[ccp4bb] keep ligand conformation

Dear all, I tried to keep a conformation of a ligand during refinement with Refmac5 (Ver. 5.7.0032), and I put a harmonic restraint as, external harmonic residues from 600 A to 600 A 600 is the residue number of the ligand. I checked structures with and without the harmonic restraint, but no ch

Re: [ccp4bb] Symmetry problem

Monika, There are several possible causes for the problem you are encountering, but your description is a little too vague to discern them. Scenario 1) You ran phaser with the option "all possible spacegroups", for several different components of your crystal, setup individually, and the runs d

Re: [ccp4bb] Can not see density map when I turn off normalization in PYMOL

Hi Hongshi, I think Dale is right. When you turn off the normalization, the level value you need to put in the isomesh command should be the absolute electron density value of the map instead of how many RMSD. In your command window log, this line shows the range of the density values in your

Re: [ccp4bb] Can not see density map when I turn off normalization in PYMOL

When you don't normalize the map you have to specify your contour level in whatever units the map came in. Your output says the "stdev" is 0.075 so I guess you need to contour at 0.225 to see the equivalent image. Dale Tronrud P.S. I feel compelled to note that what the program is reporting a

Re: [ccp4bb] Can not see density map when I turn off normalization in PYMOL

Dear Hongshi - I cant help but to first suggest that as this is the CCP4bb, the first thing you should try is using CCP4mg, if you want to make pretty pictures. If you just want to look at the map and work with it, you should use Coot. If still for some reason you want to use Pymol, you should a

[ccp4bb] Can not see density map when I turn off normalization in PYMOL

Hello there, I am making a fo-fc map for one ligand using pymol. I strictly followed the pymol wiki protocol (Display CCP4 Maps). Finally, I can get the ligand map using command: isomesh fo-fc_ligand, omitmap, 3, ligand, carve=2. However, the problem is the map I got from pymol is smaller tha

[ccp4bb] New position

Dear colleagues, We have an opening for a structural biologist here in Frederick, MD. If not interested, please forward this email to those who might be. Thank you. Best regards, Bill htt

[ccp4bb] Postdoctoral research associate position in structural biology at the University of LIverpool

THE UNIVERSITY OF LIVERPOOL FACULTY OF HEALTH AND LIFE SCIENCES INSTITUTE OF INTEGRATIVE BIOLOGY DEPARTMENT OF BIOCHEMISTRY POSTDOCTORAL RESEARCH ASSOCIATE £31,644 - £36,661 pa An exciting opportunity has emerged to join the Molecular Biophysics Group to work on a BBSRC-supported project on st

Re: [ccp4bb] / or

Dear Folmer Fredslund, Thanks for your help. Actually, I can only find the archives until APR-30-2003 at the archives. Where is the DEC-1-2003 archives? Regards, Qixu Cai 发件人: Folmer Fredslund 日期: 2014年2月19日 星期三 下午10:09 至: Cai Qixu 抄送: "CCP4BB@jiscmail.ac.uk" 主题: Re: [ccp4bb] / or Dear

Re: [ccp4bb] High Salt Cryo

Dear All, I would like to point out that the conditions 1.8 - 2.0 M NaCl are not considered High Salt as NaCl is soluble to 5M and a 2X solution (i.e. 4M NaCl) is possible. Also NaCl contrary to ammonium sulfate, citrate, phosphate, etc. is compatible with polyethylene glycol without phase

Re: [ccp4bb] [ccp4bb] Symmetry problem

Hi, Monika, It sounds like you got the two domains separately in the asymmetric unit. You could do the symmetric operation for one of the domains in pymol by generating the symmetric mates (say 10 Å). Then you should see several same ones there. Select the one you need, and save the coordinates,

Re: [ccp4bb] High Salt Cryo

4M NaCl should work too. It worked for the conditions with 1.8 - 2.0 M NaCl. Karolina W dniu 2014-02-19 06:38, Mooers, Blaine H.M. (HSC) napisał(a): > For crystals grown out of a 2 uL drop of 1.2-1.8 M LiSO4 or 1.6-2.4 M AmmSO4, > we do in situ cryoprotection with sodium malonate. We add

Re: [ccp4bb] / or

Dear Qixu Cai, You can find information about where to find the archives here: http://www.ccp4.ac.uk/ccp4bb.php#archives Best regards, Folmer 2014-02-19 14:44 GMT+01:00 Cai Qixu : > Dear Richard Gillilan, > > Where to find the archives of Dec 2003? I can only find the archives until > 2007 a

Re: [ccp4bb] / or

Dear Richard Gillilan, Where to find the archives of Dec 2003? I can only find the archives until 2007 at jiscmail. Thanks. Regards, Qixu Cai 发件人: Richard Gillilan 答复: Richard Gillilan 日期: 2014年2月16日 星期日 上午12:19 至: 主题: Re: [ccp4bb] / or There was an informative discussion on this ver

Re: [ccp4bb] High Salt Cryo

For crystals grown out of a 2 uL drop of 1.2-1.8 M LiSO4 or 1.6-2.4 M AmmSO4, we do in situ cryoprotection with sodium malonate. We add 2-4 uL of 1.9 M Na malonate to the crystallization drop, wait 10 seconds and add 2-4 uL of 2.4 M sodium malonate, repeat with 2.8 M and then 3.4 M. We do not bo

[ccp4bb] AW: [ccp4bb] Symmetry problem

Another option would be the "merge molecules" option in coot (calculate -> merge molecules). In coot you would also be able to move the molecules to the same asymmetric unit if that would be necessary. However, depending on the space group the MR solutions could have different origins and with p

Re: [ccp4bb] Ask for recommendation: crystal screening kit

Dear Wenhe, You could also consider one of the screens available from Rigaku Reagents, former Emerald Bio (http://www.rigakureagents.com/). These include the Classic Wizard Screens, the JCSG+ and PEG Ion screens as well as screens for LCP and a Membrane Protein Extraction Detergent Screening K

Re: [ccp4bb] Off topic Chromatography systems

Agilent also has some decent systems. Cheers, Ronnie -- Ronnie Berntsson, PhD PostDoctoral Fellow Department of Biochemistry and Biophysics Arrhenius Laboratories for Natural Sciences Stockholm University 10691 Stockholm Sweden On 18 Feb 2014, at 17:15 , Scott Pegan wrote: > Hey every

Re: [ccp4bb] Symmetry problem

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Monika, What program did you use for MR? I would expect the output PDB file has the correct cell and symmetry from the mtz-file you replaced against. To answer your question: you can simply concatenate the two files (e.g. with a text editor), re