Re: [ccp4bb] protein oligomer

(I presume you do FPLC). Have a look at chaotropic agents used in protein purification, The answer is generally dependent on the protein/proteins you are trying to purify and is not necessarily straightforward. Kinds regards On Sun, Jul 19, 2020 at 12:08 PM 张士军 <21620150150...@stu.xmu.

[ccp4bb] protein oligomer

Dear all: Any ideas to decrease protein polymer formation? my protein was easy to form oligomers and precipitation when do purification,I have tried add glycerol and DTT,both didn't work. Does anyone has experience to avoid it happening. Thanks! Best Regards

[ccp4bb] cannot open NOMAD-Ref server

Dear all Does anyone have used NOMAD-Ref(normal mode analysis, deformation and refinement) server (http://lorentz.immstr.pasteur.fr/nomad-ref.php)? I want to do refinement of my crystal structure, but it cannot be opened when I using "X-ray refinement", the link is

Re: [ccp4bb] muti-crystal averaging

Sent Time:2019-07-15 22:08:01 (Monday) To: "张士军" <21620150150...@stu.xmu.edu.cn> Cc: "CCP4BB@JISCMAIL.AC.UK" Subject: Re: [ccp4bb] muti-crystal averaging Do you mean these crystals have different unit cells? If so then DMMULTI is a useful technique.. Or do you mean yo

[ccp4bb] muti-crystal averaging

Dear all I want to average several sets of crystal data together, and I saw some paper used DMMULTI program in CCP4, but I didn't find this program in ccp4, but only find Blend in ccp4 which only used for unmerged reflection files. I wondering is there any programs could use HKL2000 processed

[ccp4bb] RAMACHANDRAN outlier of Thr

Dear all The problem is when I check RAMACHANDRAN outlier with coot, it shows zero, while it become one Thr outlier in phenix.vadition. so I am confusing about the standard of RAMACHANDRAN outlier in coot and phenix.validation, any difference between them? Thanks yours shijun

Re: [ccp4bb] SO4 or PO4

hate donor to acceptor hydrogen bonding contacts. Sulfate rarely has donor to acceptor hydrogen bonding contacts, as it is SO4= at any reasonable pH. Roger Rowlett On Sat, Feb 16, 2019, 4:06 AM 张士军 <21620150150...@stu.xmu.edu.cn wrote: Dear all I have got a crystal grown at the condition both ha

[ccp4bb] SO4 or PO4

Dear all I have got a crystal grown at the condition both have ion of SO4 and PO4, and the diffraction resolution is very well, but the problem is coming: how to tell which is which just from electron density? I think they are exactly same. Thanks a lot !!! Beat Regards Shijun

[ccp4bb] R-flag choose

Dear all I am confusing the choose of free R-flags recently. Rfactor means calculatted from reflection not used in refinement,so what's big the difference between different percentage of R-flags,like it's about 5% in ccp4 -refmac, while it is 10% in phenix-refinement,what's the difference

Re: [ccp4bb] disulfate bond ?

. You have spotty difference density over the ligand. Shift it left by one carbon bond and redune to see if density fits better. Artem On Wed, Jul 4, 2018, 02:26 张士军 <21620150150...@stu.xmu.edu.cn> wrote: Hi all I got a structure which has COA in it, and the SH in the tail of CO

[ccp4bb] Rfree going up after refinement

Dear all I have got my se-phase structure with ccp4-CRANK2-SAD, and its Rfree is 0.26 when CRANK2 output, but the Rfree is higher to 0.36 when I refine it with refmac or phenix-refinement. does it mean I got a wrong phase, or I didn't got the right parameters when refinement.BTW, the

[ccp4bb] phenix refinement about cis-proline

Dear all I am refining a structure which has cis-Pro and trans-Pro, the tans-Pro is gone when I set the "threshold degrees for cis-peptide " from default 45 to 65, but still has cis-Pro. While no significant change when I set it to 15. My question is how to set in phenix refinement to clear

[ccp4bb] BUCCANEER label choose

Dear all I am confusing how to choose or enter the labels when I do density modification and autobuilding with ccp4 parrot and buccaneer or ARP/wARP, there are three different options like "use Free R-flag ","use map coefficient" and "use PHI/FOM instead of HL coefficient" in the figure I

[ccp4bb] Dials

Dear all When I run dials.index it result me "Sorry: No suitable lattice could be found", but the other software can give me C2 space group. How could I DO with this situation Best Regards Shijun

[ccp4bb] cannot read h5 data file

Dear all I just collected some data with Eiger16M whose file format is *.h5. But I cannot read it with HKL2000, because I don't have the Eiger16M detector license now, while, I have *.cbf detector license. So I transfered the *.h5 to *.cbf files, but the problem is XDSGUI still cannot read

[ccp4bb]

Hi all It always fail when I run ccp4-AMPLE, and log file says Cannot find executable theseus in PATH. Please give the path to theseus *** * Information from CCP4Interface script

[ccp4bb] high Rfree

Hi everyone I have got a anti-parallel coiled-coil structure in a short fragment recently, then I want to solve a longer fragment structure with phenix-MR using this short fragment structure as a model.The result is not good because of the Rwork and Rfree is high.So I think the longer

Re: [ccp4bb] SAD phasing

> by ccp4i, to complete the structure. > Please note that for the final refinement stages (which involve manual model > adjustment), one should switch from this SHELXE-provided file to a .mtz file > written by XDSCONV or (C)TRUNCATE because SHELXE does not use the > French

[ccp4bb] SAD phasing

Hello everyone I am learning phasing SAD data now ,and I got some files(like i.phs , .pdb ,fa.res, fa.pdb) when I using SHELXC/D/E,and I know fa.pdb and fa.res (which contain heavy atom information) are used for the further solution searching ,and .phs file can read by coot. my question

[ccp4bb] merge different crystal data

Hi ccp4 guys I have a crystal whose spacegroup is I4,and the cell dimension are a=b=83，while ,the C axis is 315.SO the diffraction data is very bad when the crystal started to rotate to some degree ,and it is difficult to process the data .So I wondering there any strategy to resolve this