Re: [ccp4bb] calculate buried area between antibody and antigen

ructures deposited into the PDB > database the number might changes. > > Thank you ! > > yamei > -- Jiamu Du, Ph.D. Postdoctoral Research Fellow Laboratory of Structural Biology Memorial Sloan-Kettering Cancer Center RRL 269, 430 E 67th Street New York, NY, 10021 E-mail: d...@mskcc.org Tel: (217) - 417 - 9897

Re: [ccp4bb] how to combine the experimental phase and molecular replacement phase

phasing. > Here is the procedure > http://www.globalphasing.com/sharp/manual/chapter4.html#ExternalPhaseInformation > Cheers > David > > > Le 12 juil. 2011 à 18:08, Jiamu Du a écrit : > > Dear All, > I am now working on a low resolution phase determination (around 3.3 A

[ccp4bb] how to combine the experimental phase and molecular replacement phase

. The homologue region has a good map while other region only show a poor map. I think the combination of experimental phase and MR phase might improve the map. Is there anybody can help find which program can work on this? Thanks. -- Jiamu Du, Ph.D. Postdoctoral Research Fellow Laboratory of

[ccp4bb]

uit unusual > .Kindly help me sort out this problem. > Some basic information regarding the data are given below. > > Resolution range 41.24-2.7 > Rsym -15 > I/Sigma-17.2 > I/Sigma -4.2 > (In highest resolution shell) > Rfactor -21.4 > R free -24.2 > > Tha

Re: [ccp4bb] about RMSD bond lengths and angles

> structures and that it should be close to small molecule values is not > correct. > > > > br > > > > *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of > *Jiamu > Du > *Sent:* Wednesday, April 13, 2011 2:06 PM > *To:* CCP4BB@JISCMAIL.AC

[ccp4bb] about RMSD bond lengths and angles

Dear All, I am wondering about the ranges of RMSD bond lengths and angles. What are the acceptable ranges for these two values? Is there some statistics for them? Thanks and best wishes.

Re: [ccp4bb] where to buy stereo glasses for making stereo figures?

esearch.com/product_detail.aspx?cid=26&sid=145&pid=439 > Jürgen > > On Mar 30, 2011, at 10:24 PM, Jiamu Du wrote: > > For side by side stereo figures. > Thanks. > > On Wed, Mar 30, 2011 at 9:42 PM, Ingrid Attinost < > ingrid_attin...@hotmail.com> wrote: > >>

Re: [ccp4bb] where to buy stereo glasses for making stereo figures?

P4BB@JISCMAIL.AC.UK > > Dear All, > I want to buy a stereo glasses for making stereo figures, especially for > the labeling. Is there a company sell it? > > Thanks and best wishes. > -- Jiamu Du, Ph.D. Postdoctoral Research Fellow Laboratory of Structural Biology Memorial Sloan-

[ccp4bb] where to buy stereo glasses for making stereo figures?

Dear All, I want to buy a stereo glasses for making stereo figures, especially for the labeling. Is there a company sell it? Thanks and best wishes.

[ccp4bb] about SUPEROSE 6 PG XK 16/70

the dead volumn and whole column volumn? Thanks and best wishes. -- Jiamu Du, Ph.D. Postdoctoral Research Fellow Laboratory of Structural Biology Memorial Sloan-Kettering Cancer Center RRL 269, 430 E 67th Street New York, NY, 10021 E-mail: d...@mskcc.org Tel: (917) - 292 - 4616

Re: [ccp4bb] about the Hampton Research FoldIt kit

kFoldProteinRefoldingKit.php > > François > = > > > Francois Hoh, PhD > CENTRE de BIOCHIMIE STRUCTURALE > 29 rue de Navacelles > 34090 MONTPELLIER > France > > Tel : (33) 4 67 41 77 06 > Fax : (33) 4 67 41 79 13 > e-mail francois@cbs.cnrs.fr > (http://www.cbs.cnr

[ccp4bb] about the Hampton Research FoldIt kit

Hi, everyone, I remembered that there was a Hampton kit called FoldIt for testing the refolding buffer. But now, I can not find it on their website. Is there anyone who knows about it? Thanks. -- Jiamu Du, Ph.D. Postdoctoral Research Fellow Laboratory of Structural Biology Memorial Sloan

Re: [ccp4bb] Softwares for Protein-Protein docking!

have got some parsing related error! > (indicative of some errors in the input PDB files.). I have checked my pdb > files and did not figure out anything wrong. > May I please get some suggestions about it from any of the experienced ones > in this area? > > regards, > Anil >

Re: [ccp4bb] Softwares for Protein-Protein docking!

idea where the protein will bind to the receptor. Is there something > like AUTODOCK for macromolecules? > > It will be amzing if I get some suggestions. > > Thanks in advance, > Ivan > -- Jiamu Du, Ph.D. Postdoctoral Research Fellow Laboratory of Structural Biology Memori

Re: [ccp4bb] scala statistics and reindexing

ext. 221 > fax: (53-7) 272 0644 > email: talav...@cim.sld.cu > * > -- Jiamu Du, Ph.D. Postdoctoral Research Fellow Structural Biology Program Memorial Sloan-Kettering Cancer Center RRL 269, 430 E 67th Street New York, NY, 10021 E-mail: jiam...@gmail.com

Re: [ccp4bb] Questions about Phaser

ee many positive or negative densities). The 5th solution didn't > fit the density at all. I saw many empty density in the map, indicating I > still need to find more solutions.The space group I am using is P3 2 1. > Could this be caused by a wrong space group? > Could anyone give me s

[ccp4bb] how to generate the figure of buried surface area

Dear all, I am analyzing a complex structure and generate figure using the program Pymol. Here I want to generate a figure to show the buried surface area. How to generate this type figrues? Thanks and best wishes. -- Jiamu Du, Ph.D. State Key Laboratory of Molecular Biology Institute of

Re: [ccp4bb] question of extra high B factor

: 4 > 6.580 - 8.970 : 18 > 8.970 - 11.360 : 41 > 11.360 - 13.750 : 50 > 13.750 - 16.140 : 34 > 16.140 - 18.530 : 9 > 18.530 - 20.920 : 3 > 20.920 - 23.310 : 3 > 23.310 - 25.700 : 5 > > > > > -- Jiamu Du, Ph.D. State Key Laboratory of Molecular Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 320 Yue-Yang Road Shanghai 200031 P. R. China Tel: +86-21-5492-1117 E-mail: jiam...@gmail.com

Re: [ccp4bb] question of extra high B factor

Dear Vonrhein, On Fri, Jul 31, 2009 at 12:47 AM, Clemens Vonrhein < vonrh...@globalphasing.com> wrote: > Dear Jiamu, > > On Fri, Jul 31, 2009 at 12:00:25AM +0800, Jiamu Du wrote: > > I am refining a structure of a complex between of 50kD protein and a 20kD > > glycos

Re: [ccp4bb] question of extra high B factor

Arlington Ave.phone 419 > 383 5414 > Toledo OH 43614 fax > 419 383 3785 > > _________ > > > -

Re: [ccp4bb] question of extra high B factor

I am using TLS refinement with Phenix for the structure refinement. On Fri, Jul 31, 2009 at 12:00 AM, Jiamu Du wrote: > Dear All, > I am refining a structure of a complex between of 50kD protein and a 20kD > glycosylated protien. The data is of 2.9 A resolution. The wilson B facto

[ccp4bb] question of extra high B factor

this value acceptable? 3. In the same of similar resolutionIs, is there some other structures like this situation? A component or a subunit of the protein has a extra high B factor as high as 130. Thanks and best wishes. -- Jiamu Du, Ph.D. State Key Laboratory of Molecular Biology Institute of

Re: [ccp4bb] problem of Refmac refinement on twinning data

On 22 Jun 2009, at 11:26, Boaz Shaanan wrote: > > I observe the same oddity for linux refmac 5.5.0092 >> >> Boaz >> >> - Original Message - >> From: Jiamu Du >> Date: Monday, June 22, 2009 7:11 >> Subject: Re: [ccp4bb] problem of

Re: [ccp4bb] problem of Refmac refinement on twinning data

I am using Refmac on a windows xp system. On Mon, Jun 22, 2009 at 12:05 PM, Jiamu Du wrote: > Dear all, > I am using Refmac version 5.5.0088. The data are twinning, so the key word > 'twin' was added into the scripts. > The refinement result is as pasted below: >

[ccp4bb] problem of Refmac refinement on twinning data

BIN FREE R VALUE SET COUNT, BIN FREE R VALUE all zero? Another question is that, my data is of 2.38 angstron resolutiom, but refinement result lists a high resolution of 2.3 angstrom. If I did not add the keyword 'twin', all the results are normal. Thanks and best wishes. -- Jiamu

[ccp4bb] Refmac5 error

and model are tested to be refined well on a Linux system. Is there any suggestion? Thanks and best wishes. -- Jiamu Du, Ph.D. State Key Laboratory of Molecular Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 320 Yue-Yang

[ccp4bb] How to chemically modify the side chain of Glu?

neutralize its negative charge at least. While these chemicals should not have cytotoxic effects to cell. Because the experiment must be carried out with live cells. Is there any suggestions or references? Thanks. -- Jiamu Du, Ph.D. State Key Laboratory of Molecular Biology Institute of Biochemistry and

Re: [ccp4bb] generating omit maps

sfcheck -f data.mtz -m model.pdb -omit 2 -map On Tue, Dec 16, 2008 at 6:29 PM, Alexei Vagin wrote: > SFCHECK (method unknown) >> >> > please see CCP4 documentation > -- Jiamu Du, Ph.D. State Key Laboratory of Molecular Biology Institute of Biochemistry and Cell Biolog

Re: [ccp4bb] about the PEG molecules in crystals

here are many others, as I said. I don't > know what's there to discuss. It's either you see their density and fit them > or you don't. > > Cheers, > > Boaz > > > - Original Message - > From: Jiamu Du <[EMAIL PROTECTED]>

[ccp4bb] about the PEG molecules in crystals

Dear all, Are there some articles or reviews discussing about the PEG molecules in crystals or the biochemical features of PEG? Thanks. -- Jiamu Du, Ph.D. State Key Laboratory of Molecular Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese

[ccp4bb] [Summary] How to present the surface of a channel.

g the mask, and IDENT operator, no expansion gives a new map with a surface just around the tunnel. Hope it will be helpful. Thanks and best wishes. -- Jiamu Du, Ph.D. State Key Laboratory of Molecular Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Scienc

[ccp4bb] how to present the surface of a channel

other program can be used for preparing these figures? Thanks. -- Jiamu Du, Ph.D. State Key Laboratory of Molecular Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 320 Yue-Yang Road Shanghai 200031 P. R. China Tel: +86-21

[ccp4bb] about microbatch

sufficient for cover the drop? Thanks. -- Jiamu Du, Ph.D. State Key Laboratory of Molecular Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 320 Yue-Yang Road Shanghai 200031 P. R. China Tel: +86-21-5492-1117 E-mail: [EMAIL

[ccp4bb] How to dissolve a hydrophobic peptide?

, such as DMSO. But organic solvent is harmful to protein. Is there any sugestions for this situation? Thanks. -- Jiamu Du State Key Laboratory of Molecular Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences (CAS)

Re: [ccp4bb] unknown symmetric density

-aventis > Chemical Sciences Department > 16 rue d'Ankara > 67000 Strasbourg > France > > -- > *From:* CCP4 bulletin board [mailto:[EMAIL PROTECTED] *On Behalf Of *Jiamu > Du > *Sent:* Tuesday, February 26, 2008 3:33 PM > *To:* CCP4BB@J

Re: [ccp4bb] how to model glycosylated residues?

=>} carbo_use_2=true; > {===>} carbo_patch_2="A13"; > {===>} carbo_i_segid_2="C"; carbo_i_resid_2=3; > {===>} carbo_j_segid_2="C"; carbo_j_resid_2=2; > > {+ choice: true false +} > {===>} carbo_use_3=true; > {===>} carbo_patch_3="B12&

Re: [ccp4bb] how to model glycosylated residues?

Dear All, Thank you for your previous response. I have built a 3-mer oligosaccharides in the electron density by using coot. I prefer to refine my structure in CNS due the resolution is only 2.6 Ang. I found there are only topology and parameter files for carbohydrate in CNS but no linkage file for

Re: [ccp4bb] how to model this density?

4. If you still have more > density to fit, check the N-glycan biosynthesis pathway here: > http://www.genome.ad.jp/kegg/pathway/map/map00510.html. I think CHO cells > predominantly produce the complex type N-glycans. CHO cells may also add > an alpha1,6 fucose to the first GlcNAc. > &

[ccp4bb] how to model glycosylated residues?

Dear All: As mentioned before, I am working on a 2.6 A resolution structure. There might be a glycosylated Asn. I want to model some carbohydrate molecule into my structure. My question is how to model them? Should I treat them as small molecules? Best Regards. -- Jiamu Du State Key Laboratory

Re: [ccp4bb] how to model this density?

otif (N-X-S/T). You might have > the first NAG attached to the Asn if the motif is there. > > Jeff > > > On Jan 7, 2008, at 7:19 PM, Jiamu Du wrote: > > Dear All: > I am refining a structure at 2.6 A reslution. The protein is expressed in > CHO cell, so it might b

Re: [ccp4bb] the B facot of soaked substrate

an fine enough. Say with value > results in R-factors in the range of the surrounding protein. > > Again, I would advice against publishing a structure with B-factors you > are sure they are wrong. > Herman > > -- > *From:* Jiamu Du [mailto:[EMAIL PROT

Re: [ccp4bb] the B facot of soaked substrate

* CCP4 bulletin board [mailto:[EMAIL PROTECTED] *On Behalf Of *Jiamu > Du > *Sent:* Thursday, November 01, 2007 1:05 PM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* [ccp4bb] the B facot of soaked substrate > > > Dear All: > I am refining a protein structure with a soaked subs

[ccp4bb] the B facot of soaked substrate

this situation in the PDB bank? Thanks. -- Jiamu Du State Key Laboratory of Molecular Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences (CAS)

Re: [ccp4bb] a question about procheck

tion programs can fix this. > In Coot, one would use the fix-nomenclature-errors function. > > Hope that is clearer, > > Paul. > > On Fri, Aug 10, 2007 at 07:19:44PM +0800, Jiamu Du wrote: > > Dear Eleanor: > > But in my structure, the atom labelles are all right

Re: [ccp4bb] a question about procheck

or > example > > It doesnt change the electron density of structure calns an iouta but > conventions are conventions! > > Eleanor > > Jiamu Du wrote: > > Dear All: > > I have refined a structure. When I run procheck, a messege apears in > > the log file as bel

[ccp4bb] a question about procheck

these residues. All this residues are all right. Is there anyone who have the same experience? How to deal with this situation? Thanks. -- Jiamu Du State Key Laboratory of Molecular Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of

[ccp4bb] about Procheck

k at this part of my strucutre model with its well defined density. Is there anyone who have met the same warning? How to deal with it? Thanks -- Jiamu Du State Key Laboratory of Molecular Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese A

Re: [ccp4bb] how to convert matrix to angle

CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] how to convert matrix to angle Jiamu Du schrieb: > Dear all: > I want to calculate the rotation angle between two similar domains. By > using Coot, I can superposr the two domain and get the rotation matrix. > But how to convert this matrix to an a

Re: [ccp4bb] how to convert matrix to angle

Thanks a lot. You are so kind. On 7/7/07, Kay Diederichs <[EMAIL PROTECTED]> wrote: Jiamu Du schrieb: > Dear all: > I want to calculate the rotation angle between two similar domains. By > using Coot, I can superposr the two domain and get the rotation matrix. > But h

[ccp4bb] how to convert matrix to angle

Dear all: I want to calculate the rotation angle between two similar domains. By using Coot, I can superposr the two domain and get the rotation matrix. But how to convert this matrix to an angle. Is there any program can calculate this ? Thanks. -- Jiamu Du State Key Laboratory of Molecular

[ccp4bb] extra high B factor - Summary

last for 24 hours. This two reasons result in the lost of peptide in crystal. The low occupancy of the peptide leads to the extra high B fator when I set the occupancy to 1.0. Thank you ALL. -- Jiamu Du State Key Laboratory of Molecular Biology Institute of Biochemistry and Cell Biology Shanghai

Re: [ccp4bb] extra high B factor

be seen in the 2FoFc map but can not be seen in the composite omit map. On 4/30/07, mesters <[EMAIL PROTECTED]> wrote: Dear Jiamu Du, what were the exact concentrations (Molar values please) of protein and peptide in the co-crystallization experiment? This may help in estimating the (po

Re: [ccp4bb] extra high B factor

the other .. Even the overall Wilson plot B is not very well determined, so I wouldnt worry too much.. Eleanor Jiamu Du wrote: > Dear All: > According to your suggestion, I have set the peptide's occupency to > 0.5. Two strategies were employed. > 1. Direct using Refmac restrained ref

Re: [ccp4bb] extra high B factor

g cedex tel: +33 (0)3 88 41 70 02 [EMAIL PROTECTED] -Message d'origine- *De :* CCP4 bulletin board [mailto: [EMAIL PROTECTED] la part de*Jiamu Du *Envoyé :* lundi 30 avril 2007 05:57 *À :* CCP4BB@JISCMAIL.AC.UK *Objet :* [ccp4bb] extra high B factor Dear All: I am refining a protein

Re: [ccp4bb] extra high B factor

factor of peptide close to protein. After you get the responses, can you make a summary and post it in the newsgroup? I think your final refinement will be OK. Jackie Vitali On 4/29/07, Jiamu Du <[EMAIL PROTECTED]> wrote: > Dear All: > I am refining a protein-peptide complex strutu

[ccp4bb] extra high B factor

if this high B factor acceptable. And another question is if this high B fator will influence the final refiment level. Thanks. -- Jiamu Du State Key Laboratory of Molecular Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences

Re: [ccp4bb] buried surface area

fessor Interests: Cancer, Biochemistry, DNA Metabolism, Protein Crystallography, Modulated Crystals, Crystal Perfection, X-ray Topography, Varley, Rowling, Avatar, BRAN, RAGBRAI, swimming & soccer ** -- Jiamu Du

Re: [ccp4bb] phaser oprn error

ad_peak.mtz" - EXIT STATUS: FAILURE I donnot know what is wrong with the mtz file, it is simply converted from a sca file with scalepack2mtz, and now I am using molrep, it didnot give such wrong information. What is the problem? Thanks! Li Yang

Re: [ccp4bb] a question about O

Got it. Turn down the resolution of the monitor. The characters will be large enough to see. But the map looks not so soomth as before. On 3/20/07, Jiamu Du <[EMAIL PROTECTED]> wrote: Dear All: I have a question about the new version O.v11. In the new version, the characters displayed

[ccp4bb] a question about O

O.v11. Thanks. -- Jiamu Du State Key Laboratory of Molecular Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences (CAS)

Re: [ccp4bb] In CCP4, How to perform anneal?

Thanks! PHENIX sounds magic. It makes many thing easy to handle. I must try it. Thank you all. On 2/21/07, Pavel Afonine <[EMAIL PROTECTED]> wrote: Dear Jiamu Du: You can do annealing using phenix.refine (part of CCI APPS and PHENIX). With the latest version of CCI APPS (part of PHEN

Re: [ccp4bb] In CCP4, How to perform anneal?

Thank you all. It seems that I have to install CNS in my notebook for running CNS. On 2/20/07, Eleanor Dodson <[EMAIL PROTECTED]> wrote: It cant be done Eleanor Jiamu Du wrote: > Dear All: > Only by using CCP4, how to perform anneal refinement ? > Thanks > -- > Jiamu D

[ccp4bb] In CCP4, How to perform anneal?

Dear All: Only by using CCP4, how to perform anneal refinement ? Thanks -- Jiamu Du Key Laboratory of Proteomics Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences (CAS)

Re: [ccp4bb] Rfactor does not drop

suggestions? Thank you in advance, Emmanuel Prata -- Jiamu Du Key Laboratory of Proteomics Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences (CAS)

Re: [ccp4bb] Is Kabat or Chothia numbering necessary?

58-784-7976 http://www.scripps.edu/imm/ollmannsaphire/ -- Jiamu Du Key Laboratory of Proteomics Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences (CAS)

Re: [ccp4bb] Is Kabat or Chothia numbering necessary?

And another question I found I have to modify the residue number manually. Is there some software or webserver can do this, or typically people did this manually? Thanks again. On 1/29/07, Jiamu Du <[EMAIL PROTECTED]> wrote: I have found the Kabat numbering scheme for my fab. Thank y

Re: [ccp4bb] Is Kabat or Chothia numbering necessary?

f Lee, Ph.D. Research Associate The Scripps Research Institute Department of Immunology 10550 North Torrey Pines Rd. Room R212 Mail Drop: IMM-2 La Jolla, CA USA 92037 858-784-7976 http://www.scripps.edu/imm/ollmannsaphire/ -- Jiamu Du Key Laboratory of Proteomics Institute of Biochemist

[ccp4bb] Is Kabat or Chothia numbering necessary?

Dear All: I am solving a fab structure. I am not sure if it is necessary to number the fab residues in Kabat or Chothia numbering mode. Or the common numbering is also acceptable for publishing the structure. Thanks -- Jiamu Du Key Laboratory of Proteomics Institute of Biochemistry and Cell