[ccp4bb] Postdoctoral positions at Washington University in St Louis

Dear Colleagues, Postdoctoral positions in membrane protein biochemistry and structural biology are available in the laboratory of Peng Yuan at Washington University School of Medicine in St Louis, Missouri. The lab is interested in understanding molecular mechanisms and physiological

Re: [ccp4bb] How to define the DNA bond between P and O3’ from two different symmetric units?

molecules in all these space groups. Actually, I am really confused about that because 20pb-DNA was used in crystallization. Peng 在2018年01月30 16时58分, "Nicolas FOOS"写道: Dear Peng, to me your problem sound a bit strange, except if it's a palindromic se

[ccp4bb] How to define the DNA bond between P and O3’ from two different symmetric units?

Hello, everyone， Recently, we solve a protein-DNA complex. 20bp-DNA was used for crystallization, but only 6bp was found in one symmetric unit. My question is： How to define the DNA bond between P and O3’ from two different symmetric units during my refinement? Peng

[ccp4bb] How can I use a reference model in Phenix refinement?

.. It seemed my reference.eff was not recognized. How can I use the reference model in Phenix refinement? Thanks, Peng

[ccp4bb] How can I refine B-factors only in CCP4 REFMAC?

Dear all, How can I refine B-factors only in CCP4 REFMAC? I do not want to refine the XYZ coordinations. Thanks Peng

[ccp4bb] How to merge two cif files of ligands.

Hello, I was wondering how to merge two cif files of ligands for refinement. Thanks, Peng

Re: [ccp4bb] zalman 3d monitors

Hi Tom, I think any passive 3D monitor may work. I have several LG monitors (e.g. model D2342P ) and one Zalman monitor in my lab and they all work fine with Pymol and Coot. Peng  Peng Gong, PhD Principal Investigator Wuhan Institute of Virology Chinese Academy of Sciences No.44 Xiao Hong Shan

Re: [ccp4bb] 3D Monitors

Sabine, I am using LG D2342P and it works fine with coot and pymol. Peng --- Peng Gong Wuhan Institute of Virology, CAS --- From: Sabine Schneider To: CCP4BB@JISCMAIL.AC.UK Sent: Friday

Re: [ccp4bb] Bicarb at low pH

发自我的 iPad 在 Oct 2, 2011，4:22 PM，Roger Rowlett 写道： > You can't change the pKa of CO2, which is 6.3. Any attempt to grow bicarb > complexes below pH 7.5 will be problematic due to CO2 bubble formation, which > may crack the crystal. What we do in these situations is to soak crystals in > a cr

[ccp4bb] Off-topic: ligand enrichment

PENG, Ph.D. student Structural Biology Group Shanghai Institute of Biochemistry and Cell Biology (SIBCB) Shanghai Institute of Biological Sciences (SIBS) Chinese Academy of Sciences (CAS) 320 Yue Yang Road, Shanghai 200031 P. R. China 86-21-54921117 Email: yjp...@sibs.ac.cn

Re: [ccp4bb] Twinning for P31

gt; > wrong point group, they can be very misleading.. > > > > From the information you have provided I would guess the PG is P321 but > I > > need the TRUNCATE plots to be happy about saying that; they give some > > feeling for data quality. > > Eleanor &

Re: [ccp4bb] Twinning for P31

pected value of 2 for >>> untwinned data. (1.5 for perfectly twinned data) >>> However it can be distorted by non-crystallographic translation, but you >>> dont seem to have that.. >>> Or by experimental errors and you need to inspect it in resolution >>>

[ccp4bb] Twinning for P31

Best regards, Yingjie Yingjie PENG, Ph.D. student Structural Biology Group Shanghai Institute of Biochemistry and Cell Biology (SIBCB) Shanghai Institute of Biological Sciences (SIBS) Chinese Academy of Sciences (CAS) 320 Yue Yang Road, Shanghai 200031 P. R. China 86-21-54921117 Email: [EMAIL PROTECTED]

Re: [ccp4bb] CCP4i can NOT run

p in ccp4.setup seems to be incorrect. > You should have: > setenv CCP4_MASTER/home/prog > > and then you would have: > > echo $CCP4 /home/prog/ccp4-6.0.2 > > I don´t think your problem has anything to do with tcl setup. > >Boaz > > - Origin

Re: [ccp4bb] CCP4i can NOT run

I have checked /etc/hosts, it is similar to what you say. I also tried to set it exactly the same as yours. But it did NOT work. Thanks! On Tue, Sep 30, 2008 at 10:24 PM, Ben Eisenbraun <[EMAIL PROTECTED]>wrote: > On Tue, Sep 30, 2008 at 10:48:27AM +0800, Yingjie Peng wrote: > > I

Re: [ccp4bb] CCP4i can NOT run

xecutable is called something like "tclsh8.4" then CCP4i will > not recognise it..you have to make a symbolic link to the executable, in the > same directory, as below: > > ln -s tclsh8.4 tclsh (or the other way round, check)..also make sure you > have read (and possibly execu

[ccp4bb] CCP4i can NOT run

ry much in advance. Best wishes, Yingjie Yingjie PENG, Ph.D. student Structural Biology Group Shanghai Institute of Biochemistry and Cell Biology (SIBCB) Shanghai Institute of Biological Sciences (SIBS) Chinese Academy of Sciences (CAS) 320 Yue Yang Road, Shanghai 200031 P. R. China 86-21-5492

[ccp4bb] Degradation and phasing

ce on preventing protein degradation during purification or preventing phasing during crystallization. Any comments or suggestion are welcome. Thanks in advance. Yingjie Yingjie PENG, Ph.D. student Structural Biology Group Shanghai Institute of Biochemistry and Cell Biology (S

[ccp4bb] Problem with the DLS instrument

. Many thanks in advance. Yingjie Yingjie PENG, Ph.D. student Structural Biology Group Shanghai Institute of Biochemistry and Cell Biology (SIBCB) Shanghai Institute of Biological Sciences (SIBS) Chinese Academy of Sciences (CAS) 320 Yue Yang Road, Shanghai 200031 P. R. China 86

[ccp4bb] Generating .top and .param for metal-benzene coordination

also be due to some other reasons that I am not aware of for now. Any information will be highly appreciated. Thanks! Best, Peng

Re: [ccp4bb] Mico-focus beamline

Thank you so much for all you guys' replies, It looks like APS is a realistic option, I have been to 23ID D before, I didn't know they now have the micro focus capability. Thanks again for all your help! Best, Peng On 7/20/07, Martin Austin Walsh <[EMAIL PROTECTED]> wrote:

[ccp4bb] Mico-focus beamline

the hair through a layer of oil used for microbatch to seed new drops. It will be great if anybody has some hands on experience on doing microseeding in microbatch can give me some insights on this problem. Thanks you very much in advance for all your help! Best, Peng

[ccp4bb] Torsion of acetyl coenzyme a

OAQ OAR OAS OAQ torsion T022 0 O4* C1* N9 C4 C8 N7 C5 C4 N3 C2 \ N1 C6 N6 -- Peng Zhang, Ph.D. Student Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 320 Yue-Yang Road Shanghai

[ccp4bb] Binding pocket volume

Dear all, Is there anyone who can tell me how to calculate the volume of substrate binding pocket in a protein structure? I want to use it to the quantify the conformational change caused by induced fitting. Thanks very much. Yingjie Peng Yingjie PENG, Ph.D. student Structural Biology Group

Re: [ccp4bb] modelling with sad/mad data

data sets - then run uniqueify -f FreeRflag merged.mtz > > That will keep the existing flags and generate new ones for the new > reflections.. > > Then if you want to you can convert back to the CNS format. > Eleanor > > > Peng Zhang wrote: >> Hi, Peter, >> >

Re: [ccp4bb] modelling with sad/mad data

data sets - then run uniqueify -f FreeRflag merged.mtz > > That will keep the existing flags and generate new ones for the new > reflections.. > > Then if you want to you can convert back to the CNS format. > Eleanor > > > Peng Zhang wrote: >> Hi, Peter, >> >

Re: [ccp4bb] modelling with sad/mad data

a and peak data.I try to compare them because I want to make it clear that the difference may be caused by the mad data while not the model itself. Thanks. > Hi Peng Zhang, > > The presence of radiation damage might cause some problems. > Do so see any obvious features in the difference ma

Re: [ccp4bb] modelling with sad/mad data

e Free R set from the native to the Se data? > Eleanor > > > Peng Zhang wrote: >> Dear friends, >> >> Recently, I have solved a structure using mad method. When using the >> peak >> data(2.3A) as the native for structure refinement, the gap between R >&g

[ccp4bb] modelling with sad/mad data

real native one(2.7A),it seems OK with R=0.24 and Rf=0.28. Does anyone have the similar experience? what should I pay attention to when using the sad/mad data as the native one for modelling and refinement? Thanks in advance. -- Peng Zhang, Ph.D. Student Institute of Biochemistry and Cell

Re: [ccp4bb] Filament lifetime on Rigaku Micromax007

-161-275-5090/5658 > Fax: +44-161-275-1505 > email: [EMAIL PROTECTED] > Intranet:http://www.intranet.ls,manchester.ac.uk/facilities/research/xraycrystallography > Internet:http://www.ls.manchester.ac.uk/research/facilities/xray > > -- Peng Zhang, Ph.D. Student Institute of Bi