[ccp4bb] E.coli RNA polymerase

wishes, Vipul -- Vipul Panchal, PhD University of Bergen (M)-+47 46359545 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message

Re: [ccp4bb] Contradictory result between ITC and cocrystal structure

Hi Monika, If the protein cocrystalize with ligand doesn't mean it interacts with protein. You have provided insufficient information here. Does the ligand is bound to mutant protein with atleast 2 or 3 hydrogen bonds (how many residues are mutated?) ? If no that means, it is just cocrystalizing b

Re: [ccp4bb] translational NCS & twinning

Hi Donghyuk, I feel you went ahead with right strategy. For 2.1 A datasrt, the appropriate drop in Rfree/ Rwork is a strong indicator, i believe. If you have already build all possible model, using tls can be of further help. Cheers, Vipul On Thu 10 Jan, 2019, 3:52 PM Donghyuk Shin Dear all,

Re: [ccp4bb] cavities in protein structures

Hi Claudia, For the identification of cavities and residues linning them, metapocket is one of the preferred choice as it uses prediction from various program. Output of the server is pdb file. I found caver program represent cavities in a best manner. There is caver plugin available for pymol. Ou

Re: [ccp4bb] RMSD between superposed structures without moving

May be you should try pdbefold server. It provides rmsd between equivalent CA atoms of superimposed structures. All the best. Vipul Panchal, Ph.D. student CSIR-IGIB (M)- 091 7678617949 On 27-Aug-2017 4:50 PM, "Johannes Sommerkamp" < 155b9e78396e-dmarc-requ...@jiscmail.ac.uk>

Re: [ccp4bb] Ramachandran oultliers increase upon restrained refinement

I do agree with Eleanor. When I was solving structure at 2.16A resolution, outlier residues were having stearic clash or required side chain flipping. At 2.76A resolution, hydrogen bonds would be difficult to visulize. I found phenix.refine more user friendly. You may too find it useful. Vipul

Re: [ccp4bb] Bond length and angle outlier fixing

gy, the Joint BioEnergy Institute > Laboratory Research Manager, ENIGMA Science Focus Area > > Building 33, Room 347 > Building 80, Room 247 > Building 978, Room 4126 > Tel: 1-510-486-4225, Fax: 1-510-486-5909 > http://cci.lbl.gov/paul > > Lawrence Berkeley Laboratory > 1

[ccp4bb] Bond length and angle outlier fixing

indly find the image of relevant details attached herewith. Can somebody suggest me how to fix them? Sincerely, -- Vipul Panchal Senior Research Fellow, Respiratory disease and biology, CSIR-IGIB (M)-9540113372

Re: [ccp4bb] Poor density fit.

o zero and let the invisible > atoms be accounted for by high B-factors (either set manually or just > letting refinement do its thing). > > > Bert > > > ------ > *From:* CCP4 bulletin board on behalf of Vipul > Panchal > *Sent:* 04 May

[ccp4bb] Poor density fit.

t set occupancy for atoms without density(CG, CD1, CD2) to zero. Hopeful for the response. -- Vipul Panchal Senior Research Fellow, Respiratory disease and biology, CSIR-IGIB (M)-9540113372

Re: [ccp4bb] very high B-factor

the pdb file. I'm not sure whether the B-factor in "B factor variance Graphs" belong to residue or atom, but i guess 417 belongs to residue. What's the relationship of the two factor? Best regards, Qiaoling Yan At 2017-05-04 15:58:36, "Vipul Panchal" wrote: Hi, 1&g

Re: [ccp4bb] very high B-factor

hs", but in PDB file the b > factor is 76. Does the two factor mean the same thing? > 3. If i want to set the weight manually, which parameter should i set, > wxc/wxc_scale? or others? > > Thanks in advance. > > Best regards, > Qiaoling Yan > > > > > -- Vipul Panchal Senior Research Fellow, Respiratory disease and biology, CSIR-IGIB (M)-9540113372

[ccp4bb]

Provided your protein is >90 pure as per 15% SDS-PAGE analysis, you should try seeding. On 28-Apr-2017 12:43 PM, "李霞" wrote: Dear all: My protein is a demethylase,has failed to obtain protein crystals,then adopt the method of in situ enzyme and get protein crystals,but the crystal is still very

Re: [ccp4bb] AW: [ccp4bb] NCS difference

hould superimpose > the NCS symmetry molecule(s) and see which conformation would fit best and > fit this conformation in the other molecules as well. > > > > Best, > > Herman > > > > *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von &g

Re: [ccp4bb] NCS difference

ake it less red (blue or may be green)? Otherwise Rw/Rf~20/25 is just fine at 2.2A resolution. What exactly your worry is about? Pavel On Mon, Apr 24, 2017 at 12:48 AM, Vipul Panchal wrote: Hi all, I am solving structure of one of the acyltransferse protein. We have collected data at 2.16A resolu

[ccp4bb] NCS difference

red bar. *Can some one suggest me how may i minimize it if i am expected to do it?* -- Vipul Panchal Senior Research Fellow, Respiratory disease and biology, CSIR-IGIB (M)-9540113372

Re: [ccp4bb] Pymol point mutagenesis turns out to be deletion of a residue

I am not experienced with pymol. However if you are familiarized with coot, you can mutate and set rotamer. It is really simple. On 12-Apr-2017 12:15 AM, "Alex Lee" wrote: > Dear All, > > I am using MacPymol 1.8.6, I did Pymol point mutagenesis using Wizard, > everytime after I choose a residue

Re: [ccp4bb] Accidental crystallization of E. coli protein

with an rmsd of about 0.3 A but our data resolution is a > bit higher. This is perhaps unsurprising as the unit cells are very similar > (in fact, I just did a quick RBR). Should we bother depositing and > publishing this observation? > > Thanks. > Mohamed > -- Vipul Panch

Re: [ccp4bb] Using a codon-optimised gene to improve protein solubility

rs the translation rate of a gene, I believe this should > affect solubility as well; but I'd like to know what the community > thinks/has observed before I order an exorbitantly priced gene! > > Thank you in advance, > Sutapa > > -- > Sutapa Chakrabarti, Ph.D. > I