[ccp4bb] Protein Purification
Dear All I am purifying a protein from liver. In first step I spotted protein in Flow Through and could see intense band in SDS PAGE. I pooled the fraction and did second column. Surprisingly I could not see UV absorbance or even any band in the SDS. I used PMSF as protease inhibitor from begining of purification. First column I used Tris buffer (pH 8) and for second column I used MOPS buffer (pH 6). What could be the reason? Thanks in advance Sajid
[ccp4bb] ITC thermogram
Dear All I am running ITC experiment for my protein. At 250 nm Ligand concentration (protein was 40nm) I was getting exothermic thermogram. But it was not saturated. I reduced Ligand concentration to 15 nm and checked again. I got endothermic thermogram. I dont understand why I am getting both endothermic and exothermic thermogram for same protein and ligand. Can some one explain Thank you Sajid
[ccp4bb] ITC with heterogeneous protein
Dear All, This is an off-topic question. I have protein solution of heterogeneous (contains both monomer and dimer). I want to perform ITC with this protein. I doubt whether this heterogeneity will interfere the binding study. Any advice please. Thank you Sajid
[ccp4bb] column profile
Hi all If anyone have, please post the calibration profile for GE Sephacryl S100 26/60 Hiprep column. Sorry I could not locate in the GE Healthcare site. Thankx in advance Sajid
[ccp4bb] NADP - ADP binding
Dear All Can any one mention some reference regarding the binding of NADPH or ADP in the surface of the protein. Is there any rules that dominate these two cofactors to select the surface istead of typical Rossmann fold. Thank you Sajid Yahoo! India has a new look. Take a sneak peek http://in.yahoo.com/trynew
[ccp4bb] Peg3350 model
Hi All I have some density and I can fit a peg molecule in their. I am confused and when I search database for peg3350, I have no hit. How can I build a model for Peg 3350. I found some PDB's with peg; but they they have used peg400; Is there any difference in the model between peg3350 and peg400. Can any one define where the peg ion could bind. Thanks Sajid Add whatever you love to the Yahoo! India homepage. Try now! http://in.yahoo.com/trynew
[ccp4bb]
Dear All Is there any easy to way write topology and parameter file for a cofactor with specific conformation. Thanks a lot Sajid Love Cricket? Check out live scores, photos, video highlights and more. Click here http://cricket.yahoo.com
[ccp4bb] Auto Sharp - problem
Hi all I am trying to run autoSHARP. When I submit the job I got following message and the job is not running. Does any one have got error like this when you start autoSHARP Any advice please Sajid ** (In case of remotely submitted jobs, the go to log file will not work until the job is actually started) USAGE: /home/sajid/sharp/sushi/submit/interactive/start.sh -h $BDG_home -u $BDG_user -p $BDG_project -j $BDG_job -t $BDG_type -l $BDG_log -e $BDG_err -v $BDG_var -b -a -h $BDG_home= Home directory of BDG installation -u $BDG_user= user name -p $BDG_project = project name -j $BDG_job = job ID (name + number) -t $BDG_type= (buster|sharp|denmod) -l $BDG_log = log file -e $BDG_err = standard error file -v $BDG_var = variable setting -b = flag for backgrounding job -a = flag to do everything apart from actually running the job Maybe you are using the old syntax (Sushi 3.0.16) in your $BDG_home/submit.local/*/ subdirectories? Have a look at the new syntax in $BDG_home/submit/*/ Your actual command was: /home/sajid/sharp/sushi/submit/interactive/start.sh -h /home/sajid/sharp -u syed -j MIRAS_with se.0 -p None -t detect -l LISTautoSHARP -e STDERR -b ** From Chandigarh to Chennai - find friends all over India. Go to http://in.promos.yahoo.com/groups/citygroups/
[ccp4bb] mrBUMP - proxy to internet
Dear All I want to run MrBump. We have dynamic internet system in our institute. So I am not able to locate the proxy address. Any help please Sajid From Chandigarh to Chennai - find friends all over India. Go to http://in.promos.yahoo.com/groups/citygroups/
[ccp4bb] phasing at low resolution
Hi All I have a data set of Se-Met crystal 3.65A resolution collected at Inflection and peak wavelength. Also I have a data set at same resolution in native form. The protein size is 28000 dalton. I dont have any model for this protein. So I started to find the heavy atom peak search to find out Se positions using Shelx programe. From ShelxD and E, I got refined 12 Se sites with two molecules per AU. This prediction is consistent with the expected number of Se incorporation per molecule. Since I dont have any model for my protein, I am not able to go beyond this. Though I'm trying to reproduce good diffracting crystals, they diffracts at this level only. Some native crystals diffaracting upto 3.29A. But they are twinned data set. So it is tough to process those data set. Can I do phasing for the model with the present 12 sites. Please give me your suggestions for this problem. Thank you Sajid From Chandigarh to Chennai - find friends all over India. Go to http://in.promos.yahoo.com/groups/citygroups/
[ccp4bb] refmac5
Dear All Thanks for your suggestions to run revise. Suggestions from Mike Latchem helped me to overcome the problem. I have another question. I am trying to run REFMAC5. It is giving some warning message. # There is no file name for parameter MAPOUT1 The CCP4 program is lable to fail. Please enter a file name and Run again # After dismissing the warning message the program is not running. I do not know about this parameter file. Any suugestions please Thank you Syed Bollywood, fun, friendship, sports and more. You name it, we have it on http://in.promos.yahoo.com/groups/bestofyahoo/
[ccp4bb] Potassium Nitrate
Hi All Sorry for non CCP4 question. I want to make Pottasium Nitrate solution of pH 6.9 (ofcourse for crystallisation trails only). I'm adjusting pH by using NaOH. But it seems the pH is not stable after sometime. Is there any good way to do it. Thank you Sajid Now you can chat without downloading messenger. Go to http://in.messenger.yahoo.com/webmessengerpromo.php
[ccp4bb]
Hi All I'm getting clusters of crystals (tiny and long needles) and I'm trying to get good single crystals. Even I'm getting the same result at low salt concentrations. I reduced the temperature to slow down the evaporation, still no change. So I'm trying with mineral oil. Here I'm getting somewhat thicker needles and the number of needles is reduced. But my drop seems to be dried out in two or three days (I dont think there is a sealing problem). Can anyone suggest me to overcome this and to get good crystals. Thankz in advance Sajid Download prohibited? No problem! To chat from any browser without download, Click Here: http://in.messenger.yahoo.com/webmessengerpromo.php
