Re: [ccp4bb] Looking for a student and/or help with finalizing new virus spike structures

I am willing to help for your work. Can we communicate for the issue throgh my e-mail fenghui...@163.com with fanfeng...@mail.tsinghua.edu.cn cced? Dr Fenghui Fan Replied Message | From | Grant Hansman | | Date | 07/09/2024 12:52 | | T

Re: [ccp4bb] recombinant protein-based fluorophores

eGFP, for example, can be fused to the C- terminal of your target protein. Fluorescent proteins were usually highly soluble, especially if you select to express in insect cells, which has the tendency to express proteins in soluble states. Smith | | Smith Liu | | 邮箱：smith_liu...@163.com | 签

Re: [ccp4bb] AW: Re: [ccp4bb] AW: Re: [ccp4bb] coordinate transformation

sorry, how i move the mtz into the transformed pdb for the question in my previous email? | | Smith Liu | | 邮箱：smith_liu...@163.com | 签名由 网易邮箱大师 定制 在2017年12月18日 23:37，Smith Liu 写道： thanks. i may mean something other. for example, if i rotate the pdb by 30 degree (or 29.5 degree), or i

Re: [ccp4bb] AW: Re: [ccp4bb] AW: Re: [ccp4bb] coordinate transformation

thanks. i may mean something other. for example, if i rotate the pdb by 30 degree (or 29.5 degree), or i shift the pdb along x-axis by something for example 0.123*a, then how i move the mtz map correspondingly for the fitting of mtz into the transformed map? | | Smith Liu | | 邮箱：smith_liu

Re: [ccp4bb] coordinate transformation

Dear All, If I have a set of PDB with the corresponding density map, after I transform the PDB based on the suggestion of everybody, is any way to transform the map so that the map will be fit with the transformed PDB? Smith At 2017-12-18 18:39:34, "Eleanor Dodson" <176a9d5ebad7-d

Re: [ccp4bb] secondary structure prediction

yes | | Smith Liu | | 邮箱：smith_liu...@163.com | 签名由 网易邮箱大师 定制 在2017年12月07日 09:11，zheng zhou 写道： Thanks for many advices. I was not clear in the previous email. I know the close homologous protein (20% identity, total 500aa), but the fragment hits (30~40aa, identity 40~50%) are from other

Re: [ccp4bb] secondary structure prediction

Rosetta | | Smith Liu | | 邮箱：smith_liu...@163.com | 签名由 网易邮箱大师 定制 在2017年12月06日 22:14，zheng zhou 写道： Dear CCP4 community, Sorry for the off-topic question. I am trying to design constructs for structure studies. It only has a homolog structure in PDB with sequence identity ~20%. When I

Re: [ccp4bb] script for shape complementarity

how about modify your selected part of protein into two molecules | | Smith Liu | | 邮箱：smith_liu...@163.com | 签名由 网易邮箱大师 定制 在2017年12月03日 16:21，joy yang 写道： Dear All, can anyone shed a clue on how to define the suface area used in ccp4 sc (shape complementarity) script? The script

Re: [ccp4bb] RMSD calculation for large assemblies

how about mean square deviation of the rmsd of each c alpha？ | | Smith Liu | | 邮箱：smith_liu...@163.com | 签名由 网易邮箱大师 定制 在2017年12月02日 22:48，Reza Khayat 写道： Hi, I'm analyzing the RMSD between 60 subunits of a virus. Can someone identify a program that can generate a spread fo

Re: [ccp4bb] Vacuum pump in cold room

use the brand of vacuum pump without oil 发自网易邮箱大师 在2017年10月29日 01:17，Denis Rousseau 写道： Does anyone have experience with a vacuum pump in cold room? We have been told they may not start because of the viscosity of the oil? Thanks Denis Rousseau From: CCP4 bulletin board [CCP4BB@JISCMAIL.

Re: [ccp4bb] OFF topic (Protein degrades during Dailysis)

suppose protease is the issue, then avoid overnight dialysis 发自网易邮箱大师 在2017年10月26日 22:18，Anamika Singh 写道： Dear All, I am purifying the His-tagged proteins ( 21Kda) using buffer 20mM Tris, 150mM Nacl, and 5mM MgCl2 with 500mM imidazole. Earlier I was facing the precipitation problem during

Re: [ccp4bb] Off topic: denaturing urea gels

your enzyme cannot give definite fragment. thus smear 发自网易邮箱大师 在2017年09月30日 19:28，Mohammad Khan 写道： Dear all, I am working with an exonuclease and I run the digested DNA on a 8Murea-20%acrylamide gel in TBE buffer. I use the Mini-Protean BioRad system and cast gels of about 8.6x6.5 cm dimen

Re: [ccp4bb] Biotin binding protein

if necessary, phage or yeast display to screen 发自网易邮箱大师 在2017年09月24日 07:05，Reza Khayat 写道： Hi, Sorry for the non crystallography question. Is anyone aware of monomeric proteins (<20kDa) that can bind to biotin? We need this for a couple of different projects where biotin covalently modifies

Re: [ccp4bb] Difficult purification with imac columns

change buffer，or use different resin matrix from another compny 发自网易邮箱大师 在2017年09月15日 19:53，Narayanan Ramasubbu 写道： Hi. We are working on a periplasmic protein that breaks naked glycans in peptidoglycans. There is truncated structure available but our target is the full length protein. The di

Re: [ccp4bb] Fast searching of articles related to your PubMed indexed paper

can you updated the server so that the most recent articles can be found? 发自网易邮箱大师 在2017年07月25日 11:49，Yaoqi Zhou 写道： Fast searching of articles related to your PubMed indexed paper Are you spending too much time searching the literature to prepare your grant proposals, manuscripts and kee

Re: [ccp4bb] Off topic: Flourescence anisotropy measurement

May i ask, whether the fluoresnce anisotropy method was reliable enough to determine the stoichiometry of a protein complex? 发自网易邮箱大师 在2017年07月22日 03:44，Phoebe A. Rice 写道： You might also be getting aggregation. If you do an old-fashioned EMSA ("gel shift") assay, does it hang up in the well?

[ccp4bb] 回复：[ccp4bb] suggestions are welcome

please characterize your a and b to see they really what they are 发自网易邮箱大师 在2017年07月18日 10:25，高艺娜 写道： Hi all , It has been reported the Negative stain EM of a protein A-B complex, but according to my gel filtration results (I purified A and B respectively for incubation) , I found that A co

Re: [ccp4bb] long loop

Fab fragment binding towards long loop 在2017年07月04日 23:22，dongxiaofei 写道： Dear ALL, I want to make a protein crystal,but there is a long loop between domains of protein , which contains two small domains owning about 40 amino acids respectively and a loop about 70 amino acids. Loop is so lo

Re: [ccp4bb] Separating Monomers and Dimers

it was not stable for frozen storage. if necessary，using protein fresh without frozen 发自网易邮箱大师 在2017年06月27日 20:22，jai mohan 写道： Dear all, I am working on a Red Fluorescent Protein (His-Tag) molecular weight around 27kDa. After purification I ran a SDS page, the band at 27kDa confirms the mono

[ccp4bb] Fw:[ccp4bb] on Cell & Symmetry in coot

Dear All, I mean if the radius set in the Coot "Cell Symmetry" was too small, not enough monomers (less than 6) can be displayed to show the "continuous helix with a six-fold screw axis". If the radius was too large, as for the "continuous helix with a six-fold screw axis" can be regarded as

[ccp4bb] on R-free label

Dear All, Will you please tell me how to know whether my mtz file has the R-free label or not? SMith

Re: [ccp4bb] Rfree below Rwork

If both the PDB and mtz for the pdb have been assigned to P1 space group for some reason, can this lead to Rwork higher than Rfree during refinement? If after converting my PDB and mtz to P1 space group, and I have forgotten what is the original space group for my PDB and mtz before conversion

[ccp4bb] on mosaicity estimation by iMosflm

Dear All, When I do mosaicity estimation by iMOSFLM, it shows, "The mosaicity estimation has not worked for some reason. Message from Mosflm is - Unable to estimate mosaicity automatically from this image-determine a value visually. You should enter an estimated value to replace 0.05". First I

[ccp4bb] on secondary structure restraint

Dear All, Even with the Coot secondary structure (for example helix) restraint selected and by this way we keep the secondary structure, I find the protein secondary structure formed in this way was not so typpical, for example, not all CO ( i) and NH (i+4) forms H-bonds, and there are H-bonds

[ccp4bb] on resolution and explaination of the intersubunit bonds

Dear All, In order to acceptably explain the salt bridges, hydrophobic interactions and H-bonds among subunits in the crystal structure of a protein complex, is there a threshold resolution of the crystal, for example, if the crystal is poorer than 4A or 5A, the crystal structure solved cannot

[ccp4bb] on b-factor

Dear All, In the PDB file, the b-factors were only determined by the quality of the map, is this view right or not? Smith

[ccp4bb] HIS related crystallography issue

l's phenix plug. PDB_REDO does HQN-flips automatically based on WHAT _CHECK results and refines your model in Refmac. Cheers, Robbie Sent with my Windows Phone Van: Robbie Joosten Verzonden: ‎20-‎5-‎2015 14:30 Aan: Smith Liu; CCP4BB@JISCMAIL.AC.UK Onderwerp: RE: [ccp4bb] HIS related crysta

[ccp4bb] HIS related crystallography issue

Dear All, Suppose the protein crystal resolution is about 2-3A, then in the map it should be rather difficult to distinguish the C and N in the sidechain of HIS. In this way we may regard the sidechain of HIS is flippable. But suppose in one flipped conformation of the HIS, the free N in the s

[ccp4bb] how to actively assign H to N of His

Dear All, After CCP4 or phenix refinement, I find the H position of N in specific His residues needs to be regularized based on the function of that His. Will you please advise on how to actively assign H to one or two of the 2 N in the His residue in the PDB file? Or do we have a server, whi

[ccp4bb] on the contour level in Coot

Dear All, For the contour level in the Properties in the Dssplay of the Display Manager in Coot, the contour level should be exacly the sigma value we see in the published crystallography paper, am I right? But I have paid attention to a paper which has a sigma level of 6-7 for its densty. Wil

[ccp4bb] on space group

Dear All, Alhough there are on-line explainations on the space group, I found it was difficult to fully understand. Here we take P 1 21 1 as an exmaple, will you please explain to me with easy language what each number indicates？Or do we have a on-line server which can demonstrate the meaning

[ccp4bb] on the contour level in Coot

If for both a mtz density and mrc map I set the contour level as 0.15, does the 015 has the comparable significance for the mtz density and mrc map? Smith

Re: [ccp4bb] self-rotation in the absence of NCS

I recently solved a 4-identical chain protein structure. First I got it from initial model with NCS, good enough. Then from the initial model I process it without NCS, quality better than solved with NCS. Smith At 2015-04-30 02:07:31, "Eleanor Dodson" wrote: Hmm - I think these peaks

[ccp4bb] on the electron microscopy function of refmac5

Dear All, The CCP4 document says refmac can process electron microscopy map for refinement. But I cannot localize that function in the refmac5 of the CCP4. Will you please advise how to have the refmac process the electron microscopy map? Smith

Re: [ccp4bb] on NCS restraint

Dear Jurgen, My understanding is that NCS restraint can significantly enhance the speed of calculation, but considering the subunits even with the eactly same sequence may not be identical, to have NCS restraint may be not necessary or may be not good for the refinement, am I right? Smith

Re: [ccp4bb] Problem in optimization

Additive screening At 2015-04-11 18:00:21, "高艺娜" wrote: >Dear all >I have tried a variety of methods on regular optimization of the crystal ,but >all have failed,the 17 kDa protein crystal still have many nucleation and poor >diffraction also poor resolution(the best 3.5－4.0Å） >The cry

[ccp4bb] on building a helix fragment by coot

graphical interface there are "Sequence closest fragment" and "Sequnece all fragments!"? I ask these questions in order to avoid my failling to do something which Coot can do. I am looking forward to getting your reply. Smith Forwarding messages Fr

Re: [ccp4bb] on building a helix fragment by coot

gments into density. > >Good luck, > >Rhys > >From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Smith Liu >[smith_liu...@163.com] >Sent: 01 April 2015 05:58 >To: CCP4BB@JISCMAIL.AC.UK >Subject: [ccp4bb] on building a

[ccp4bb] on building a helix fragment by coot

Dear All, If I need to build a fragment of helix to a fragment of density by coot, should I use baton build method or should I use place Helix here function? I have tried both, but I find it is difficult to place the sidechains to the map mosition which looks like where shold be occupied by th

[ccp4bb] on refinement by coot

Dear All, Suppose there is a 10-residue helix, there are 2 of the 10 Calphas do not position so well so the sidechains of the 2 Calphas do not align with the density. Is any Coot commands which can refine the 2 Calpha positions and the corresponding sidechains? By the way, if I use Wincoot, wi

[ccp4bb] on Baton build

Dear All, In coot when I try to build a peptide by baton method, I find the starting point of the baton starts from somewhere in the sidechain rather than from the Calpha position. In addition, when I try to changing the starting residue by Baton-build params, the starting point of the Baton d

[ccp4bb] on openning the PDB file and the mtz file by Coot

Dear All, When we by Coot open the PDB fle and the mtz file from the same refinement, the protein backbone (and the sidechains) and the electron density always fit automatically. Will you please tell me the mechanism of the Coot how the PDB file automatically fit the mtz file in its graphical

Re: [ccp4bb] how to recover my data

(such as reprocessing the images). Cheers -- Ian On 7 March 2015 at 06:29, Smith Liu wrote: Dear All, The current version of CCP4 does not contain mtzdump. I use UCLA MBI — mtzdump to process it. For a mtz file, the output says there was no valid reflection data. For another mtz fi

Re: [ccp4bb] how to recover my data

the file with random programs has even less chance of working than I have of winning the lottery! As others have suggested there are much easier ways of recovering your data (such as reprocessing the images). Cheers -- Ian On 7 March 2015 at 06:29, Smith Liu wrote: Dear All, The current

Re: [ccp4bb] how to recover my data

Dear All, The current version of CCP4 does not contain mtzdump. I use UCLA MBI — mtzdump to process it. For a mtz file, the output says there was no valid reflection data. For another mtz file, it only gave about 50 lines information (not a new mtz file). As for the original mtz is very large,