Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

On 12/16/10 03:06, Ian Tickle wrote: > Dale > >> The reward of the >> full calculation is that all the complications you describe disappear. >> An atom that sits 0.001 A from a special position is not unstable >> in the least. > > That's indeed a very interesting observation, I have to admit that

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

On Thu, Dec 16, 2010 at 1:18 PM, wrote: > Of course there is no dicontinuity, but you create one the moment you decide > that certain symmetry operators no longer apply to certain atoms. Change 'atoms' in that statement to 'reflections', or to 'map grid points', then read it again. Does the (-

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

Ooops sorry that's only the executable, I guess to have to contact David for the source. -- Ian On Thu, Dec 16, 2010 at 1:14 PM, Jon Wright wrote: > On 16/12/2010 12:24, Ian Tickle wrote: >>> >>> I think this is how the Oxford CRYSTALS software ( >>> http://www.xtl.ox.ac.uk/crystals.html ), whic

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

, Herman -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Ian Tickle Sent: Thursday, December 16, 2010 1:31 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms > You still have an arbitrary thresh

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

Hi Jon, try this: http://www.xtl.ox.ac.uk/download.html -- Ian On Thu, Dec 16, 2010 at 1:14 PM, Jon Wright wrote: > On 16/12/2010 12:24, Ian Tickle wrote: >>> >>> I think this is how the Oxford CRYSTALS software ( >>> http://www.xtl.ox.ac.uk/crystals.html ), which has been around for at >>> lea

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

On 16/12/2010 12:24, Ian Tickle wrote: I think this is how the Oxford CRYSTALS software ( http://www.xtl.ox.ac.uk/crystals.html ), which has been around for at least 30 years, deals with this issue, so I can't accept that it can't be made to work, even if I haven't got all the precise details str

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

> You still have an arbitrary threshold: at high resolution you see two > disordered atoms off-axis and at low resolution you see one ordered atom > on-axis. However, somewhere in between you or the program has to decide > whether you still see two atoms or if the data (resolution) does not warr

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

Ian Tickle Sent: Wednesday, December 15, 2010 6:57 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms That's my whole point, it's not an arbitrary threshold, it's determined completely by what the data are capable of telling you about

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

Or you could write and ask the author, who is always willing to help (sorry, David!)... On 16 Dec 2010, at 11:24, Ian Tickle wrote: >> I think this is how the Oxford CRYSTALS software ( >> http://www.xtl.ox.ac.uk/crystals.html ), which has been around for at >> least 30 years, deals with this is

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

> I think this is how the Oxford CRYSTALS software ( > http://www.xtl.ox.ac.uk/crystals.html ), which has been around for at > least 30 years, deals with this issue, so I can't accept that it can't > be made to work, even if I haven't got all the precise details > straight of how it's done in pract

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

Dale > The reward of the > full calculation is that all the complications you describe disappear. > An atom that sits 0.001 A from a special position is not unstable > in the least. That's indeed a very interesting observation, I have to admit that I didn't think that would be achievable. But th

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

cule suddenly becomes >> > special and the occupancy is set to 1.0. So depending on rounding errors, >> > different thresholds etc. different programs may make different decisions >> > on whether a water is special or not. >> > >> > For me, this is confusing.

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

. >> >> For me, this is confusing. >> >> Best regards, >> Herman >> >> -Original Message- >> From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Ian >> Tickle >> Sent: Wednesday, December 15, 2010 3:47 PM >>

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

ions on whether > > a water is special or not. > > > > For me, this is confusing. > > > > Best regards, > > Herman > > > > -Original Message- > > From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Ian > > Tickle &

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

fferent decisions on whether a water is special or not. > > For me, this is confusing. > > Best regards, > Herman > > -Original Message- > From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Ian > Tickle > Sent: Wednesday, December 15, 2010 3:47

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

...@jiscmail.ac.uk] On Behalf Of Ian Tickle Sent: Wednesday, December 15, 2010 3:47 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms Dear George I notice that the Oxford CRYSTALS program, which is what I used when I did small-molecule crystallography

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

Dear George I notice that the Oxford CRYSTALS program, which is what I used when I did small-molecule crystallography and which is still quite popular among the small-molecule people (maybe not as much as Shel-X!), uses the CIF convention: OCC= This parameter defines the site occupancy EXCLUDING

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

Dear Ian, Yes. Once an atom has been identified as on a special position because it is within a specied tolerance, SHELXL applies the appropriate contraints to both the coordinates and the Uij so there is no danger of the atom wandering off the special position. Usually, when an atom it very cl

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

Dear George I would say that an atom has fractional occupancy (but unit multiplicity) unless it's exactly on the special position (though I can foresee problems with rounding of decimal places for an atom say at x=1/3), so that effectively once the atom is fixed exactly on the s.p. the symmetry co

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

Dear Ian, Of course I could convert the occupancy on reading the atom in and convert it back agains on reading it out. This is not quite so trivial as it sounds because I need to set a threshold as to how close the atom has to be to a special position to be treated as special, and take care t

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

Dear George Is applying the multiplicity factor to the occupancy internally in the program such a issue anyway? It need only be done once per atom on input (i.e. you multiply each input occupancy by the multiplicity to get the combined multiplicity*occupancy value that you would have reading in d

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

>   Personally I find it disturbing to have the occupancy of "B  31" > set to 0.33 and that of "D  31" set to 1.00 simply because of an > insignificant shift in the position of the atom. > > Dale Tronrud H2O on or near a 3-fold must be disordered because obviously H2O only has 2-fold symmetry. It

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

uld call this a Wyckoff position, but side chains of proteins do sit on top of crystallographic symmetry axes. Best, Herman -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Ralf W. Grosse-Kunstleve Sent: Thursday, December 09, 2010 3:47 AM To: CCP4

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

> > No disorder is involved. > > > > The occupancy of an (fully occupied) atom on an n-fold rotation axis is > 1/n > > If a two-fold, 1/2 > > If a three-fold, 1/3 > > > > When you sum over all the atoms in the unit cell, application of the > symmetry operations to atoms lying on the rotation axis g

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

SHELXL also expects that the occupancy of a fully occupied atom on a threefold axis should be set at 1/3, and will generate this automatically if necessary. It will also generate automatically the necessary constraints for the x, y and z parameters (and for the Uij if the atom is anisotropic). I

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

ckle Date: Saturday, December 11, 2010 0:41 Subject: Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms To: CCP4BB@JISCMAIL.AC.UK > No that surely can't be right.  Application of a symmetry > operator to > a point on a special position which is unchanged by the operator > do

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

On Fri, 2010-12-10 at 22:40 +, Ian Tickle wrote: > Application of a symmetry operator to > a point on a special position which is unchanged by the operator > doesn't generate a symmetry copy of the point, because there is no > symmetry copy of such a point! Why not? Symmetry-related copy may

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

On Fri, 2010-12-10 at 21:53 +, Ian Tickle wrote: > Hmmm - but shouldn't the occupancy of the Zn be 1.00 if it's on the > special position Shouldn't 1/3 be better for programming purposes? If you set occupancy to 1.0, then you should specify that symmetry operators do not apply for these atom

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

No that surely can't be right. Application of a symmetry operator to a point on a special position which is unchanged by the operator doesn't generate a symmetry copy of the point, because there is no symmetry copy of such a point! For general Wyckoff positions it does, for sure. If you look at

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

The proper occupancy for an atom on a special position depends on how one defines the meaning of the number in that column. In the past, refinement programs, at least I know mine did, simply expanded all atoms in the coordinate file by the symmetry operators to determine the contents of the uni

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

Good point Colin! 2-Zn insulin is of course a classic example of this, where the two independent Zn2+ ions both sit on the crystallographic 3-fold in R3. It doesn't matter whether you count the metal ion as part of the protein or not: if I understand Gloria's original question correctly, all that

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

Colin Nave wrote: .. Also Acta Cryst. (2002). D58, 29-38 "The 2.6 Å resolution structure of Rhodobacter capsulatus bacterioferritin with metal-free dinuclear site and heme iron in a crystallographic `special position' "D. Cobessi, L.-S. Huang, M. Ban, N. G. Pon, F. Daldal and E. A. Berry ( h

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

Does one regard the metal atom in a metalloprotein as being part of the protein? If so, a shared metal could occupy a special position in a dimer for example. In Acta Cryst. (2008). D64, 257-263 "Metals in proteins: correlation between the metal-ion type, coordination number and the amino-acid

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

: Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms The forces acting on an atom at a special position must have the same symmetry on average as the special position, so the atom will be in equilibrium, and there will at first sight be no net force (i.e. zero energy gradient) to push

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

positions. > > Best, > Herman > > -Original Message- > From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of > Ian Tickle > Sent: Thursday, December 09, 2010 3:35 PM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

onal cases will occupy "true" Wyckoff positions. Best, Herman -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Ian Tickle Sent: Thursday, December 09, 2010 3:35 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positio

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

> cases out there (and so far I have heard of a disulfide bond on a > 2-fold connecting two homodimers). I'm slightly puzzled by this example. If the S-S bond is on the special position, then the rest of the molecule can't have 2-fold symmetry, so would have to be rotationally disordered with occ

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

y axes. > > Best, > Herman > > -Original Message- > From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of > Ralf W. Grosse-Kunstleve > Sent: Thursday, December 09, 2010 3:47 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff pos

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

] On Behalf Of Ralf W. Grosse-Kunstleve Sent: Thursday, December 09, 2010 3:47 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms Hi Gloria, My hobby is space group symmetry. My interest phenix development. > so I can't imagine a protein crys

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

that it isn't important to handle them in a special way. So Wyckoff positions remain foreign in the macromolecular context. Ralf - Original Message > From: Gloria Borgstahl > To: CCP4BB@JISCMAIL.AC.UK > Sent: Wed, December 8, 2010 12:16:54 PM > Subject: [ccp4bb] Fw

[ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

I've gotten some interesting responses, that I will summarize for the group later, but I thought I should clarify why I asked. I was worrying about this because I have been working out the steps in how to determine the (3+1)D superspace group for a protein crystal. The last step listed in IT vol C

[ccp4bb] [Fwd: Re: [ccp4bb] Space group and R/Rfree value]

Original Message Subject:Re: [ccp4bb] Space group and R/Rfree value Date: Wed, 01 Dec 2010 09:44:06 -0700 From: Maia Cherney To: Xiaopeng Hu References: <643947201.129232.1291191478190.javamail.r...@zmbx0.sysu.edu.cn> A dimer could be with a symmetry-relate

[ccp4bb] [Fwd: Re: [ccp4bb] Graphics for notebook]

--- Begin Message --- Kay Diederichs wrote: "" Datum: Sun, 14 Nov 2010 21:37:10 + Dear all, Thanks for your suggestions. From what I learned new GPUs from NVIDIA are using the Optimus technology which does not support Linux, meaning that only the dedicated graphics on the system will be

[ccp4bb] Fwd: [ccp4bb] tlsanl *NOW ALSO REFMAC* and phenix TLS results

On Thu, Oct 21, 2010 at 11:42 AM, Ian Tickle wrote: > There are a number of things that don't look right here, both with the > Refmac and the Phenix runs: [...] interesting, thanks for these comments. > S should not have been symmetrized to actually display the principal axes in molscript, i me

Re: [ccp4bb] Fwd: [ccp4bb] Fill map/mask with dummy atoms?

Doesnt arp/warp start with doing something like this? If you gave a 0/1 mask I wonder what the first build would look like.. You would have to invent a "reflection" file for the map ... E On 10/13/2010 12:49 PM, Dirk Kostrewa wrote: ... maybe, to clarifiy my question a little bit: I want to f

[ccp4bb] Fwd: [ccp4bb] Fill map/mask with dummy atoms?

... maybe, to clarifiy my question a little bit: I want to fill an essentially flat cryo-EM-map with dummy atoms. So, a peak search doesn't work. I would need a program that fills this map with dummy atoms for a few things that I want to try with this "atomic" representation. Best regards, D

[ccp4bb] Fwd: [ccp4bb] Summary: measure detergent concentration

Hi Folks, The paper Phil recommended looks very nice. Below is a summary when last time I asked people about this. Regards, Weikai Original Message Subject: [ccp4bb] Summary: measure detergent concentration Date: Wed, 28 Oct 2009 16:49:32 -0400 From: wei...@crystal.harvard

[ccp4bb] [Fwd: [ccp4bb] Permanent X-ray Lab Manager Post London UK]

There is just over a week left to apply for this X-Ray Lab Manager job in central London. Best wishes Nick -- Prof Nicholas H. Keep Executive Dean of School of Science Professor of Biomolecular Science Crystallography, Institute for Structural and Molecular Biology, Department of Biological Scie

Re: [ccp4bb] Fwd: [ccp4bb] XSCALE

Another very nice script to run and collect statistics from XDS is xdsme from Pierre Legrand http://code.google.com/p/xdsme/ Daniel Le 05/08/2010 16:55, Jovine Luca a écrit : WRT the redundancy, I am afraid you have to recompute an approximate value yourself using the number of observation

[ccp4bb] Fwd: [ccp4bb] XSCALE (II)

Apologies for the repetition, but only the first link: http://cc.oulu.fi/~pkursula/xdsi.html is for the xdspub program that produces the output I attached. The other one has the same name, but does something else! Luca

[ccp4bb] Fwd: [ccp4bb] XSCALE

> WRT the redundancy, I am afraid you have to recompute an approximate value > yourself using the number of observations and number of unique reflections > (this is what I do all the time). I suppose one could always write a jiffy > program to compute the correct values using both files INTEGRA

[ccp4bb] Fwd: molecule name from pdb id and chain identifier

Apologies if this has been posted already but I couldn't see it yet! Hi, Sorry for the off topic question! I'm looking at Dali search results and find the molecule names are not always the same as the ones for the chain identifier from the pdb entry (maybe the molecule names are always of chain

[ccp4bb] Fwd: postdocs

Prof. Gebhard Schertler Head of Biology and Chemistry Biomolecular Research Laboratory Paul Scherrer Institute Anfang der weitergeleiteten E-Mail: Von: Daniel Oprian Datum: 8. Juli 2010 17:16:43 MESZ An: gebhard schertler Betreff: postdocs Dear Gebhard, I am writing to find out if you

[ccp4bb] Fwd: [ccp4bb] error in running Phaser NMA mode

Forgot to also post this response to the BB. Randy Begin forwarded message: > From: Randy Read > Date: 25 June 2010 12:59:12 GMT+01:00 > To: Yong Y Wang > Subject: Re: [ccp4bb] error in running Phaser NMA mode > > Dear Yong, > > Sorry about that! I suspect the example script in the document

[ccp4bb] Fwd: Re: [ccp4bb] creating new ligand cif file

Received from Peter Zwart: Original Message Subject:Re: [ccp4bb] creating new ligand cif file Date: Mon, 21 Jun 2010 07:08:18 -0700 From: Peter Zwart To: Vellieux Frederic References: <4c1f4f26.2070...@ibs.fr> it is the same format actually. 2010/6/21 V

[ccp4bb] Fwd: Referee report for Nature Reviews Molecular Cell Biology almost due

This very rapid reply to my withdrawal as a reviewer for NPG journals contains a response issued last night purporting to clarify issues obfuscated by the UC Digital Library in their letter. They claim that the data cited by the UCDL are misleading. I can neither verify or refute this claim. Wha

Re: [ccp4bb] Fwd: creating a metal plane model to fit a protein.

Well - try the coordinate utility recommended by Martyn Winn to convert cif to pdb coord_format xyzin ./1ivo.cif xyzout 1ivo.pdb

[ccp4bb] Fwd: creating a metal plane model to fit a protein.

Dear all, I have a coordinates CIF file of an interested metal from "CRYSTMET Toth Materials Toolkit" with the atoms coordinates. I want to create a metal plane according to the cell symmetry of the metal and to convert the coordinates so it be used in a pdb format file for exploring the protein fi

Re: [ccp4bb] Fwd: calculate the real space R factor using OVERLAPMAP

On Tue, May 25, 2010 at 6:58 AM, Pavel Afonine wrote: > Yes, because all the information you need is encapsulated in 1 number > per region of interest! > > I agree it's a good reason. Actually what I described doesn't quite achieve this, because you need to keep a record of both the RMSD Z-score

Re: [ccp4bb] Fwd: calculate the real space R factor using OVERLAPMAP

On Tue, May 25, 2010 at 6:22 AM, Frank von Delft wrote: > Hi Ian, I read with great interest.  But got stumped here: > >>> - how you compute sigma(rho)? >> >> See my reply to George Sheldrick's post. >> > > I think your reply did not make it out to the BB, certainly neither to my > inbox nor to th

Re: [ccp4bb] Fwd: calculate the real space R factor using OVERLAPMAP

Hi Ian, thanks for very detailed reply! - do you think it is better than looking at three values {map CC, 2mFo-DFc, mFo-DFc} and why? Yes, because all the information you need is encapsulated in 1 number per region of interest! I agree it's a good reason. But I don't understand wha

Re: [ccp4bb] Fwd: calculate the real space R factor using OVERLAPMAP

Hi Pavel Phew! Lots of questions - this could take a while: > - where this formula come from and what are the grounds for this? It's just the RMSD of the density divided by its standard uncertainty (sigma), which we're assuming is the same for all grid points: this isn't quite true, sigma is hi

Re: [ccp4bb] [Fwd: Is it possible for the Tris buffer to strip the Zn ions from the Zinc Finger motif of a protein?]

sometimes change in ph also dissocaites the complex,so you need to screen best buffer ph for your protein complex. atul kumar On Sun, May 23, 2010 at 8:18 PM, Maia Cherney wrote: > Original Message > Subject:Is it possible for the Tris buffer to strip the Zn ions > fro

Re: [ccp4bb] Fwd: calculate the real space R factor using OVERLAPMAP

Hi Ian, On 5/23/10 5:01 AM, Ian Tickle wrote: Thanks a lot! Actually my map has very weak density at only certain region, and I want to numerically say that this region is "weakly" correlated to the atomic map at this region. But according to the CC formula, if investigating by residue, CC only

[ccp4bb] [Fwd: Is it possible for the Tris buffer to strip the Zn ions from the Zinc Finger motif of a protein?]

Original Message Subject: Is it possible for the Tris buffer to strip the Zn ions from the Zinc Finger motif of a protein? Date: Sun, 23 May 2010 08:45:55 -0600 From: Maia Cherney To: ruheng The complex can dissociate without loosing Zn. For example, if you dilut

Re: [ccp4bb] Fwd: calculate the real space R factor using OVERLAPMAP

On Sun, May 23, 2010 at 5:24 AM, Pavel Afonine wrote: > Hi, > > > On 5/22/10 8:23 PM, Zhang, Hailiang wrote: >> >> Thanks a lot! Actually my map has very weak density at only certain >> region, and I want to numerically say that this region is "weakly" >> correlated to the atomic map at this regio

Re: [ccp4bb] Fwd: calculate the real space R factor using OVERLAPMAP

Hi, On 5/22/10 8:23 PM, Zhang, Hailiang wrote: Thanks a lot! Actually my map has very weak density at only certain region, and I want to numerically say that this region is "weakly" correlated to the atomic map at this region. But according to the CC formula, if investigating by residue, CC only

Re: [ccp4bb] Fwd: calculate the real space R factor using OVERLAPMAP

Dear Nasos & Hailiang, Gerard Kleywegt's MAPMAN calculates the RSR, discussed here: http://xray.bmc.uu.se/usf/mapman_man.html#S41 Mark On 21 May 2010 23:54, Athanasios Dousis wrote: > Hello all, > > I'm forwarding a question from my labmate Hailiang Zhang reg

Re: [ccp4bb] Fwd: calculate the real space R factor using OVERLAPMAP

Hello, I was just wondering whether there is some other tools in eg CCP4, Phenix or CNS to calculate real-space R in the general way in absolute values. related to your question: in PHENIX you can get a table of map CC (computed between model and 2mFo-DFc maps), and the value of mFo-DFc a

[ccp4bb] Fwd: calculate the real space R factor using OVERLAPMAP

Hello all, I'm forwarding a question from my labmate Hailiang Zhang regarding OVERLAPMAP and real-space R factors. Thanks in advance for your suggestions. Nasos Dousis Rice University P.S. Can someone please add haili...@bcm.tmc.edu to the CCP4BB listserv? Original Message

Re: [ccp4bb] Fwd: regarding purification of DNA binding protein

Hi Arpit, You can use PEI (polyethyleneimine). Adding PEI at low conc. (e.g. 0.25%) after cell lysis should precipitate most of the DNA. Note, it is best to do the addition step-wise at 4 deg with gentle steering over a period of time 10-15 min or so. Ibrahim On 5/12/10 10:20 AM, "Tim Gr

Re: [ccp4bb] Fwd: regarding purification of DNA binding protein

Hello Arpit, don't you use DNAse during lysation of the cells? Or do you mean that you want to get rid of unspecific DNA and want to add some specific DNA after purification? In that case I'd understand you don't want to use DNAse. Tim On Wed, May 12, 2010 at 06:23:56PM +0530, Arpit Mishra wrote:

Re: [ccp4bb] Fwd: regarding purification of DNA binding protein

Dear Arpita, For Getting rid of DNA you can incubate the lysate with DNase and incubate it before lysing the cells with sonication or french press (or anyother method of your choice) cheers Rashmi On Wed, May 12, 2010 at 8:53 PM, Arpit Mishra wrote: > > > -- Forwarded message

[ccp4bb] Fwd: regarding purification of DNA binding protein

-- Forwarded message -- From: Arpit Mishra Date: Wed, May 12, 2010 at 6:20 PM Subject: regarding purification of DNA binding protein To: ccp...@jiscmail.ac hi all i am trying to purify DNA binding protein, but i couldnt get rid of the DNA after performing hi-trap heparin column,

[ccp4bb] Fwd: [ccp4bb] control of nucleation

I mistakenly sent this off to Enrico, rather than to the CCP4BB. Apologies to Enrico. Begin forwarded message: > From: "Charles W. Carter, Jr" > Date: May 6, 2010 6:50:23 AM EDT > To: est...@cea.fr > Subject: Re: [ccp4bb] control of nucleation > > In fact, there is quite good experimental evid

[ccp4bb] Fwd: Re: [ccp4bb] SUMMARY: scala and xds data

Well, there's one one very good reason to scale XDS data with scala: scala prints out per-image statistics, which are fantastically useful. My particular favourite: the scaling B-factor, which is as direct a read-out of dose (i.e. decay) as we have: 1A^2 per MGy. (Lots and lots of cave

[ccp4bb] Fwd: Biophysical specialist scientist position. Laboratory of Molecular Biology, Cambridge, UK

The Laboratory of Molecular Biology (LMB) in Cambridge, UK wishes to recruit an Investigator Scientist to support a range of collaborative projects involving biophysical methods for studying macromolecules and their interactions. The individual will also conduct workshops and informal tr

Re: [ccp4bb] Fwd: [ccp4bb] Blue color upon X-ray exposure?

@JISCMAIL.AC.UK Subject: [ccp4bb] Fwd: [ccp4bb] Blue color upon X-ray exposure? > > I have personally noticed that the blue color only appears when the pH of the > hyperquenched solution is higher than 7 or so. I assume this is because > solvated electrons react with protons to form the

[ccp4bb] Fwd: [ccp4bb] Blue color upon X-ray exposure?

> > I have personally noticed that the blue color only appears when the pH of the > hyperquenched solution is higher than 7 or so. I assume this is because > solvated electrons react with protons to form their conjugate base: the > hydrogen atom. The latter species is highly reactive as well,

[ccp4bb] Fwd: phases using XDS and SHELX after I3C magic triangle soak

Dear All, I am currently attempting to phase a protein domain target after soaking the crystal with Tobias Beck's I3C magic crystal compound, using XDS and SHELX. After XDS processing, I was able to detect 27% anomalous signal. I used ccp4 to generate an .mtz file. After attempting to convert the

[ccp4bb] Fwd: Kit Do Brasileiro

-- Mensagem encaminhada -- De: Educação Física Data: 20 de fevereiro de 2010 19:11 Assunto: Kit Do Brasileiro Para: Adriene Melo , Alysson Simões < alyssonsimo...@hotmail.com>, Arthur Araújo , ass...@hotmail.com, bulhoesmarce...@gmail.com, Caio , Cyntia Nislane , Dryelle Raíssa < d

[ccp4bb] Fwd: [ccp4bb] anomalous difference fourier maps

Begin forwarded message: From: "Charles W. Carter, Jr" Date: February 19, 2010 10:28:55 AM EST To: "George M. Sheldrick" Subject: Re: [ccp4bb] anomalous difference fourier maps I'm also inclined to join this discussion. I agree with both Gérard and George. I also sympathize with Ivan. Ove

[ccp4bb] Fwd: summer internship in structural biology

Hello, May the pouch of your Holiday Wombat overflow with presents! I would like to draw your attention to a summer internship in our lab at Monsanto. If you are an interested student, or know someone who may be interested - please apply using http://www.monsanto.com/careers/opportunities/ and t

[ccp4bb] Fwd: Postdoc Position at UCSD

Postdoc Position at UCSD: A full-time postdoctoral position is available at UC San Diego. We are looking for a highly motivated postdoctoral research fellow to join our laboratory. We are interested in structure-function studies of Protein-DNA and Protein–RNA complexes using a combination o

[ccp4bb] [Fwd: Re: [ccp4bb] off-topic: crystal optimization without buffer]

Forgot to hit the "Reply all" button (sorry :-( ) --- Begin Message --- Katja Schleider wrote: Hi everybody, sorry for my off-topic question. I got small initial crystals in 200mM NaSulfat and 20% PEG 3350. There is no buffer in this condition. How can I optimize these crystals? Just vary the

[ccp4bb] [Fwd: Re: [ccp4bb] video that explains, very simply, what Structural Molecular Biology is about]

Just thought this will be of interest to all. Subbu --- Begin Message --- Narayanan Ramasubbu wrote: Vellieux Frederic wrote: Narayanan Ramasubbu wrote: Hi: Could someone point out the name and where to get these crystallization plates used in the video? By the way, this is a wonderful vide

[ccp4bb] Fwd: Unit of electrostatic potential in PyMol

Oops.., I meant to ask a different quesition. Let me try again: I used PyMol to generate a qualitative Vacum Electrostatic surface (without APBS calculations). The potential is displayed in the range -56.3 to +56.3. Is it possible to change this scale in PyMol, if so how? Thank you, -Partha ---

[ccp4bb] Fwd: [ccp4bb] measure detergent concentration

To measure detergent concentrations in protein samples, the way that I recommend is ATR-FTIR, it is very accurate, fast (10min ) and requires as low as 10uL of protein sample. Here is the reference: · PVeesler, D. et al. Production and biophysical characterization of the CorA transport

[ccp4bb] [Fwd: Re: {Disarmed} [cnsbb] CNS installation on ubuntu]

Hi there, Would there be a kind soul that could pass this message on to cnsbb? I am registered with e-mail address velli...@ibs.fr but the e-mail address has changed to frederic.velli...@ibs.fr 12 months ago perhaps. I am not very good at all these e-mail diffusion lists and cannot see how to

[ccp4bb] [Fwd: Re: [ccp4bb] latest version of coot (having a small problem with it though)]

I pass the following comment received privately, could be of use to either the Coot developpers (Paul & Kevin) or to simple Coot users (like me). Fred. --- Begin Message --- Fred, the same thing happened to me the other day. All of a sudden, Coot simply would not do rsr complaining of lacking r

[ccp4bb] [Fwd: Re: [ccp4bb] Activation of ShelxCDE module of CCP4i(Linux OS version)]

Thanks~ Original Message Subject: Re: [ccp4bb] Activation of ShelxCDE module of CCP4i(Linux OS version) From:"Clemens Vonrhein" Date:Thu, October 15, 2009 2:24 am To: CCP4BB@JISCMAIL.AC.UK -

[ccp4bb] [Fwd: NCS in REFMAC (was Re: [ccp4bb])]

--- Begin Message --- NCS. I don't think REFMAC can handle yet NCS (help me there Garib). CNS FYI there's documentation for NCS options in REFMAC, although I haven't actually used them yet (haven't been lucky enough to have NCS in my structures). Pete --- End Message --- <>

[ccp4bb] Fwd: [ccp4bb] electron density slabs

This could be due to biscuit contamination of your protein - did you eat cake before setting up your crystallisation drops?Alternatively it could be a Fourier ripple - a very strong 5.4 Å resolution 00l reflection which is not correctPoulBegin forwarded message:From: hayato Jumonji

[ccp4bb] Fwd: IPTG

Subject: IPTG In response to your email thread discussion please also add Carbosynth (www.carbosynth.com) offering IPTG 10g $85.They are bulk producers (100kg batches)

[ccp4bb] [Fwd: [ccp4bb] CCP4 / Ubuntu 9.04 64-bit]--Coot

Thanks to all who helped with this, especially Paul Emsley, Ed Pozharski, Robert Orru, Partha Chakrabarti, and Michael Strickler. Here is a brief summary of the results: 1. It's easy to compile Coot for 64-bit Ubuntu 9.04 using the autobuild script *IF* you have all the the prerequisites. S

[ccp4bb] Fwd: [ccp4bb] structure <-> function

Begin forwarded message: From: Richard Gillilan Date: June 23, 2009 9:43:20 AM EDT To: "Nadir T. Mrabet" Subject: Re: [ccp4bb] structure <-> function A very interesting question. Stephan Jay Gould was well known for his argument that evolution is contingent on all kinds of factors (like met

Re: [ccp4bb] [Fwd: totheboard]

Sascha M. Marek wrote: Dear crystallographers! My basic question is, how can electron density maps be moved along with the respective PDB coordinates? If you have Coot, you can try Extensions -> Maps -> Transform map by LSQ model fit.

[ccp4bb] [Fwd: totheboard]

Dear crystallographers! My basic question is, how can electron density maps be moved along with the respective PDB coordinates? I would like to superimpose two structures from different space groups (P21 and P212121) along with some omit ligand density in the active center to later highlight the

[ccp4bb] Fwd: Aussie synchrotron sports sponsorship - very funny

I hope this helped our Australian friends get more funding! Ho The TV show 'Thank God You're Here' goes to the synchrotron! http://www.youtube.com/watch?v=N_zbySqumaA&feature=related

Re: [ccp4bb] Fwd: [ccp4bb] Crystal vacuum cleaner

the dewar? Jacob - Original Message - From: Patrick Loll To: CCP4BB@JISCMAIL.AC.UK Sent: Friday, March 27, 2009 8:35 AM Subject: [ccp4bb] Fwd: [ccp4bb] Crystal vacuum cleaner Pretty cool, but the examples shown are all gigantic. Having just spent a frustrating sev

<    1   2   3   4   5   6   >