.  Your
 second matrix is nearly the equivalent position (x,-y,-z).  This
 is a two-fold rotation about the x axis.  You also have a translation
 of about 31 A along x so if your A cell edge is about 62 A you have
 a 2_1 screw.

 Dale Tronrud

 On 10/15/2013 12:29 PM, Yarrow Madrona wrote:
 Hi Phil,

 Thanks for your help.

 I ran a Find-NCS routine in the phenix package. It came up with what
 I
 pasted below:
 I am assuming the the first rotation matrix is just the identity. I
 need
 to read more to understand rotation matrices but I think the second
 one
 should have only a single -1 to account for a possible perfect 2(1)
 screw
 axis between the two subunits in the P21 asymetric unit. I am not sure
 why
 there are two -1 values. I may be way off in my interpretation in
 which
 case I will go read some more. I will also try what you suggested.
 Thanks.

 -Yarrow

 NCS operator using PDB

 #1 new_operator
 rota_matrix1.0.0.
 rota_matrix0.1.0.
 rota_matrix0.0.1.
 tran_orth 0.0.0.

 center_orth   17.72011.4604   71.4860
 RMSD = 0
 (Is this the identity?)

 #2 new_operator

 rota_matrix0.9994   -0.02590.0250
 rota_matrix   -0.0260   -0.99970.0018
 rota_matrix0.0249   -0.0025   -0.9997
 tran_orth   -30.8649  -11.9694  166.9271
 Hello Yarrow,

 Since you have a refined molecular replacement solution I recommend
 using that rather than global intensity statistics.

 Obviously if you solve in P21 and it's really P212121 you should have
 twice the number of molecules in the asymmetric unit and one half of
 the
 P21 asymmetric unit should be identical to the other half.

 Since you've got decent resolution I think you can determine the real
 situation for yourself: one approach would be to test to see if you
 can
 symmetrize the P21 asymmetric unit so that the two halves are
 identical.
  You could do this via stiff NCS restraints (cartesian would be
 better
 than dihedral).  After all the relative XYZs and even B-factors would
 be
 more or less identical if you've rescaled a P212121 crystal form in
 P21.
  If something violates the NCS than it can't really be P212121.

 Alternatively you can look for clear/obvious symmetry breaking
 between
 the two halves: different side-chain rotamers for surface side-chains
 for example.  If you've got an ordered, systematic, difference in
 electron 

[ccp4bb] DNA interaction 2D plot software

2013-10-16 Thread Eike Schulz
Hello everyone, 

I would like to display the interactions of a protein dsDNA complex in a
simplified 2D plot, similar to what LIGPLOT does for protein ligand
interactions. In many articles you find interactions displayed in such a way
but as far as I know those are hand-made. In my experience LIGPLOT itself
is suboptimal if there are too many interactions to display Š

Thanks a lot in advance for your suggestions.

Eike






Re: [ccp4bb] DNA interaction 2D plot software

2013-10-16 Thread Nicolas Foos

Hello,
you can try Nucplot. http://www.ebi.ac.uk/thornton-srv/software/NUCPLOT/

Very usefull and tunnable to find and show dsDNA/protein complex.

Hope to help.

Nicolas

Le 16/10/13 21:23, Eike Schulz a écrit :

Hello everyone,

I would like to display the interactions of a protein dsDNA complex in 
a simplified 2D plot, similar to what LIGPLOT does for protein ligand 
interactions. In many articles you find interactions displayed in such 
a way but as far as I know those are hand-made. In my experience 
LIGPLOT itself is suboptimal if there are too many interactions to 
display …


Thanks a lot in advance for your suggestions.

Eike




[ccp4bb] Problems with key bindings in coot0.7.2 CCP4 install

2013-10-16 Thread Bernhard Lechtenberg
Hi all,

I recently installed CCP4 6.4 under Mac OS X 10.8.5 and now have problems using 
key bindings in the Coot version (0.7.2) that comes with CCP4. Although most of 
the standard key bindings still work, some of them (e.g. 'o' for other NCS 
chain) and most of the user-defined key bindings do not work. The key bindings 
file seems to be correctly loaded by Coot and the correct keys are listed in 
'Extensions - Settings - Key bindings' and the linked functions work when I 
click on the buttons in that list. The terminal shows the following message 
when I hit one of the keys that are not working:

(skip-to-next-ncs-chain 'forward)
((safe_scheme_command) Error in proc: key:  unbound-variable  args:  (#f 
Unbound variable: ~S (skip-to-next-ncs-chain) #f))

Everything works correctly in a separately installed Coot v0.7.1 with the same 
.coot.py file.

Any suggestions on what the problem might be?

Thanks for the help

Bernhard



Bernhard C. Lechtenberg, PhD
Postdoctoral Fellow
Riedl Lab
Sanford-Burnham Medical Research Institute
10901 North Torrey Pines Road
La Jolla, CA 92037, USA
Phone: 858.646.3100 x 4216
Email: blechtenb...@sanfordburnham.orgmailto:blechtenb...@sanfordburnham.org