[ccp4bb] Shrodinger prime

Hello Everyone, I am sorry for off topic question, Is someone has Shrodinger prime license only for protein structure prediction? How much they charge for only for cloud version I need this figure urgently, just to put in the proposal. Please let me know Regards Dr. Rohit Kumar Singh Scientist

Re: [ccp4bb] Resampling CryoEM Density map to XRD Density map for Difference Map

Dear Paul, Thank you Regards Devbrat On Thu, Jun 6, 2024, 8:53 AM Paul Emsley wrote: > > On 06/06/2024 04:00, Devbrat Kumar wrote: > > > -- > Dear Paul, > > Thank you for your response. I wanted to compare a Coulomb potential map > to an electron density map. Be

Re: [ccp4bb] Resampling CryoEM Density map to XRD Density map for Difference Map

this clarifies my query. Sorry for any confusion. Thank you again. Regards Devbrat On Wed, Jun 5, 2024, 7:56 PM Paul Emsley wrote: > > On 05/06/2024 07:00, Devbrat Kumar wrote: > > > -- > > Hello Everyone, > > Hello Devbrat, > > I have a query regarding the resa

Re: [ccp4bb] Resampling CryoEM Density map to XRD Density map for Difference Map

;> Gemmi (mainly for crystallography, included in CCP4) >> https://gemmi.readthedocs.io/en/latest/grid.html >> >> Maybe there are also some relevant features in CCTBX (included in CCP4 >> and Phenix). >> >> Cheers, >> Martin >> >> On 05/06/2024 07:

Re: [ccp4bb] Resampling CryoEM Density map to XRD Density map for Difference Map

rystallography, included in CCP4) >> https://gemmi.readthedocs.io/en/latest/grid.html >> >> Maybe there are also some relevant features in CCTBX (included in CCP4 >> and Phenix). >> >> Cheers, >> Martin >> >> On 05/06/2024 07:00, Devbrat Kumar wr

Re: [ccp4bb] Resampling CryoEM Density map to XRD Density map for Difference Map

t; EMDA (for cryoEM maps, included in CCP-EM) >> https://gitlab.com/ccpem/emda >> https://doi.org/10.1016/j.jsb.2021.107826 >> >> Gemmi (mainly for crystallography, included in CCP4) >> https://gemmi.readthedocs.io/en/latest/grid.html >> >> Maybe there ar

Re: [ccp4bb] Resampling CryoEM Density map to XRD Density map for Difference Map

tps://gemmi.readthedocs.io/en/latest/grid.html > > Maybe there are also some relevant features in CCTBX (included in CCP4 and > Phenix). > > Cheers, > Martin > > On 05/06/2024 07:00, Devbrat Kumar wrote: > > Hello Everyone, > > Greetings! > > I have a query r

[ccp4bb] Resampling CryoEM Density map to XRD Density map for Difference Map

density difference map. Thank you in advance for your help. *Warm Regards-* *Devbrat Kumar* To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

[ccp4bb] Voidoo cavity volume tool: cavity.lib file

Dear All, I want to use voidoo cavity volume tool (Uppsala software facility) to determine cavity volume around a specific set of residues (G.J. Kleywegt & T.A. Jones (1994)). Unfortunately, I don't have the cavity.lib file that is required for this tool. I tried downloading the files from the

Re: [ccp4bb] Multi-lattice crystal data processing strategy for structure solution

Dear Prof John Thank you for your valuable time and insight. I will do as you have suggested. *Warm Regards-* *Devbrat Kumar* On Wed, Nov 15, 2023 at 11:28 PM John Bacik < b45abf420e1f-dmarc-requ...@jiscmail.ac.uk> wrote: > > Hi Devbrat, here are a couple of other t

Re: [ccp4bb] Multi-lattice crystal data processing strategy for structure solution

Dear Prof Gerard Thank you for your in-depth analysis of the possibilities I am facing. The image slicing was at 0.1 degrees. *Warm Regards-* *Devbrat Kumar* On Wed, Nov 15, 2023 at 5:21 PM Gerard Bricogne wrote: > Dear Devbrat, > > With the unit-cell geometry you have, name

Re: [ccp4bb] Multi-lattice crystal data processing strategy for structure solution

model building and refinement cycling, along with phases from MR (2.7 Angstroms). I will revisit this process. I will follow your advice for the peak search. If I cannot find any leads, I hope to seek your guidance. Thank you again for your support. *Warm Regards-* *Devbrat Kumar* On Wed, Nov

Re: [ccp4bb] Multi-lattice crystal data processing strategy for structure solution

p the MR-SAD pipeline (for > SAD after MR and for model rebuilding using anomalous > data) of Crank2. > > If you want me to take a look at your raw data, upload the best datasets > (native and SeMet) to a cloud service and send me the link. > > Good luck, > Kay > > On T

Re: [ccp4bb] Multi-lattice crystal data processing strategy for structure solution

Dear Professor Phil Thank you for highlighting and providing input. Yes, The space group is P21. *Warm Regards-* *Devbrat Kumar* On Wed, Nov 15, 2023 at 5:39 PM Phil Evans wrote: > Is the space group really P2? P21 is MUCH more common > Phil > > > On 14 Nov 2023, at 15:55

[ccp4bb] Multi-lattice crystal data processing strategy for structure solution

Hello everyone, The issue with the crystal is its multi-lattice nature; even the truncated protein, which has been crystallized, exhibits multi-lattice characteristics (detectable only after XRD). I have multiple native and selenium datasets with similar unit cell parameters. (One axis is excessi

Re: [ccp4bb] How to calculate experimental residual electron density map

Dear Prof. Eleanor Dodson, Thank you for the response. I will try generating difference map as told and will update. - Regards, Ankur K Singh Ph.D. Student From: Eleanor Dodson Sent: Monday, July 24, 2023 5:31 PM To: Ankur Kumar Singh Cc: CCP4BB

[ccp4bb] How to calculate experimental residual electron density map

Dear Members, I am trying to generate an experimental residual electron density map for a protein structure resolved at 1.1 Angstrom. One way to do this is by refining the structure using an aspherical model of charge distribution (Multipole density proposed by Hansen and Coppens) in MoPro. Howe

Re: [ccp4bb] Adding metal ions

Dear Jose, I want to simulate the copper/protein complex to track the movement of copper ion from the surface to its binding site. Best Veerendra -Original Message- From: CCP4 bulletin board On Behalf Of Jose Brandao-Neto Sent: Tuesday, June 20, 2023 11:23 AM To: CCP4BB@JISCMAIL.AC

Re: [ccp4bb] Adding metal ions

Sent: Friday, June 16, 2023 5:40 PM To: Veerendra Kumar Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] Adding metal ions Take a protein structure with waters, replace surface waters with Cu++ and run some very basic MD to optimize distances. Many of the atoms will move since Cu++ will find

[ccp4bb] Adding metal ions

Dear All, I want to add about 200 copper ions on protein surface randomly. Is there any program available to serve the purpose? Thank you Best regards Veerendra Get Outlook for Android To unsubscrib

Re: [ccp4bb] India EMBO Lecture course on Tumour Metabolism-Dealine extended 28th February 2023

Dear All, Deadline for registration and abstract submission extended till 28th February, 2023. Registration link- https://meetings.embo.org/event/23-tumour-metabolism Thank you Best Regards Veerendra Kumar, PhD Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

Re: [ccp4bb] issue with running ccp4i2

Doc File "src/lxml/parser.pxi", line 711, in lxml.etree._handleParseResult File "src/lxml/parser.pxi", line 640, in lxml.etree._raiseParseError File "", line 1 lxml.etree.XMLSyntaxError: Document is empty, line 1, column 1 From: Bo

[ccp4bb] issue with running ccp4i2

Hi Group I currently updated my ccp4 to the latest version. I have also made python3.7 the default version. The log when I run ccp4i2 & from the command line is appended below. I suspect it is the python version but please guide me for the same. Python 3.7.12 (default, Jan 6 2022, 21:30:12) [

[ccp4bb] Multiplicity is more than 20

Hi All: I have collected a dataset for a crystal of a 30 residues long helical peptide that makes a trimer in the solution. I also solved the structure to get a trimer. My issues start when I start preparing for a deposition. Details about the data: space group: I 21 3 Resolution: 1.6 Current

[ccp4bb] Helix class identifier in Helix Record of PDB

Hi All Happy New Year to All. I have a PDB file that has left-handed 310 helices. However, the helix class in PDB documentation (https://www.wwpdb.org/documentation/file-format-content/format33/sect5.html) does not have any number assigned to the left-handed 310-helix. The auto annotation soft

[ccp4bb] Excellent Opportunity for Postdoc in Ion-Channel Structural Biology

/public <https://urldefense.com/v3/__https:/www.ncbi.nlm.nih.gov/myncbi/claudio.grosman.1/bibliography/public__;!!DZ3fjg!rQbPPU9HmgERY4wmiV22sCEFfhgBKyPAgmAjAc4NIwePpODucsYnvVtDcXV3NFUKog$> ). *Recent Select Publications * *· Kumar P, Cymes GD, Grosman C. Structure and function at the lipid-p

Re: [ccp4bb] Validation of structure prediction

Hi, try SAVES online tool,and ProSa. On Mon, 20 Dec, 2021, 9:40 pm Reza Khayat, wrote: > ​Hi, > > > Can anyone suggest how to validate a predicted structure? Something > similar to wwPDB validation without the need for refinement statistics. I > realize this is a strange question given that the

Re: [ccp4bb] Refmac is changing the bond lengths, torsion angle of modified residues

, Winfried Sent: 16 November 2021 19:24 To: Prasun Kumar Subject: Re: [ccp4bb] Refmac is changing the bond lengths, torsion angle of modified residues Dear PR, 0.1Angstrom is not a general disaster - you should talk to a chemist. Best, Winfried Hinrichs

[ccp4bb] Refmac is changing the bond lengths, torsion angle of modified residues

Hi Group I am refining one of the structures that has modified amino acid and it is not defined in the CCP4 dictionary. I got the restrains using ELBOW and used it for refinement. However, when I refine the structure using REFMAC, the bond length deviates significantly from the ideal/ given val

[ccp4bb] Protein's C-terminal neutral

e end, which is not the end residue of my purified protein) and I want to make it neutral (possibly a peptide bond in solution). Please let me know if I am clear enough with my question. Thank you -- Regards Dr. Rohit Kumar Singh Postdoctoral fellow Aurora C

[ccp4bb] convert loop into a sheet

am using ccp4-Refmac5 for the refinement. Thank you Rohit -- Regards Dr. Rohit Kumar Singh To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&

[ccp4bb] Specifying achiral residue as D-amino acid

Hi All: I am trying to solve a structure that has got D-amino acids. The sequence has also got few achiral residues but is mentioned as a part of L-peptide in the monomer library. For example GLY or AIB. Since my sequence has all D-amino acids, I was thinking of some method by which these achir

Re: [ccp4bb] E.coli cell lysis using glass beads

Veerendra Kumar, PhD Associate Professor & Ramalingaswami Fellow Amity Institute of Molecular Medicine & Stem Cell Research (AIMMSCR) J-3 108, Amity University Campus Sector-125, Noida-201303 UP, INDIA http://amity.edu/aimmscr/Faculty.asp Google Scholar: https://scholar.google.com/citati

Re: [ccp4bb] Suggestions to improve resolution of protein crystals

that as well. I wish you all the best with your trials. Best Ashish Kumar On Sun, Mar 21, 2021 at 11:04 AM Saurabh Upadhyay wrote: > Dear All, > > I am trying to crystalize a protein, which occurs in monomeric (60kDa) and > tetrameric (240kDa) form. *The protein during crystallization

[ccp4bb] E.coli cell lysis using glass beads

Dear All, Sorry for the off topic. May I ask your experience about bacterial cell lysis using glass beads beating? How is the cell lysis compared with sonication and French press? Does the glass beads affect the protein quality? Thank you in advance. Best Regards Veerendra Kumar, PhD Associate

Re: [ccp4bb] Suggestions to improve resolution of protein crystals

e the cryosolution as well. I was able to get up to 2.6 angstrom data at home source. Hope this helps. *Regards* *Adarsh Kumar, PhD* *Suo Lab* *Florida State University College of Medicine* *Tallahassee, FL - 32304* On Sun, Mar 21, 2021 at 2:04 PM Saurabh Upadhyay wrote: > Dear Al

Re: [ccp4bb] Saving multi-state obj in Pymol

I think the chain identifier for both the states is same. If it is, change it and hopefully it should work . Cheers, Prasun From: CCP4 bulletin board on behalf of Sam Tang Sent: 30 January 2021 13:24 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Saving multi-sta

[ccp4bb] (scattering factors) f and f" for Sr Heavy atom

te or where to find these f and f" values for Sr heavy atoms? Please let me If you need any information from my side. Thank you in advance -- Regards Dr. Rohit Kumar Singh Postdoctoral fellow To unsubscribe from the C

[ccp4bb] Data 3 A

for Refmac the final R/Rfee is 23/30 and with satisfactory Ramachandran statistics as well as electron density and model in agreement with each other in coot. Does It mean that I have correct solution? Please suggest, -- Regards Dr. Rohit Kumar Singh Postdoctoral fellow

Re: [ccp4bb] Problem in finding a MR solution

u have solved for molecular > Replacement of the other crystals. > I have only two things in mind currently. I hope it will work for you. > > On Fri, Dec 11, 2020, 4:48 PM Suraj Kumar mandal > wrote: > >> Dear All, >> >> We are trying to solve a structure of a pr

Re: [ccp4bb] Problem in finding a MR solution

eat each data set as a "run" and see how > well they ageee. > Eleanor > > On Fri, 11 Dec 2020 at 11:18, Suraj Kumar mandal > wrote: > >> Dear All, >> >> We are trying to solve a structure of a protein, for which we have >> collected five different

[ccp4bb] Problem in finding a MR solution

Dear All, We are trying to solve a structure of a protein, for which we have collected five different home source data at 3.2-3.5 Ang resolution. We are processing the data using iMOSFLM and the program suggests P3 (and related) space groups for all the data. We are able to get a solution with one

[ccp4bb] Crystal dissolved while checking under microscope

Hi Group: I have a peptide that got crystallized within 20-25 minutes after putting down the tray. The condition has 1.8M Ammonium Salt, 0.01 Cobalt (ii) Chloride hexahydrate and MES (0.1M) pH 6.5. I dissolved my peptide in 25 mM Sodium Accetate (pH=5). PI of my peptide is 10.2 When I checked

[ccp4bb] Help to fight COVID-19

and we would do our level best. Pramod Kumar, Ph.D. Postdoctoral research associate, Grosman Lab Department of Molecular and Integrative Physiology University of Illinois at Urban-Champaign. To unsubscribe from the

[ccp4bb] Running CCP4_Blend on Mac

/external programs/add a program/. When i start the blend program, it is showing Dependency error: BLEND requires R. Am I missing something here. Please advise me running blend through ccp4 interface? Thank you, -- ravi kumar To

[ccp4bb] Post doc position available at Florida State University

Dear all One postdoctoral position is available immediately in an enzymology laboratory to elucidate mechanisms of DNA/RNA synthesis, DNA lesion bypass, and base excision repair catalyzed by various human and viral DNA/RNA polymerases, and to mechanistically investigate gene editing enzymes inc

[ccp4bb] One postdoc position available at Florida State University

Dear all One postdoctoral position is available immediately in an enzymology laboratory to elucidate mechanisms of DNA/RNA synthesis, DNA lesion bypass, and base excision repair catalyzed by various human and viral DNA/RNA polymerases, and to mechanistically investigate gene editing enzymes inc

Re: [ccp4bb] how to get protein crystal

Hi Amala, In addition to Limbini´s suggestions. 1. You can always do MALS, SLS, Native Page or cross linking experiments to check whether your protein is monodisperse in the solution or not. This is very important step. 2. When you set up crystallization and if you have 40-50% drops precipit

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] 1 out of 2 proteins in asymmetric unit does not fit density

Hi Jessica You may try the following (if you haven't already): 1. Try solving it using P222 space group. 2. Re-index using different axes. *Regards* *Adarsh Kumar* *Florida State University College of Medicine* *Tallahassee, FL - 32304* On Mon, Dec 16, 2019 at 2:30 PM Jessica

[ccp4bb] Postdoc position available in an enzymology laboratory at Florida State University

Dear all One postdoctoral position is available immediately in an enzymology laboratory to elucidate mechanisms of DNA/RNA synthesis, DNA lesion bypass, and base excision repair catalyzed by various human and viral DNA/RNA polymerases, and to mechanistically investigate gene editing enzymes inc

[ccp4bb] Issues with stero in Wincoot

Dear all, We are trying to install stereo in Wincoot in windows 10 pro, 64 bit computer. We have installed nvidia quadro K4000 graphics driver in our system. The stereo is working well with Pymol, but keep crashing on Wincoot. Can you anyone experienced the same issue and how can I f

[ccp4bb] Postdoc position available in an enzymology laboratory at Florida State University

One postdoctoral position is available immediately in an enzymology laboratory to elucidate mechanisms of DNA/RNA synthesis, DNA lesion bypass, and base excision repair catalyzed by various human and viral DNA/RNA polymerases, and to mechanistically investigate gene editing enzymes including CRI

[ccp4bb] mar2mtz command

Hi, While using mar2mtz command in linux ubuntu, we are getting the following error. mar2mtz: error while loading shared libraries: libccp4f.so.0: cannot open shared object file: no such file or directory Can anyone suggest how to proceed further. Thanks #

[ccp4bb] mar2mtz command

Hi, While using mar2mtz command in linux ubuntu, we are getting the following error. mar2mtz: error while loading shared libraries: libccp4f.so.0: cannot open shared object file: no such file or directory Can anyone suggest how to proceed further. Thanks Raj #

[ccp4bb] One postdoc position available at Florida State University

, Biochemistry, Biology, Biophysics, Structural Biology, and Biomedical Sciences Position Type: Full Time Organization Type: Academia Job Type: Postdoc Regards Adarsh Kumar, PhD Suo Lab Florida State University School of Medicine Tallahassee, FL - 32304

Re: [ccp4bb] Racemic crystallography and structure solving problem

replacement is a problem for me. However, I am on it. Regards Prasun From: Tim Gruene Sent: 05 March 2019 10:02:53 To: Prasun Kumar Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] Racemic crystallography and structure solving problem Dear Prasun, in case you

Re: [ccp4bb] Racemic crystallography and structure solving problem

Thank You Pierre! I will have a look and let you know. Regards Prasun From: LEGRAND Pierre Sent: 04 March 2019 16:33:56 To: Prasun Kumar; CCP4BB@JISCMAIL.AC.UK Subject: RE:[ccp4bb] Racemic crystallography and structure solving problem Hi Prasum, In such

[ccp4bb] Racemic crystallography and structure solving problem

Hi All: I have performed racemic crystallography and got crystals that diffracted. The automatic processing softwares, XIA2 DIALS, (available in Diamond, UK) gives the space group as P1 and cell dimension 42.78 52.16 54.49 114.11 92.16 92.31. Challanges start from here: 1) How much

Re: [ccp4bb] OT: Nvidia 3D vision 2 glasses with Ubuntu workstation

or: Asus VG248QE Used method detailed in the following link: https://devtalk.nvidia.com/default/topic/1004126/general-discussion/nvidia-3d-stereo-under-linux-ubuntu-16/ Thank you for all your help. *Regards* *Adarsh Kumar, PhD* *Suo Lab* *Florida State University College of Medicine*

Re: [ccp4bb] OT: Nvidia 3D vision 2 glasses with Ubuntu workstation - Fwd: 3D graphics under linux for coot, pymol and chimera

Hi Wim Thank you for sharing your experience. I have almost the same setup, except for the stereo connector. i will place order for that today and will share how things go from there. *Regards* *Adarsh Kumar, PhD* *Suo Lab* *Florida State University College of Medicine* *Tallahassee, FL

Re: [ccp4bb] OT: Nvidia 3D vision 2 glasses with Ubuntu workstation

Thank you, Guenter. I will keep that in mind. *Regards* *Adarsh Kumar, PhD* *Suo Lab* *Florida State University College of Medicine* *Tallahassee, FL - 32304* On Thu, Dec 20, 2018 at 5:33 PM Guenter Fritz < guenter.fritz.phenix.c...@gmail.com> wrote: > Dear Adarsh, > >

Re: [ccp4bb] OT: Nvidia 3D vision 2 glasses with Ubuntu workstation

Hi Did you use 3-DIN connector? Regards Adarsh Kumar, PhD Suo lab Florida State University School of Medicine Tallahassee FL - 32304 On Thu, Dec 20, 2018, 16:48 Guillermo Montoya we are using a similar setup ( i do not know if the asus monitor is the > same) > and I managed to make i

Re: [ccp4bb] OT: Nvidia 3D vision 2 glasses with Ubuntu workstation

Thank you Jim. I will try that. *Regards* *Adarsh Kumar, PhD* *Suo Lab* *Florida State University College of Medicine* *Tallahassee, FL - 32304* On Thu, Dec 20, 2018 at 3:55 PM Jim Fairman wrote: > If you want to use it with linux, the 3-pin connector is required. You > can

[ccp4bb] OT: Nvidia 3D vision 2 glasses with Ubuntu workstation

(unfortunately doesn't have a 3-pin DIN socket) Monitor: Asus VG248QE Thanks and regards Adarsh Kumar Suo Lab Florida State University College of Medicine To unsubscribe from the CCP4BB list, click the following link:

[ccp4bb] One postdoc position available at Florida State University

: Full Time Organization Type: Academia Job Type: Postdoc Regards Adarsh Kumar, PhD Suo Lab Florida State University School of Medicine Tallahassee, FL - 32304 To unsubscribe from the CCP4BB list, click the following link: https

Re: [ccp4bb] R-merge is too high !!

I totally agree with Berry. Please consider Rpim, CC1/2 and I/sigI for cutting the data. Rmerge is old approach as it is data redundancy dependent. Thank you Rajesh ---x With regards Rajesh K. Harijan, Ph.D. Schramm Laboratory Albert Einstein College of Medicine 1300 Morris Park Ave., Bro

[ccp4bb] Postdoc position available at Florida State University

Type: Postdoc *Regards* *Adarsh Kumar, PhD* *Suo Lab* *Florida State University School of Medicine* *Tallahassee, FL - 32304* To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk

Re: [ccp4bb] Open SESAME & Instruct-ERIC Workshop on Remote X-ray Data Collection from European Synchrotrons at the Weizmann Institute of Science on 14-18 May 2018

Dear Rik and Joel, Thank you very much for organizing this great workshop for students. I followed it online from New York. It was nice to see some familiar faces as the speaker. Hoping to see you all in coming future. regards, Rajesh ---x With regards Rajesh K. Harijan, Ph.D. Schramm

Re: [ccp4bb] Open SESAME & Instruct-ERIC Workshop on Remote X-ray Data Collection from European Synchrotrons at the Weizmann Institute of Science on 14-18 May 2018

Dear Rik and Joel, This is really great. Thank you very much. I will follow it from New York. Have a great workshop. regards, Rajesh ---x With regards Rajesh K. Harijan, Ph.D. Schramm Laboratory Albert Einstein College of Medicine 1300 Morris Park Ave., Bronx, NY 10461 Tel: 718.430.2777

Re: [ccp4bb] Suggestions on Dynamic Light Scattering instruments

__ Debasish Kumar Ghosh CSIR- Senior Research Fellow (PhD Scholar) C/o: Dr. Akash Ranjan Computational and Functional Genomics Group Centre for DNA Fingerprinting and Diagnostics Hyderabad, INDIA Email(s): dkgh...@cdfd.org.in, dgho

Re: [ccp4bb] Unknown density

gt; > > With best regards, > Ivan Shabalin, Ph.D. > Research Scientist, > Department of Molecular Physiology and Biological Physics, > University of Virginia, > 1340 Jefferson Park Avenue > <https://maps.google.com/?q=1340+Jefferson+Park+Avenue&entry=gmail&s

Re: [ccp4bb] Unknown density

d be > cacodylate? Or water, am not sure. > > Cheers, > Hussain > > > On 7 Mar 2018, at 9:19 am, Rajesh Kumar wrote: > > > > Dear All, > > > > Have you had experience with this kind of density? I am wandering what > this could be? > > > > Thank you very much for the help. > > > > -Rajesh > > > > > > > > >

Re: [ccp4bb] COOT problem

Dear Paul, It seems that XQuartz 2.7.7 is working in my macbook and I can run COOT a bit faster. Thank you for the help. -Rajesh On Wed, Feb 28, 2018 at 5:42 AM, Paul Emsley wrote: > On 27/02/2018 21:11, Rajesh Kumar wrote: > >> >> I just had installed new SSD and latest

Re: [ccp4bb] COOT problem

Dear Paul, Thank you very much. Only COOT is giving problem. Other programs work very well. I will change XQuartz to 2.7.8 and see if COOT works. regards, Rajesh On Wed, Feb 28, 2018 at 5:42 AM, Paul Emsley wrote: > On 27/02/2018 21:11, Rajesh Kumar wrote: > >> >> I just

[ccp4bb] COOT problem

Dear All, I just had installed new SSD and latest macOS High Sierra 10.13.3 into my macbook pro. It seems my macbook is much faster but running COOT is a bit problem. When I open COOT, screen becomes gray for a second and then it opens. When I try to move from one residue to next, it does not mo

Re: [ccp4bb] protein quasicrystals?

gt; > I have been trying to crystallize a protein complex and keep getting > sphere shape crystals. The diffraction is around 3 angstrom, but looks like > multiple lattices. I am wondering if it could be a quasi crystal? Is there > anyone has such experience? > > > > Tha

[ccp4bb] Publishing structure of a protein

Hi, We purified a protein whose structure (apo) is already known in pdb database and determined the crystal structure with a component of buffer. Can we submit this structure in pdb database and publish it as a research paper (only structure)? Also can anyone suggest some journals for this? Thanks

[ccp4bb] 3 Scientist positions in SM drug discovery at Biogen, Cambridge, MA

5658#jobDetails=795658_5140> Thank you. Best regards, Rajesh Kumar Prakash

[ccp4bb] Iron Oxidising state

Dear All, I am solving a structure (resolution 2 A) of an enzyme having Iron as a metal cofactor. How could I know oxidising state of the bound Iron (Fe+2 or Fe+3)? Thank you in advance -- WITH REGARDS Dr. Rohit Kumar Singh

Re: [ccp4bb] Electron density map for publications

gt; Usually, fo-fc is the best way to show. > > > best, > > > ------ > chenzhonghao...@163.com > > > *From:* raj kumar > *Date:* 2017-12-19 13:07 > *To:* CCP4BB > *Subject:* [ccp4bb] Electron density map for publications > Hi > W

[ccp4bb] Electron density map for publications

Hi Which electron density map (fo-fc or 2fo-fc) should I use for representing the density of the bound ligand? Thanks Raj

[ccp4bb] Scientist position in SM protein science - Biogen - #33174BR

wUI/Search/home/HomeWithPreLoad?PageType=JobDetails&noback=0&partnerid=169&siteid=5140&jobid=798102#jobDetails=798102_5140> Best regards

Re: [ccp4bb] Density around PEG

Thanks, I'll check it out. On Wed, Dec 13, 2017 at 8:06 PM Anthony Addlagatta < anthonyaddlaga...@gmail.com> wrote: > This could be 2-mercaptoethanol. > > Anthony > > On Wed, Dec 13, 2017 at 11:24 PM, sanjeev kumar > wrote: > >> Hi all, >> Can som

Re: [ccp4bb] domain prediction of a membrane protein

Hi Firdous, The question, if I am understanding correctly, is to find the topology of the regions of a membrane protein, that is cytoplasmic, membranous or extra-cellular. You can do it by site directed cystine mutagenesis nearby to the the preferred region/domain followed by MAL-PEG analysis.

Re: [ccp4bb] Predict effects of mutations on protein stability and protein-protein interaction

Hi Wenhe , You can mutate the desired residue in 'pymol' (save the new pdb structures) and run them for molecular dynamic simulations (in Gromacs, Desmond etc.) to see the stability of your protein [for the full length protein or its segments] (by checking RMSD and RMSF values). You can analyz

[ccp4bb] Regarding Patents

Sorry for asking out of context question. Can a mutated DNA or protein molecule be patented. Thanks Raj

[ccp4bb] Beam-line Scientist and Engineer Positions Elettra, Italian Synchrotron Source, Trieste, Italy

Dear all, Two beam-lines dedicated to high pressure X-ray diffraction and macromolecular crystallographic studies have been commissioned at the Elettra Synchrotron Source in Trieste, Italy, as a part of an Indo-Italian collaboration funded by the Department of Science and Technology on the Indian s

Re: [ccp4bb] Precipitation issue during refolding

Dear Dipankar, Your problem is quite tricky to solve. I have two opinions which worked for me for a very high aggregation prone protein (Huntingtin, which always used to go in inclusion bodies and precipitate even in elution buffer). 1. First have 4-5M Guanidinum Hydrochloride in the lysis buf

Re: [ccp4bb] doubt regarding MR search model

&source=g> >> E-28049 Madrid, Spain >> tel. (+34) 91 585 4616 <+34%20915%2085%2046%2016> >> http://wwwuser.cnb.csic.es/~mjvanraaij >> Editor of Acta Crystallographica F, Structural Biology Communications >> http://journals.iucr.org/f/ >> >> On 19 Sep 2017

Re: [ccp4bb] doubt regarding MR search model

MR solution is: does it refine - give it 20 cycles of > mindless refinement and see if the R and FreeR go down. > > Then look at the maps and see if there are obvious corrections to be made.. > > Eleanor > > On 18 September 2017 at 14:59, Satvik Kumar > wrote: > >

Re: [ccp4bb] PAK=0 problem

options correctly during refinement? On 15-Sep-2017 12:36 PM, "Eleanor Dodson" wrote: > PAK=0 is GOOD - i.e. there are no clashes between symmetry equivalent > molecules. > So I think you have solved your structure. > Eleanor > > On 15 September 2017 at 07:20, rohit

[ccp4bb] PAK=0 problem

know what strategies I can use to get correct solution. As I have tried all the combination in PHASER. Here I am attaching the result of PHASER . [image: Inline image 3] Thank you in advance -- WITH REGARDS Dr. Rohit Kumar Singh

[ccp4bb] Fix sidechain outliers

Dear All, Could anyone help me, how I can fix my sidechain outliers or clashscore in coot or in CCP4 tools. Or by using any online severs. Its urgent Thank You in advance -- WITH REGARDS Dr. Rohit Kumar Singh School of Life Sciences, Jawaharlal Nehru University New Delhi -110067

Re: [ccp4bb] Hydrophobic hotspots

Hi Hugh, Waltz is an excellent web-server to give very good results on amyloidogenic regions based on sequence stretches (correlate the regions with hydrophobic patches by hydropathy plot obtained from Expassy-Protscale). Aggrescan and PASTA are two other reliable servers for the same kind of p

Re: [ccp4bb] Primer design

"Debasish Kumar Ghosh" , CCP4BB@JISCMAIL.AC.UK Sent: Monday, July 24, 2017 6:48:25 PM Subject: RE: Primer design Or sequence the whole exome for what, $500-1000? JPK -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Debasish Kumar Ghosh S

Re: [ccp4bb] Primer design

Dear Syed, The process is very trivial to clone your gene of interest. Assuming your gene is transcribed as mono-cistronic mRNA, take the oligodT primer as reverse primer. First isolate the total RNA from the tissue or cells and do the cDNA synthesis using oligodT primer followed by gene specif

Re: [ccp4bb] weird diffraction pattern

Hi Chenjun, Few suggestions from my side. Process the data with XDS and look into acentric intensity distribution (it indicates any twinning possibility). Run XTRIAGE and SFCHECK to understand any twinning or pseudo translation possibilities. Twinning can confuse the program and suggest you smalle

Re: [ccp4bb] Ramachandran oultliers increase upon restrained refinement

Dear Meytal, PHENIX-REFINE has an option for Ramachandran outlier refine. If you check this on, it will do the work. But after this refinement, you must check every residues to make sure residues are in the density. Thank you Rajesh ---x With regards Rajesh K. Harijan, Ph.D. Schramm La

Re: [ccp4bb] Separating Monomers and Dimers

monomer and higher oligomers. Best regards, Debasish Kumar Ghosh CSIR- Senior Research Fellow (PhD Scholar) C/o: Dr. Akash Ranjan Computational and Functional Genomics Group Centre for DNA Fingerprinting and Diagnostics Hyderabad, INDIA Email(s): dkgh...@cdfd.org.in, dgho...@gmail.com Telephone

Re: [ccp4bb] Protein or DNA crystals

croscope but > no Trp fluorescence (6 Trp in 256 aa). It may due to low Trp. > > This is our first time to work on protein/DNA complex crystals and we > are not certain if this is just DNA or protein/DNA crystals. Can you > provide your comments on our hits? > > Thank you fo

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