Re: [ccp4bb] off topic: Alternatives to GE HiTrap columns

You can also try products from Bio-rad. http://www.bio-rad.com/featured/en/nickel-columns-nickel-resin.html Best! -- 卢作焜 南开大学新生物站A202 Lu Zuokun, Ph.D. Candidate College of Life Science, Nankai University At 2017-02-18 04:31:08, "Kevin Jin" wrote: Sorry, the company was CloneTech, now

Re: [ccp4bb] phenix installtion problem

Dear Weifei, You'd better ask this question on phenixbb as here is ccp4bb. But the environment variable file (.bashrc or .bash_profileis) in your home folder(specific user) or in /etc/profile (all user). Source Phenix in this file. Next time you run the terminal, the file will be source

Re: [ccp4bb] Request

Dear Neeraj, Do you mean the H3C protease ( trade name: PreScission protease provided by GE)? This protease can specifically cleavage the sequence encode by plasmid pGEX-6p, which possess the GST tag. Best wishes! Lu Zuokun -- 卢作焜 南开大学新生物站A202 Lu Zuokun, Ph.D. Candidate College of

Re: [ccp4bb] manufacturers of protein purification systems

Dear Ruth, Aligent and Shimadzu have their own liquid chromotagraphy instrument, as I know. Regards! Lu Zuokun -- 卢作焜 南开大学新生物站A202 在 2015-06-22 16:38:30，"Ruth Brenk" 写道： >Hi, > >does anybody known a manufacturer of a protein purification system >besides Biorad and GE Healthcare

[ccp4bb] ppGpp purification and concentrate

Dear ccp4bb members, Sorry for asking a non-crystallographic question where google search cannot provide any valuable answer. pppGpp was synthesized by relQ enzyme using ATP and GTP, the product was purified by anion exchange chromatography. The problem is that the concentration of pp

Re: [ccp4bb] 1st NJUST/CCP4 Crystallography School Announcement

-- 卢作焜 南开大学新生物站A202 在 2015-05-27 10:44:28，"Chang Qing" 写道： Dear Eva I checked the application information on the Web page and can only find the information below: Thank you for your interest in the 2015 CCP4/APS Summer School. The application system for the 2015 school is now closed.

Re: [ccp4bb] 1st NJUST/CCP4 Crystallography School

Dear Eva, I still got the same information at: http://www.ccp4.ac.uk/schools/china-2015/application.php Thank you for your interest in the 2015 CCP4/APS Summer School. The application system for the 2015 school is now closed. The 2016 workshop will be advertised towards the end of 20

Re: [ccp4bb] Fwd: Re: [ccp4bb] coot space bar translate rather slow at host machine but not in virtual machine

Dear Jorge, A virtual machine simulates a physical machine based on the host OS. Almost all the hardware resources is simulated by the virtual machine, BIOS,CPU,RAM Of course, all these instruction will finally be carried out by the really hardware. Your action on the guest OS will fir

Re: [ccp4bb] coot space bar translate rather slow at host machine but not in virtual machine

Dear Jorge, I got the same problem several month ago, coot works fluently in a virtual machine of centos 5 or ubuntu but not in a host machine of the same OS. Just 2 days ago, in order to run program more quickly, I convert the virtual machine of Ubuntu 14.04 to a physical machine. And

Re: [ccp4bb] XDS INP

Dear Natalie, I try to run my images with fast_dp, but got the error message: Fast_DP installed in: /home/lu/bin/fast_dp_20141205 Starting image: /home/lu/Documents/hg6l3/Hg6_L3_1_2.mccd Number of jobs: 1 Number of cores: 0 Processing images: 1 -> 360 Phi range: 112.50 -> 472.50 Template: Hg6

Re: [ccp4bb] XDS INP

Tue, 12 May 2015 14:50:26 +0100, Huw Jenkins wrote: > >>On 12 May 2015, at 13:09, luzuok wrote: >> >>> STANDARD DEVIATION OF SPINDLE POSITION (DEGREES) 11.13 >> >>Is the oscillation range and rotation axis direction correct in your XDS.INP >>file? >> >> >> >>Huw

Re: [ccp4bb] XDS INP

Yes! two data sets from one crystal with 2 different wave length. -- 卢作焜 南开大学新生物站A202 在 2015-05-12 22:14:16，"Huw Jenkins" 写道： >Hi, > >Also the IXDREF.LP files from yesterday and today suggest that you are having >problems with 2 different datasets. Is that correct? > >IDXREF from yesterda

Re: [ccp4bb] XDS INP

DS.INP), so I would >try with the above first, run COLSPOT, inspect with the gnuplot technique I >described, and then modify the parameters until the plot looks more >meaningful, at which point IDXREF will most likely happily index. > >No, this is not fully automatic, but at le

Re: [ccp4bb] XDS INP

ownload please see > > http://www.globalphasing.com/autoproc/ > >Cheers > >Clemens > >On Thu, May 07, 2015 at 04:33:38PM +0800, luzuok wrote: >> Dear all, >> I'm a XDS beginner and the first problem I encounter was the INP file. >> The detector type i

Re: [ccp4bb] XDS INP

Fred. On 07/05/15 10:33, luzuok wrote: Dear all, I'm a XDS beginner and the first problem I encounter was the INP file. The detector type is MX300. Is the detector supported by XDS? How to modified the INP file? The sitefile of HKL2000 was attached. Can anyone provide some tut

[ccp4bb] XDS INP

Dear all, I'm a XDS beginner and the first problem I encounter was the INP file. The detector type is MX300. Is the detector supported by XDS? How to modified the INP file? The sitefile of HKL2000 was attached. Can anyone provide some tutorial to use XDS? Best wishes! Lu zuokun

Re: [ccp4bb] on openning the PDB file and the mtz file by Coot

Dear Smith, Coot calculates electronic map from data columns in the mtz file. If a correct model (atomic coordinates) in a PDB file is generated from the mtz file (Model building). This mode (PDB file) will " fit " the mtz file. Yours Sincerely! Lu Zuokun -- 卢作焜 南开大学新生物站A202 在 2015-0

[ccp4bb] Some practical questions regarding heavy atom derivatives soaking

Dear all, I have some questions when soaking heavy atom derivatives, 1. How to prepare HA derivative stock solution? I use 10 mM Bis-tris pH 6.8 to dissolve my heavy atom derivatives ( Hampton Research Heavy Atom Screen M1 and Heavy Atom Screen Hg), the concentration is 100 mM. Apparentl

[ccp4bb] Assess anomalous signal?

Dear all, I'm doing Hg SAD phasing for the first time, and I met some problem: 1. How to assess the anomalous signal after I process the data and get my mtz file? My labmate doesn't scan the fluorescence signal. Actually, I don't quite understand why we use fluorescence to detect anom

Re: [ccp4bb] question related to MTZ file

How "initial" this MTZ file? Does this mtz file contain phase information? Lu Zuokun -- 卢作焜 南开大学新生物站A202 在 2015-01-02 00:52:53，"Jurgen Bosch" 写道： I assume you mean with initial mtz file the one derived from Mosflm after processing your images. If so, then how about running that file thr

Re: [ccp4bb] AW: [ccp4bb] water at the same exactly position

n Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von luzuok Gesendet: Donnerstag, 30. Oktober 2014 04:54 An:CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] water at the same exactly position Dear Nicolas, It is really time-consuming! Philip told me to run the s

Re: [ccp4bb] water at the same exactly position

Dear Nat, But if there are other solvent molecules, such as Mg2+, SO4-,, in the same position. How can this problem be solved? Lu Zuokun -- 卢作焜 南开大学新生物站A202 在 2014-10-30 12:57:31，"Nat Echols" 写道： On Wed, Oct 29, 2014 at 8:53 PM, luzuok wrote: I think it is bette

Re: [ccp4bb] water at the same exactly position

lecules. >In coot you can remove it graphically, but according to my knowledge not >automatically, and it maybe time consuming. > >Hope to help >Nicolas > > >De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de luzuok >[

[ccp4bb] water at the same exactly position

Dear all, I found that there are some water molecules in my pdb that share the same position. This maybe cause by merging molecules in coot. It seems that I have mereged water molecules into my protein for more than one time. Does anyone tell me how to fix this problem? Best regards! Lu Zu

Re: [ccp4bb] Cacodylate won't stay in place

Dear Oarabile, You may try automated ligand fitting programme, in Coot-Calculate- Other modelling tool- Find ligands. There are also other Liand fit programme in Phenix or ccp4. Good luck! Lu Zuokun -- 卢作焜 南开大学新生物站A202 At 2014-10-26 02:51:01, "Kgosisejo, Oarabile" wrote: Hell

Re: [ccp4bb] Merge PDB chains

CMAIL.AC.UK >> Subject: Re: [ccp4bb] Merge PDB chains >> >> Edit the ATOM records? >> >> >> Sent on a Sprint Samsung Galaxy S® III >> >> >> Original message >> From: luzuok >> Date:10/23/2014 6:51 AM (GMT-05:00) &

[ccp4bb] Merge PDB chains

Dear all, Sorry to ask a simple question. There are many SO4 in my PDB file, one belongs to a different chain. I want to merge them into one chain, can anyone tell me how to do this? Best regards! Lu Zuokun -- 卢作焜 南开大学新生物站A202

Re: [ccp4bb] R free flag missing after ARP/wARP?

gards, >Tim > >On 10/20/2014 04:41 AM, luzuok wrote: >> Dear all, >> I was using ARP/wARP in ccp4i, the input mtz file certainly has free R >> flag, but the output mzt file doesn't have the free R flag label? >> I chose " do not use the Fr

[ccp4bb] R free flag missing after ARP/wARP?

Dear all, I was using ARP/wARP in ccp4i, the input mtz file certainly has free R flag, but the output mzt file doesn't have the free R flag label? I chose " do not use the Free R flag" in the ARP/wARP GUI. Can anyone tell me what's wrong with this? best reagrds! Lu Zuokun -- 卢作焜 南开大学新生