Re: [ccp4bb] Unidentified blob
Hi - At higher resolution like you have, it seems common to me to detect alternate conformations for the larger solvent molecules, making it more difficult to decide at first glance what occupies the density. After you put in something, the new difference peaks should tell you if there is another conformation, which, may not occupy the same overall space, that may need to be added. There will be water shifts due to this too. These cases are easier to spot if the protein also has alternate conformations adjacent to the blob in question. Data near 1 angstrom can be a lot of work. D On Thu, Dec 12, 2013 at 4:17 AM, Danilo Belviso danilo.belv...@ic.cnr.itwrote: Dear Afshan, Maybe what I suggest you have already tried: have you tried to fit a citrate molecule? The blob seems to be branched, thus compatible with such organic molecule. Danilo On Thu, 12 Dec 2013 03:34:07 -0800, Afshan Begum afshan...@yahoo.com wrote: Dear Experts, I collected a data set (1.12A) of one of my target proteins, and built a model by molecular replacement. I then exam the model by Coot and found one unidentified blob. I am unable to to identified a blob which appeared on the surface of the molecule its close to residues 115 SER the protein purified in 10 mM Na-phosphate buffer, 100mM KCl and crystallized in 1.6 M sodium citrate, 3.5% _v/v _glycerol I have attached the picture of the blob. I would be thankful for your kind suggestions. Best Regards AFSHAN -- David Shin, Ph.D Lawrence Berkeley National Labs 1 Cyclotron Road MS 83-R0101 Berkeley, CA 94720 USA
Re: [ccp4bb] molrep question - how get our ducks in a row?
Hi Gloria, It depends on if you mean hard as in thinking up a slick trick, or hard as in maybe 20-30 mins of tedious work. I had the same problem with 18 in the ASM, where the solution had scattered models, but didn't want to think about it, so just used pymol. 1) open the first model with the original 6 models 2) then make separate files with each of the other subunits (with the CRYST line) - with short names like m1.pdb, m2.pdb, m3.pdb etc. (this is so you can read easily in the gui later for saving) 3) then open m1.pdb 4) on the left, go to the A or action menu for m1 .pdb generate symmetry mates within 100 Angstroms (this can be smaller or larger, just need to see them) 5) then you'll have the symmates on the screen and the list of each right listed as m1_100-1-100 etc. So you can just click them on and off to see which one you like, then save that molecule. 6) Then delete the symmates delete m1_* so you can check 7) Open the saved symmate to check 8) go to step 3 for the next model, ie. m2.pdb not a slick answer, but can be done when tired with minimal error. On Thu, Feb 23, 2012 at 4:07 PM, Gloria Borgstahl gborgst...@gmail.comwrote: Hello all, We are solving a superstructure of a protein complex with 2 parts. Built 6 of the first part and they are all sensibly stacked next to each other. Then we read this into molrep as the fixed model and solved for the second part. The solution was found but the 6 for the second model are in different ASU's and unit cells. What is the easiest way to get everyone together in one asu? We can think of hard ways to do it, but any advice? Thanks, Gloria -- David Shin, Ph.D Lawrence Berkeley National Labs 1 Cyclotron Road MS 83-R0101 Berkeley, CA 94720 USA
Re: [ccp4bb] SAXS collection
Hi- While the server is down at the moment, members of our lab have been working on one - www.bioisis.net Currently, I believe the page is being updated. Try accessing in the near future. Dave On Wed, 12 Jan 2011, Rojan Shrestha wrote: Hello: I am searching for SAXS data depositor like protein data bank for protein structure and EDS from electron density map. I have no idea how can I get SAXS data. Is there a depository for SAXS collection? If not so, what is the usual way to get it? Regards, Rojan
[ccp4bb] OSX 10.6, Fink CCP4 install problem
Hi - Got a new computer, was trying to install CCP4 following the Scott Lab page (64 bit install) - http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/64-bit_Fink_for_10.5_and_10.6 First had to install fink - tried to follow that page, but didn't have the cvs command (forgot about the xcode, etc.). So installed Fink via: http://www.finkproject.org/download/srcdist.php This install put fink into the sw/ directory, not sw64/ So after fink was running, I went back to the http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/64-bit_Fink_for_10.5_and_10.6 page, and started from For now on, I will use /sw* to mean /sw or /sw64 as appropriate. ie. edited files: When it is done, edit /sw*/etc/fink.conf and change line 4 to look like this: ## Trees: local/main stable/main stable/crypto unstable/main unstable/crypto This activates the unstable branch. Then issue source /sw*/bin/init.sh fink selfupdate-cvs fink -y update-all fink scanpackages # everything was fine until I did this: First you need to edit the /sw64/etc/apt/sources.list file and add the following three lines to the bottom of that file (I changed the sources.list file in the sw/ directory) # deb http://sage.ucsc.edu/fink_intel_10.6_64bitstable main crypto deb http://sage.ucsc.edu/fink_intel_10.6_64bit unstable main crypto deb http://sage.ucsc.edu/fink_intel_10.6_64bit local main then wehn I tried to install coot and ccp4 using the next part: # fink scanpackages sudo apt-get update sudo apt-get dist-upgrade sudo apt-get install coot # I found out I killed fink. ie. here's the error message after running fink scanpackages: ERROR: Configuration file /sw64/etc/fink.conf not found. /sw/bin/dpkg: error processing fink (--configure): subprocess post-installation script returned error exit status 1 Errors were encountered while processing: fink E: Sub-process /sw/bin/dpkg returned an error code (1) I see that the previous edit made the update look for something in /sw64/ which of course didn't exist, but now my version of fink is dead... ie. I type fink scanpackages, or any fink command, and the command is not found. I type which fink and nothing returns, but everything is still in the sw/ directory. What do you think? now that I have the cvs command up and going, I just delete the sw/ directory and start over, or is there some fix I can do? Thanks, Dave
