Re: [ccp4bb] Comparison of Water Positions across PDBs

Downloading structures of the same homologous family with blast. Then superimpose them on a reference structure. You may then try to look at over lapping water molecules On 30 Oct 2013 02:23, "Elise B" wrote: > Hello, > > I am working on a project with several (separate) structures of the same >

Re: [ccp4bb] changes in small sections of secondary structure

Dear Mahesh, Instead of bothering with the secondary structure assignments why may try to superpose your structures and then view your RMSD plots(Superpose program in CCP4 can do the trick). You might then be better off focusing on the regions with high RMSD. Regards On Sat, Oct 19, 2013 at 3:20

[ccp4bb] Staining Crystals with comassie

Dear All, I am looking for a method to quickly differentiate between salt and protein crystals. I have been told thats its a popular alternative to the commercially available izit dye. I would appreciate if some one would share their comassie crystal staining protocol. Swastik

[ccp4bb] CCP4 Setup manager

Dear All, I am currently setting up a system running UBUNTU-12.04.3 (64 bit version), When I try to install CCP4 software suite by using the software suite, it kinda gets hung with the message "Now communicating with CCP4 server, please wait.." for ever Any help would be usefull. Re

Re: [ccp4bb] X-ray pattern has streaks

One standard thing to do would be to set up a grid around the condition and then try picking crystals from different well to see if any of them produce better looking diffraction patterns. If that does not work one might give any of the commercially available additive screen a try to see if diffrac

Re: [ccp4bb] video of crystal pick-up through microscope?

Hi, May be this would help https://www.youtube.com/watch?v=QcsaWowulDM On Fri, Sep 13, 2013 at 2:51 PM, Frank von Delft wrote: > Hi all - does anybody know where I can find a video of a crystal being > harvested, but taken through a microscope? > > The Google has not been helpful, but I'm obvioul

[ccp4bb] Hydrogens from Shelxl

Dear All, I have been working on a high resolution protein structure using Shelx for refinement. In the PDB output by Shelxl the hydrogen atom names are in duplicate which is causing difficulty in PDB deposition. I am aware of the use of shelxpro's B option to prepare for pdb deposition, it unfortu

Re: [ccp4bb] Fwd: [ccp4bb] pdbset

: > -BEGIN PGP SIGNED MESSAGE- > Hash: SHA1 > > Dear Swastik Phulera, > > unless you need the ANISOU cards, you can first remove them with e.g. > > grep -v "^ANISOU" youfile.pdb > yournewfile.pdb > > before running pdbset. > > (I hope yo

[ccp4bb] Fwd: [ccp4bb] pdbset

-- Forwarded message -- From: Swastik Phulera Date: Tue, Jun 11, 2013 at 1:51 PM Subject: Re: [ccp4bb] pdbset To: Tim Gruene Dear Tim, Miguel Thanks for your suggestions, the program does work now, but it seems that it cant handle AnsioU s . It gives an error: PDBSET

[ccp4bb] pdbset

bset: Use: pdbset: Use: Times: User: 0.0s System:0.0s Elapsed: 0:00 Does any one have any idea what's wrong here? Swastik Phulera -- -- स्वस्तिक फुलेरा वरिष्ठ अनुसंधान कर्ता राष्ट्रीय कोशिका विज्ञान केंद्र पुणे विश्वविद्यालय परिसर, गणेशखिंड पुना, ४११,००७