Re: [ccp4bb] Phaser solution and solvent content for arp warp

I think I would be tempted to chainsaw one of the ensemble chains of 2IT8 (they look very similar except for side-chain disposition) and use 1 or 2 of these as search models in a Phaser run. If this works, you should see good Z-values and the final result inspected in Coot should show good mole

Re: [ccp4bb] Phaser solution and solvent content for arp warp

Just throw your phaser-placed model into Buccaneer JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of xaravich ivan Sent: Monday, June 29, 2015 3:10 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Phaser solution and solvent content for arp warp Hi everyone, I think I have

[ccp4bb] Phaser solution and solvent content for arp warp

Hi everyone, I think I have finally got a solution in Phaser (screen shot attached) as the TFZ is 10. However the solution PDB has 30 molecules in it as the search model was an NMR solution. As I have 0.944 Angs resolution data pretty complete, I thought of building the initial model in ArpWarp. I

Re: [ccp4bb] AW: [ccp4bb] Single search Model input in Phaser!!!

Thanks everyone, It works now. cheers, Ivan On Mon, Jun 29, 2015 at 8:59 AM, Gabor Bunkoczi wrote: > Hi Ivan, > > you need to tell Phaser which ensemble to use for searching. Open the > "Search parameters" tab, and select the ensemble you defined. > > HTH, Gabor > > On 2015-06-29 16:48, xaravich

Re: [ccp4bb] AW: [ccp4bb] Single search Model input in Phaser!!!

Hi Ivan, you need to tell Phaser which ensemble to use for searching. Open the "Search parameters" tab, and select the ensemble you defined. HTH, Gabor On 2015-06-29 16:48, xaravich ivan wrote: Hi Herman, CCp4bb, Attached you will find the inputs for running phaser with single pdb, and the e

[ccp4bb] AW: [ccp4bb] AW: [ccp4bb] Single search Model input in Phaser!!!

Hi Ivan, I always run phaser via my own script, but I checked the ccp4i gui: the error message indicates that you did not set a search option. In the tab “Search parameters” I found an item “Perform search using” followed by a box. When nothing is clicked here, the box is empty so Phaser does n

Re: [ccp4bb] AW: [ccp4bb] Single search Model input in Phaser!!!

You’ve got to put values in for “search parameters,” tell it how many ensembles to look for. JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of xaravich ivan Sent: Monday, June 29, 2015 11:49 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] AW: [ccp4bb] Single search Mo

Re: [ccp4bb] Heavy-atom derivatives

Hi Giulliana, here is a nice and simple method on how to select heavy atoms for phasing using native PAGE (please see Fig. 1): http://www.ncbi.nlm.nih.gov/pubmed/10903954 Structure. 2000 Jul 15;8(7):R143-9. Screening for phasing atoms in protein crystallography. Boggon TJ, Shapiro L. Hope that help

[ccp4bb] Heavy-atom derivatives

Dear all, I'm looking for a method to solve the phase problem. Thus, I would like some help about heavy-atom derivatives. What is the best heavy-atom to make soaking? I tried Iodine (because my protein have a lot of tyrosines), but no results... I read some papers about quick-soak, its a good me

Re: [ccp4bb] imosflm errors

All of the above started to work On Mon, Jun 29, 2015 at 2:27 AM, Harry Powell wrote: > Hi Ivan > > When you say "it started to work" do you mean xia2, imosflm & ccp4i, or > just one of these?? > > :-) > > On 29 Jun 2015, at 08:38, xaravich ivan wrote: > > Thanks Graeme, > I just uninstalled CCP

Re: [ccp4bb] imosflm errors

Hi Ivan When you say "it started to work" do you mean xia2, imosflm & ccp4i, or just one of these?? :-) On 29 Jun 2015, at 08:38, xaravich ivan wrote: > Thanks Graeme, > I just uninstalled CCP4 and ccp4i Tcl, then re installed ccp4i tcl+tk first > and then CCP4+arpwARP and then it started to

[ccp4bb] AW: [ccp4bb] Single search Model input in Phaser!!!

Dear Ivan, Phaser is perfectly happy with an ensemble consisting of just one molecule. Your error must lay elsewhere, but we would need more information to be able to help you here. Best, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von xaravich ivan Gesendet: Mo

[ccp4bb] Single search Model input in Phaser!!!

Now that I am able to run ccp4i, I have a new problem. I generated a search model by chainsaw and I want to run Phaser in CCP4i with this search model as input, but it seems that I only can give an ensamble input and I cannot find a way to input a single chainsaw generated search model in Phaser. A

Re: [ccp4bb] imosflm errors

Thanks Graeme, I just uninstalled CCP4 and ccp4i Tcl, then re installed ccp4i tcl+tk first and then CCP4+arpwARP and then it started to work finally. I don't know why this would be the case, but for the timing it seems to work. Thanks, Ivan On Mon, Jun 29, 2015 at 12:07 AM, Graeme Winter wrote:

Re: [ccp4bb] imosflm errors

Dear Ivan This is not a xia2 error, rather something very unhappy with ccp4i - you should be getting this error from almost any ccp4i session? I expect more ccp4i expert people will be able to help here. It is also possible (indeed, easier) to run xia2 from the command line, for more information: