Re: [ccp4bb] unidentified density

to build any peptide for my second protein. Your help is highly appreciated. regards - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG

Re: [ccp4bb] Best method for weighted averaging of Friedel pairs?

), space group P3 2 1 I+: 23841.50 sigI+: 634.01 I-: 9628.57, sigI-: 264.75 Method 1: Imean=13815.32, sigImean=186.76 Method 2: Imean=11738.95, sigIMean=244.31 Method 3: Imean=11738.95, sigIMean=7106.47 Thanks a lot! Cheers, Markus - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie

Re: [ccp4bb] DNA in coot

a structue of protein-DNA complex with coot. I add DNA by adding ideal DNA/RNA in the other model. But I cannot edit chi angle of these nucletide, neither the mutate. When I press the mutate and my DNA, coot give amino acid not nucletide. Why? Thanks Lisa - -- - -- Dr Tim Gruene

Re: [ccp4bb] Fwd: HR3699, Research Works Act

you to the petition: https://wwws.whitehouse.gov/petitions#!/petition/oppose-hr3699-research-works-act/vKMhCX9k - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU

Re: [ccp4bb] REFMAC 5.7

- -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPPRpaUxlJ7aRr7hoRAmOtAJ9myX62PYfbJ+c8hdi

Re: [ccp4bb] offtopic : Signed binaries in the next OS X

this will be the default). - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE

Re: [ccp4bb] HKL2000/3000 Error

10.5.8. Thanks in advance! Best regards, -Rajintha - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org

Re: [ccp4bb] Putting Text into Movies

be helpful for conveying some ideas... Jacob - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org

Re: [ccp4bb] about point mutation

you all the members in advance, cheers, Arun - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org

Re: [ccp4bb] Any calculation function in CCP4 to analyze coordinate file?

? --such as the total number of protein residues/water/ligand, the total atoms of protein/water/ligand, the average b-factor of protein/water/ligand, the number of residues which have alternative side chians, and so on. Thank you. King regards, Wenhe - -- - -- Dr Tim Gruene Institut fuer

Re: [ccp4bb] Desalting columns

combinations to see which buffer works. For a starting point, I'd like to use desalting colums. Does anyone have suggestions for good buffer exchange and sample recovery? I woud like to load about 250 uL onto each column. Thanks a lot! Best regards, Sangeetha. - -- - -- Dr Tim Gruene Institut

[ccp4bb] Introducing mrprep

happy to improve the program if I can. Cheers, Tim - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org

Re: [ccp4bb] Temp Fact Variance Analysis

%. Thank you for comments Ros - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org

Re: [ccp4bb] B average lower than Wilson

: Rmerge: 15.0 (51.8) I/σ(I): 7.30 (1.84) 5 monomers/AU R/Rfree: 19.7/23.3 ...ask for other infoes if you need. Any advice/suggestion is welcome!! - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE

Re: [ccp4bb] REFMAC Riding Hydrogens

or less systematic test that prove this: see On contribution of hydrogen atoms to X-ray scattering here: http://www.phenix-online.org/newsletter/ Pavel - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE

Re: [ccp4bb] setting occupancy for disordered water

in advance, Regards, ARKO - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org

Re: [ccp4bb] REFMAC Riding Hydrogens

of context: this newsletter article was written in the context of macromolecular refinement. And yes, recently may be a broad term -:) All the best, Pavel On Mon, Mar 5, 2012 at 12:45 PM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: Dear Pavel, you may want to add to the structures

Re: [ccp4bb] Restrained refinement problem

in reliance on this e-mail is strictly prohibited and may be unlawful. Visit us at http://www.aurigene.com - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux

Re: [ccp4bb] Matthews coeff. from model

coefficient from a crystallographic model of RNA-protein complex? Thanking you. James. - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG

Re: [ccp4bb] Matthews coeff. from model

Molecular Biology Division Department of Chemistry Biochemistry University of California, Los Angeles mi...@chem.ucla.edu - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (GNU/Linux

Re: [ccp4bb] How to reduce R factor

of this email or any action taken in reliance on this e-mail is strictly prohibited and may be unlawful. Visit us at http://www.aurigene.com - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version

Re: [ccp4bb] Refmac version

refmac binary? Kindly provide some suggestion. Thanking you With Regards Kavya -- This message has been scanned for viruses and dangerous content by *MailScanner* http://www.mailscanner.info/, and is believed to be clean. - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie

Re: [ccp4bb] Trying to cut the resolution of the datasets

Heslington YO10 5YW tel: 00 44 1904 328259 Fax: 00 44 1904 328266 - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http

Re: [ccp4bb] unstable refinement error in SHELXL

, and the .ins file generated from coot is good for SHELXL, but it didn't work all the time, eg. it work for the first few rounds, then there is a problem. Can you give me some suggestions about what I should do to get the SHELXL running again? Thanks, Lu - -- - -- Dr Tim Gruene Institut

Re: [ccp4bb] Defining beamstop and error during indexing- moslfm

. (it might be wrong) It will be highly appreciable if someone can please suggest if this the method we should use to define the beamstop or there is any site definition file which has to be used, as it is available for HKL2000 or how we have to define the beamstop in mosflm. - -- - -- Dr Tim

Re: [ccp4bb] Clustal omega

Institute for Biophysical Chemistry Hannover Medical School Germany. - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http

Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication]

be the radius and a the thickness of a pizza. Then the volume of that pizza is equal to pi*z*z*a ! ** - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A

Re: [ccp4bb] PEG molecule crossing a two-fold crystallographic symmetry axis

it depending on which of the two above methods you chose. Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Wed, 29 Apr 2009, Chandrika Deshpande wrote: Hello everyone, My protein crystallised in the spacegroup P6522 with one protein

[ccp4bb] Peptide on two-fold axis - was:[ccp4bb] PEG molecule crossing a two-fold crystallographic symmetry axis

closely related. In your case you can refine two peptides each with an occupancy of 0.5, one for each direction. Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Wed, 29 Apr 2009, lidefeng wrote: Hi everyone, Following

Re: [ccp4bb] phasing with se-met at low resolution

Dear Raja, FOR  HIGH ANGLE REFLECTIONS ANOMALOUS DATA BECOMES IMPORTANT.   Raja  this is the theoretical point of view. As James pointed out, in real life the intensities of reflections at high resolution becomes comparable to the noise level so that the accuracy of which the reflections

Re: [ccp4bb] phaser

to 1 in the ccp4 initialisation script AND make sure CCP4 is set up AFTER phenix 3) before starting ccp4i from a terminal, change the PATH variable manually so that $CCP4/bin comes before the phenix path Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG

Re: [ccp4bb] CCP4 compatability with other software suites

Dear Zhongren, if I remember correctly, mapman from G. Kleywegt can convert from CCP4 map format to various other formats, including CNS. Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Thu, 28 May 2009, Wu, Zhongren wrote

Re: [ccp4bb] execute problems with ccp4i

Dear Len, when you start ccp4i from the command line (a terminal), does it produce any error messages? Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Tue, 9 Jun 2009, Leonard Thomas wrote: I have ran into this problem before

Re: [ccp4bb] xds undefined data_range error

. Are you working under windows, or did you edit the XDS.INP with a windows editor? That might have placed non-unix end-of-line characters which could confuse xds. Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Wed, 10 Jun 2009

Re: [ccp4bb] Difference Map images

I know that sometimes Fo(complex)-Fo(apo) cannot be done because of nonisomorphism. We've had a lot of success with this with the dioxygenases because there is no large scale alteration in the active site. As for the technique itself, Brian Matthews drilled this into me when I was a postdoc in

Re: [ccp4bb] Difference Map images

realistic result than the MR-solution I suggested. Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Thu, 18 Jun 2009, Doug Ohlendorf wrote: Tim, Not really. Fo's can be viewed as having 3 parts. 1) F from our modeled structure, 2) F from

Re: [ccp4bb] can I try crystallization in high salt?

You may also apply salting-in: if the reservoir concentration is lower than that of the protein buffer, water may evaporate from the reservoir into the drop, lowering the protein's solubility and thus maybe grow crystals. Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D

Re: [ccp4bb] CCP4 / Ubuntu 9.04 64-bit

The 64bit version of Ubuntu should come with 32-bit versions of all libraries. These are extra packages, if you search the repositories, you should find them. -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Fri, 3 Jul 2009, Thomas J

[ccp4bb] mtz2hkl: New Version 0.3 available.

my homepage http://shelx.uni-ac.gwdg.de/~tg/mtz2x/mtz2hkl/mtz2hkl.php Tim Gruene - -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.9 (GNU/Linux) iD8DBQFKXx

Re: [ccp4bb] mosflm and hkl2000

as to what went wrong? Sincerely, Tim B.T.W.: I've seen cases where hkl2000 gets stuck, too... -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Fri, 31 Jul 2009, Marius Schmidt wrote: We have a little internal project where we want

Re: [ccp4bb] Is there Windows version of O ?

version also only has 2.5MB. You need a lot a data-files, too, if you want to enjoy the program. You get what you need from the same ftp-server. But I suggest you find someone already familiar with O to start using it. Tim   -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077

Re: [ccp4bb] cracking crystal

before going to the next concentration. This way you can check various cryo-protectants like PEG400, MPD, glycerol, sugars (fructose, sucrose)... Since you don't have to many crystal, you can use the cracked parts for this experiment, so you only have to sacrifice one or two crystals. Tim -- Tim

Re: [ccp4bb] How to improve the Se-Met crystal diffracted to 5.6A

with the native crystals? You might get better diffracting crystals. Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Fri, 4 Sep 2009, xu zhen wrote: Dear all,   I have a Se-Met crystal diffracted to 5.6A and a full data set of the same

Re: [ccp4bb] Devices Suitable to Concentrate Protein Solutions in Liter Scale

Hi, Could you not carry out Ammonium Sulfate precipitation to concentrate the protein? I never did it myself so I have no idea if it's practical in this case. Maybe it's still worth mentioning, though. Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG

Re: [ccp4bb] non-CCP4 related: HKL2MAP availabilty

You can get hkl2map through a web interface, http://webapps.embl-hamburg.de/hkl2map/hkl2map_download.php Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Thu, 10 Sep 2009, Ajit Datta wrote: Hi everyone, Sorry for a non-CCP4

Re: [ccp4bb] MSA formatting...

Hello Tommi, could you please paste one or two lines of what you've got and one or two lines of what you want. That might make the problem description a bit easier. Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Sun, 13 Sep

Re: [ccp4bb] multiple datasets in Xds

are done you can scale them together with scala, xscale, or whatever scaling program you prefer. It's worth setting REFERENCE_DATASET in XDS.INP for the low resolution data set to the XDS_ASCII.HKL from the high resolution set. That way you ensure that both are consistently indexed. Tim -- Tim

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

- better than no model at all, be it wrong or not. -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Tue, 17 Nov 2009, Morten Kjeldgaard wrote: On 17/11/2009, at 08.10, mesters wrote: Yes, but models that can be validated against

[ccp4bb] arp/warp failure on Debian testing

. The directory /tmp/tg exists and is writable on both computers. Cheers, Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A

Re: [ccp4bb] Electron density improvement with resolution graphic

You may also have a look at James Holton's page http://ucxray.berkeley.edu/~jamesh/movies/ and take a screenshot of one of his movies. Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Fri, 4 Dec 2009, Brad Bennett wrote: Hi all

Re: [ccp4bb] configuration or install issue with tk

With 'sudo' you should not have this issue. I agree, though, that having a separate user account to install crystallographic programs is quite an advantage from an administrative point of view. Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID

Re: [ccp4bb] configuration or install issue with tk

On Mon, 14 Dec 2009, Edward A. Berry wrote: Mark A. White wrote: Stuart, Are you logged-in as root or are you working in a root shell ( using su or sudo)? Depending on your security settings X-windows may not permit a program that is run from a root shell to access the display, which belongs

Re: [ccp4bb] editing phi and psi angles in coot

Hello Paul, I almost never use this tool these days. You can find out why at the study weekend :) Paul. What about those who don't attend? Tant pis? Cheers, Tim

Re: [ccp4bb] Cavity filling

If I remember correctly, arp/warp and/or phenix/resolve can do something of that kind. Did you check the documentation of these programs? Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Wed, 6 Jan 2010, Simon Kolstoe wrote

Re: [ccp4bb] Blob help

Hello Vin, have you tried fitting two glycerol molecules with complementary occupancies? Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Fri, 8 Jan 2010, Vin Purp wrote: Can a trained eye identify this blob? This is 1.65 Ang

Re: [ccp4bb] DSSP server

is perfect ;-) Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Thu, 14 Jan 2010, Jane Bailey wrote: Hello all, I am sorry for this off-topic question. I see it has been discussed many times, but somehow I got stuck in the very

[ccp4bb] arp/warp: missing 'wilsonb'

be the cause and the cure of such behaviour? Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A

Re: [ccp4bb] Molecular Replacement

with one after the other, starting from the largest one. Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Mon, 18 Jan 2010, Muhammed bashir Khan wrote: Dear All; We have solved a crystal structrure of protein at 1.8 A. I have now

[ccp4bb] coot: fit ligand

omitted. Is there a way to kindly as coot to not separate the two when trying to find a suitable home for them? Ta, Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature

Re: [ccp4bb] HKL-MTZ conversion

are not necessarily the views and opinions of The University of the Witwatersrand, Johannesburg. All agreements between the University and outsiders are subject to South African Law unless the University agrees in writing to the contrary./font/p/html -- -- Tim Gruene Institut fuer

Re: [ccp4bb] To calculate Domain-domain orientation

missed something. Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Fri, 19 Feb 2010, Jane Bailey wrote: Dear all, Problem is coming one after another. I got another question about how to calculate the domain/domain orientations (tilt

[ccp4bb] units of f0, f', f''

', and f'' is actually e (a positive charge!) and the value of f^0 of Fe at its K-edge was actually 26e or -26e - see e.g. Table 1 in http://www.ccp4.ac.uk/courses/proceedings/1997/j_smith/main.html Cheers, Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key

Re: [ccp4bb] units of f0, f', f''

Disclaimer: this answer does not involve any (mention of) CCP4 software. Mea culpa. On Fri, 26 Feb 2010, Tim Gruene wrote: Dear all, I just stumbled across the question about what is the unit of f' and f''. The first couple of hits from ixquick.com claim it was e^-. Since e

Re: [ccp4bb] Did anyone here know how to get the Rfree value of high resolution range

is not a misconception of mine. Tim On Sat, Feb 27, 2010 at 05:13:15AM +, Yuan SHANG wrote: Hi,all, I can get the R-value~resolution statistics from .lst file,but where is the Rfree value? Thanks in advance. Yuan -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen

Re: [ccp4bb] linux question

linux or ?? Any thoughts on this? Thanks Dave -- Jim Fairman, Ph D. Post-Doctoral Fellow National Institutes of Health - NIDDK Cell: 1-865-748-8672 Lab: 1-301-594-9229 E-mail: fairman@gmail.com james.fair...@nih.gov -- -- Tim Gruene Institut fuer anorganische Chemie

Re: [ccp4bb] crystallization of a macromolecular complex

will be highly appreciated. Thanks, Jan -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature

Re: [ccp4bb] Off-topic - Domain termini for construct design

you really need to Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member Department of Biochemistry (B8) Netherlands Cancer Institute, Dept. B8, 1066 CX Amsterdam, The Netherlands Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791 -- -- Tim Gruene Institut

Re: [ccp4bb] arp_warp 7.1 and CCP4 6.1.3

the refmac version is 5.5.0109. There's a conditional branch in the installation script that extracts the 0109 from this and does not like the leading zero. Solution (to be tried): re-compile refmac5 changing the version number to 5.5.109 Pedro Matias -- -- Tim Gruene Institut fuer

Re: [ccp4bb] arp/warp

? Cheers, Rafael. -- Rafael Couñago Research Fellow Department of Biochemistry University of Otago 710 Cumberland St Dunedin, New Zealand ph: (03) 479 5148 -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc

Re: [ccp4bb] Butandiol as cryopotectant

Hello Ulrike, in our lab 2,3-Butanediol has had a good reputation. Tim On Mon, Mar 22, 2010 at 01:32:33PM +, Ulrike Demmer wrote: Hi everybody, has anyone experience with Butandiol and its different isoforms as cryoprotectant ? Thanks, Ulrike -- -- Tim Gruene Institut fuer

Re: [ccp4bb] Butandiol as cryopotectant

mosaicity. I was able to switch from a three-step soaking protocol with glycerol and glucose to a quick (30 second to one minute) soak with 2,3-BD. It's a winner. Steve I Hello Ulrike, in our lab 2,3-Butanediol has had a good reputation. Tim On Mon, Mar 22... -- -- Tim

[ccp4bb] update on SeMet production

, which ones? Thanks a lot, Tim -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature

[ccp4bb] SUMMARY: update on SeMet production

expression system * in addition to E.coli, P. aeruginosa was also mentioned. Thanks to everyone who replied. Tim On Tue, Mar 23, 2010 at 01:25:56PM +0100, Tim Gruene wrote: Dear all, since I am currenty preparing a lecture on crystallography I am wondering about the status quo of the production

Re: [ccp4bb] Calculation of the net charge of an electrostatic surface for secondary structural elements

of the electrostatic surface of helices 2 and 3 versus, say, helices 3 and 4 of the same protein. Thanks in advance, Rebecca -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital

Re: [ccp4bb] debugging gfortran with gdb on MacOSX

a debugger. The gfortran manual mentions gdb once, saying that it is capable of generating such information, but then has no further mention of gdb. Any advice would be much appreciated! Thanks, Charlie -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG

Re: [ccp4bb] crystals of 1D

In case you are using a standard purification protocol (with, say, two purification steps and a polishing gel filtration) you might also try adding yet another purification step, no matter how pure your sample looks on SDS-PAGE. Tim -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr

[ccp4bb] Zalman and coot: flipping polarisation?

that one can use the maximised window? Tim -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature

Re: [ccp4bb] Need isolated crystals

. Thanks Amit Sharma -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature

Re: [ccp4bb] cysteine conformation in coot

, New Delhi-110067 -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature

Re: [ccp4bb] Need isolated crystals

. To restore crystal size follow the rest of Tim's list. Enrico. On Mon, 12 Apr 2010 23:01:10 +0200, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: Have you tried anything, yet? The list of answers can be quite long. A couple of keywords: - micro-seeding - macro-seeding - cross-seeding

Re: [ccp4bb] blt2.4z in ubuntu 10.04

’ was here make[1]: *** [bltAlloc.o] Error 1 make[1]: Leaving directory `/home/hari/tcltk++/blt2.4z/src' make: *** [all] Error 2 -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature

Re: [ccp4bb] Rejected posting to CCP4BB@JISCMAIL.AC.UK

...@gmail.com wrote: Hi Tim, Thanks a tonne Tim for the pointer on how bltwish is handled in debian. A symlink from /usr/bin/wish to /usr/bin/bltwish. Seems to at-least start ccp4i. Now to see if it will also plot my graphs Hari -- -- Tim Gruene Institut fuer

Re: [ccp4bb] Rejected posting to CCP4BB@JISCMAIL.AC.UK

I have to withdraw what I stated in the post below. I forget and overlooked that we have bltwish installed together with ccp4i. I would like to apologise, Tim On Thu, Apr 15, 2010 at 08:20:13AM +0200, Tim Gruene wrote: Dear Bill, as I pointed out in my previous post I have the impression

Re: [ccp4bb] sigma cutoff for fitting waters in model

like to know what is the acceptable sigma cut off for waters to be kept in a model if data is of about 1.6 A. thanks in advance Sudhir Kumar Research Scholar Structural Biology Laboratory SLS, JNU, New Delhi-110067 -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077

Re: [ccp4bb] Arp Waters vs coot find waters!

? Is there something specific I should look for? I apologise in advance if this question has already been asked before. Thanks, Ivan -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature

[ccp4bb] Coot does not read svg icons

be missing? Cheers, Tim -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature

Re: [ccp4bb] Coot does not read svg icons

the following dependencies? librsvg2 librsvg2-gtk librsvg2-shlibs Gabriel Gabriel Birrane Beth Israel Deaconess Medical Center RN348 99 Brookline Ave Boston, MA 02215 -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Tim Gruene

[ccp4bb] phenix error message

, in _reduce_ex dict = getstate() TypeError: 'NoneType' object is not callable snap 8 (We cannot click 'OK' because our computers are not connected to the internet. Does anyone know what the error messages mean and how we can overcome them? Thanks a lot, Tim -- -- Tim Gruene

Re: [ccp4bb] phenix error message

On Fri, Apr 23, 2010 at 01:12:36PM +0200, Tim Gruene wrote: Hello, we are using the latex phenix version (1.6.1) on PCs with Debain Stable or Sorry, I meant 'latest' version, in case this causes confusion... Testing. After starting a refinement job, the following error message shows up

Re: [ccp4bb] phenix error message

On Fri, Apr 23, 2010 at 07:20:15AM -0700, Nathaniel Echols wrote: On Fri, Apr 23, 2010 at 4:12 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: we are using the latex phenix version (1.6.1) on PCs with Debain Stable or Testing. After starting a refinement job, the following error message

Re: [ccp4bb] phenix error message

On Fri, Apr 23, 2010 at 08:23:30AM -0700, Pavel Afonine wrote: On 4/23/10 8:14 AM, Tim Gruene wrote: On Fri, Apr 23, 2010 at 07:20:15AM -0700, Nathaniel Echols wrote: On Fri, Apr 23, 2010 at 4:12 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: we are using the latex phenix

Re: [ccp4bb] Adding TER card in PDB file

at the end of chain in my PDB file. Adding TER card manually is not problem but how to add Atom serial number ? Can it be done by some kind of PDB edit ? Thank you very much. Mike -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A

Re: [ccp4bb] maximum B-factor of metal ion

complex? Thanks in advance for the help. James... -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature

Re: [ccp4bb] Ramchandran outliers

acceptable percentage of outliers in a structure that is otherwise reasonable? The Rfactor/Rfree is 23/29 at 2.1 Angs resolution. Thanks, Ivan -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital

Re: [ccp4bb] program align does not see libcxa.so.5

allow fixed field selection which is key to dealing with files that have alternate conformers). HTH, Ed. -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature

Re: [ccp4bb] How to predict the secondary structure from a protein sequence..??

..??? Thank u hsn. -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature

Re: [ccp4bb] software to represent raw reflections in hkl zones

to have a precision photograph that shows reflections only in the [0kl] plane. Does anyone know software that can transform raw data to give intensity distribution in distinct zones of hkl? Many Thanks for your help, Tillmann -- -- Tim Gruene Institut fuer anorganische

Re: [ccp4bb] control of nucleation

, does anyone have adivce about this? Best regards. -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature

Re: [ccp4bb] Processing compressed diffraction images?

cheap, we don't need the extra I/O bandwidth for anything else, and you shouldn't need to spend a fortune, particularly if there are ways of making the software more efficient, which after all will benefit everyone. Cheers -- Ian -- -- Tim Gruene Institut fuer anorganische Chemie

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

hi-trap heparin column, i have also tried high conc salt buffer (upto 1 M NaCl) and also tried o.2 M lithium sulphate, please suggest me some way to get rid of undesired DNA.. thanks Regards Arpit -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG

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