[ccp4bb] how generate maps only to cover atoms in pdb

Hi, I want to generate maps only covering atoms in the pdb file. I tried fft-creat map in ccp4i (output map to cover all atoms in pdb), but it actually also generated map in places other than pdb atoms. Are there any other ways to do this? Thank you. -- Best regards, Joe

Re: [ccp4bb] Interaction between the domains

Contact in CCP4i can calculate the distance between specified chains/residues. Pymol can display hydrogen bonds too. Joe peter hudson wrote: Hello all I have a very quick question. Is there any programme, which can calculate the H-bond pattern or residues involved in H-bonds formation betw

[ccp4bb] Refmac failed at the end of run

Hi all, I am using refmac in ccp4i 6.1.1 (installed in windows). It runs well when using automatic weight, but failed when using user-specified weight (0.12 in this case). I attach the error message as follow. Your help is very much appreciated. .. 18 0.2064 0.2348 0.8464076

[ccp4bb] Please recommend screen kits for membrane proteins

Sorry for the off-topic subject. I am new to membrane proteins. We already have Qiagen MB class I and II, Sigma Membrane, and Membrane Gold kits, but I want to know if there other kits out there you would recommend. Thanks a lot, Joe

[ccp4bb] Questions regarding Peptidoglycan-binding protein

Dear all, Thank you in advance for your expert opinions. I am working on a peptidoglycan (PG)-binding protein, which is composed of two functionally identical domains. Interestingly, when subjected to gel filtration chromatography (Superdex 200), both full-length protein and the single domains mi

Re: [ccp4bb] Fwd: [ccp4bb] crystallisation robot

Hi, Does anyone have information about how long it takes to set up a 96-well tray for the crystallization robots available? Besides cost per tray and maintenance cost, another important feature we consider is the time for setting up a 96-well tray. It is an important factor since we are talking

[ccp4bb] ---solved---Fwd: [ccp4bb] problem in running DM (NCS averaging)

7 8:13 AM Subject: RE: [ccp4bb] problem in running DM (NCS averaging) To: JOE CRYSTAL <[EMAIL PROTECTED]> Cc: [EMAIL PROTECTED] Hi Your first error seems to have been caused by invalid input. The program seems to have read the lines AVERAGE REFI and LABOUT ... correctly, so the problem

[ccp4bb] problem in running DM (NCS averaging)

Dear all, I tried to run DM for NCS averaging (DM module in CCP4i 6.0.2 installed under Windows XP), but the running failed at different stages with various error message as listed below. I was told it could be an installation problem, but I don't know how to fix it. I am wondering if you have

[ccp4bb] need help--Rfree is not decreasing

Dear all, I am refining a structure at 2.0 A. The water molecules have been added using arp/warp resulting Rwork/Rfree=21/26% (about 370 HOH for 360 residues). After 10 cycles of refmac refinement (wt 0.3), Rwork/Rfree went up about 1.5% to 22.5/27.5%. I did some minor adjustments and add/del

Re: [ccp4bb] Protein-DNA complex for crystallization

Hi Kumar, I also have the same issue. If you get any helpful response, could you forward me a copy? Thank you. P.S. Could anyone who has any comments or suggestions on this issue also forward the response to ccp4bb? Thank you in advance. Best, Joe On 7/16/07, bputcha <[EMAIL PROTECTED]>

[ccp4bb] Fwd: extend resolution in refmac

Dear all, I am refining a structure in Refmac at 2.3 A and I set resolution range to 2.2 A to extend the resolution. However, Refmac seemed to ignore my setting and still refined structure at 2.3 A. Thank you in advance for your any helpful suggestions. Best, Joe

[ccp4bb] extend resolution in refmac

Dear all, I am refining a structure in Refmac at 2.3 A and I set resolution range to 2.2 A to extend the resolution. However, Refmac seemed to ignore my setting and still refined structure at 2.3 A. Thank you in advance for your any helpful suggestions. Best, Joe