Re: [ccp4bb] regarding TLS records

Hello Yarrow, in some refinement software (phenix.refine), if you run TLS refinement and > you don't specify the TLS groups, the entire structure is considered one > TLS group if you use TLS parameterization and do not specify TLS groups, two scenarios are possible: a) each chain will be treated

Re: [ccp4bb] regarding TLS records

Hi Vipin, I'm not sure what software you are running or your refinement strategy. However, in some refinement software (phenix.refine), if you run TLS refinement and you don't specify the TLS groups, the entire structure is considered one TLS group which is not helpful. This may be why the annotat

Re: [ccp4bb] jiffy for analyzing spot.xds?

yes, and http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Generate_adx does this for all frames contributing to SPOT.XDS. HTH, Kay On Tue, 15 Apr 2014 11:38:23 +0100, T. Nakane wrote: >Dear Francis, > >You can visualize SPOT.XDS with adxv. > >Since column 3 of SPOT.XDS is the image

[ccp4bb] ipmosflm not connecting to XQuartz on Mac.

Hi all, Anyone having issues getting ipmosflm to connect to XQuartz? I'm getting a hang when running go just when I expect the old GUI to load. Thanks, F - Francis E. Reyes PhD 215 UCB University of Colorado at Boulder ---

Re: [ccp4bb] Coot error

If you are using a standalone Coot package, you may want to try one from regular CCP4 distribution instead. Coot is integrated in CCP4 6.4.0, and installation of CCP4 is fully automated so that no manual tweaking should be required. Eugene On 15 Apr 2014, at 13:24, Monica Mittal wrote: > Hi a

[ccp4bb] The 7th K.H. Kuo Summer School of Electron Microscopy and Crystallography

Dear colleagues, We are pleased to announce the “The 7th K.H. Kuo Summer School of Electron Microscopy and Crystallography” to be held in Shanghai, China from July 26 - 30, 2014. This is a biannual international summer school organized by the K.H. Kuo Education Foundation and the Chinese Academ

[ccp4bb] PDRA in Macromolecular Crystallography Methods Development

Dear All, I’d like to draw your attention to a 4yr Post Doc position available at Diamond Light Source funded jointly by Diamond and CCP4. For details of the post see http://www.diamond.ac.uk/Careers/Vacancies/All/DIA0916_CH.html or contact gwyndaf.ev...@diamond.ac.uk

[ccp4bb] BCA Bursaries for IUCr - deadline on 2nd May

Dear All, Please note that the deadline for applying for Bursaries to attend the IUCr is the 2nd May. These bursaries are open to BCA members – further details on eligibility are available on the webpage. Please see the link below: http://crystallography.org.uk/prizes/bursaries/abbf-bursaries/

Re: [ccp4bb] shelxc/hkl2map

Dear Monica, I think you are almost there. To run SHELXC, an example command is: shelxc mymad < my_shelxc.input | tee shelxc.log The command and names are as explained by Tim Gruene at . Other tutorials a

Re: [ccp4bb] Coot error

Try "yum install glib2-devel" (as root). I haven't used CentOS/Fedora in a while, but I think this is the right package. Cheers, ___ Roger S. Rowlett Gordon & Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346

[ccp4bb] Coot error

Hi all I am facing a problem while installing coot in CentOS. After configuring its showing No package'glib-2.0' found. Either it asks me to adjust PKG_CONFIG_PATH env variable if i installed in non standard prefix or i can set set env variables GLIB_CFLAGS and GLIB_LIBS to avoid need to call pkg-c

[ccp4bb] AW: [ccp4bb] AW: appropriate torsion angles

Dear Joel, I suspect that you will have a mixture of different puckers. Relaxing the restraints would not be the way to go, since it might lead to a distorted average structure. If your cif file is correct (tetrahedral nitrogens), it should not impose a specific pucker. However, you will have t

Re: [ccp4bb] jiffy for analyzing spot.xds?

Thank you all, Once again the ccp4bb delivers. F On Apr 15, 2014, at 6:38 AM, T. Nakane wrote: > Dear Francis, > > You can visualize SPOT.XDS with adxv. > > Since column 3 of SPOT.XDS is the image number of spot centroid, > you can extract spots near frame 4 like this: > > awk '{if (int($

Re: [ccp4bb] jiffy for analyzing spot.xds?

Dear Francis, You can visualize SPOT.XDS with adxv. Since column 3 of SPOT.XDS is the image number of spot centroid, you can extract spots near frame 4 like this: awk '{if (int($3+0.5) == 4) print $1, $2;}' SPOT.XDS > spots_04.adx Then you can load "spots_04.adx" into adxv. (you must load the

[ccp4bb] Shelx GUI usage with hkl2map

Hi all I am new to use the programs for anamolous data processing. I installed hkl2map as well as shelxc/d/e. I am abl to run shelx on command line but not through GUI. Kindly guide me how to use the GUI for shelx. Thanx in advance. Monica

[ccp4bb] shelxc/hkl2map

Hi all I installed shelxc/d/e on linux by unpacking and then making executable by chmod +x. I got the executables for all files. Now when i run as ./shelxc i get the infromation about the program. I guess i need to define the input file also along with shelxc. But instead of that i want to use GUI

Re: [ccp4bb] AW: appropriate torsion angles

Dear Herman and Paul, Thanks for your input. I have already looked at the CSD and it conclusively tells me that both nitrogens are tetrahedral and both have a phenyl ring. I have added appropriate chiral restraints for the nitrogens. That part I am comfortable with. What I am looking to do is

Re: [ccp4bb] jiffy for analyzing spot.xds?

Hi Francis At the risk of offending Wolfgang and Kay, why not try using other software to index & visualize spots found on the images? Mosflm is the one that comes to my mind straight away, but there are others that could probably do the job... It would certainly be possible to write a jiffy th

[ccp4bb] AW: [ccp4bb] AW: appropriate torsion angles

Dear Paul, I find it difficult to predict when a pipirazine nitrogen will be sp2 and when sp3, so I usually search the csd with the exact substituent at hand and supposed that Joel will have done the same. In general, I find that auto generate programs are overly optimistic how far delocalizati

Re: [ccp4bb] AW: appropriate torsion angles

Dear Joel and Herman, On 15/04/14 04:39, herman.schreu...@sanofi.com wrote: Dear Joel, I always tell our chemists not to include piperazine rings etc. in their compounds because of this conformational mess, but somehow they do not seem to listen. ;-) Unfortunately, do did not tell us how

[ccp4bb] AW: appropriate torsion angles

Dear Joel, I always tell our chemists not to include piperazine rings etc. in their compounds because of this conformational mess, but somehow they do not seem to listen. ;-) Unfortunately, do did not tell us how and with software you auto generated your cif file, so I can only give some genera

[ccp4bb] hkl2map

Hi all I am new to phasing experiments. I have downloaded hkl2map-0.3.i-beta.tgz and i need help to install it on linux. I would be thankful if anyone can guide me. Thanx Monica