[ccp4bb] Facility manager positions at CCMB, India
Dear All, The Centre for Cellular & Molecular Biology (CCMB) is a premier research organization in frontier areas of modern biology. The objectives of the Centre are to conduct high quality basic research and training in frontier areas of modern biology, and promote centralized national facilities for new and modern techniques in the interdisciplinary areas of biology. Recently our institute has advertised for facility manager positions in the areas of CryoEM/X-ray, Biophysics etc. at entry level. The notification can be found here: http://e-portal.ccmb.res.in/positions/regular/notif_4_2020/ Kindly bring it to the attention of interested rese archers. Best regards, Sankar ** Dr. Rajan Sankaranarayanan Chief Scientist, Structural Biology Laboratory CSIR-Centre for Cellular and Molecular Biology (CCMB) Uppal Road Hyderabad - 500 007 India. Ph: +91-(0)40 2719 2832 to 2835 (Lab) +91-(0)40 2719 2500 (CCMB Reception) Fax: +91-(0)40 2716 0252, 2716 0591 e-mail: san...@ccmb.res.in sanka...@yahoo.com Web:http://e-portal.ccmb.res.in/e-space/sankar/index.html -- P.S: Kindly reply back to san...@ccmb.res.in 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 was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Postdoctoral Research Positions in X-ray crystallography
Dear All, One postdoctoral position is available immediately in Dr. Zucai Suo’s laboratory (https://u.osu.edu/suolab/) to study protein functions, mechanisms, and interactions through protein X-ray crystallography. The ideal candidate should have a PhD in structural biology and extensive experience in all aspects of protein X-ray crystallography, including protein expression and purification, crystallization, structure determination and refinement. Experience with baculovirus expression system is a plus. The protein targets are human kinases and DNA polymerases. Please contact Dr. Suo <%20su...@osu.edu> through email at su...@osu.edu, or phone (614) 688-3706, or regular mail: 880 Bio. Sci., 484 West 12th Ave., Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210. Zucai Suo, Ph.D. and Professor Department of Chemistry and Biochemistry The Ohio State University Columbus, OH 43210 Office phone: (614) 688-3706 Email: su...@osu.edu Internet: https://u.osu.edu/suolab/ CAPA President: http://www.capachembiol.org/
[ccp4bb] Invitation to connect on LinkedIn
LinkedIn I'd like to add you to my professional network on LinkedIn. - rajan kumar rajan kumar choudhary Student at Delhi University Patna Area, India Confirm that you know rajan kumar choudhary: https://www.linkedin.com/e/ptbprq-hvwh6svb-4t/isd/15811920428/ejx-xTJH/?hs=false&tok=2ElvC1VtR4t6g1 -- You are receiving Invitation to Connect emails. Click to unsubscribe: http://www.linkedin.com/e/ptbprq-hvwh6svb-4t/XL1uAZoCTuIfF98RcTWBR3ZMc5pFnJQycC/goo/CCP4BB%40jiscmail%2Eac%2Euk/20061/I7179920246_1/?hs=false&tok=1d7KYqhdx4t6g1 (c) 2012 LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043, USA.
[ccp4bb] size of a flexible pdb structure
Dear all, sorry for asking an off topic question. My protein is composed of two domains connected by a flexible linker (15aa). after 50ns simulation i came across the fact that one domain is flexible. so my question is that how could i be able to calculate the size of molecule or radius of my molecule and which conformation i should prefer to calculate the size of molecule. your any suggestion will be very helpful. thank you all in advance with best regards -- *Rajan kumar choudhary* *Senior Research Fellow* *Department of Atomic Energy(Govt.Of India)* *ACTREC TATA Memorial Center * *Kharghar Navi-Mumbai* *Mumbai-410210* *India*
[ccp4bb] large domain motion and calculation of flip flop angle
Dear all, sorry for off topic question. My protein is composed to two domains connected by a flexible linker and shows large domain motion with large RMSD value of 9.0 A* difference with respect to the initial structure, when simulated for 20 ns. As the first domain doesn't shows any RMSD change when superimposed to initial structure but the other domain moves significantly. so my question is how i could be to calculate the angle of motion in degree of the flexible domain with respect to the initial structure after superimposition. thank you all in advance Regards *Rajan kumar choudhary* *Senior Research Fellow* *Department of Atomic Energy(Govt.Of India)* *ACTREC TATA Memorial Center * *Kharghar Navi-Mumbai* *Mumbai-410210* *India*
Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
I agree completely with Ed and made a similar suggestion when this
discussion came up last time i.e. the reviewer should reveal the identity
if he wants coordinates. Even data (including raw data if need be) can be
given in those cases. As reviewer has a reason to suspect and therefore
want to inspect the data implicated in the manuscript of the author(s), the
author(s) has every reason to suspect the motive of such reviewers
('Reviewers' are not 'gods' or a different breed, they are future 'authors'
of papers and proposals).
While almost always we find that 'reviewers' dont indulge in any kind of
malpractices and are very useful in improving the quality of manuscripts,
there are rarest of rare scenarios when one also encounters reviewer
'misconduct'. More so if you do not belong to certain clubs or the high
profile niches/regions of research.
A reviewer(may be a competitor but one who does not come out explicitly
with a conflict of interest) need not use just data only, but can also get
clues/ideas presented in the manuscript to scoop. To narrate a situation
that happened to us several years back, this 'reviewer' played a delaying
tactics by asking for more data to be included in the manuscript (did not
reject though), which were not relevant at all. The editor who handled the
manuscript was a serious one, luckily for us, and accepted our argument
that it was not required. The paper was accepted but it had to wait for
publication in the journal. Before it was published, we saw a paper
appearing in another journal (submitted after acceptance of our paper) and
accepted for publication in a few days with Immediate Online Publication.
The paper had the claims, very similar to ones made in our paper, from a
half baked story on a structure of a homologous system. The corresponding
author of the paper was the first reviewer (as we thought he/she was an
authority in the area!!!) whom we suggested. When we contacted the editor
to reveal the identity of the 'reviewer' by mentioning the case, a mute
reply(apology!) came that they are sorry that this has happened. Also, I
must add that these situations are more likely when the claims are high
(read as higher journal impact factor!).
The above scenario, if it happens when one is reasonably established, would
not affect the individual as much as it would have affected someone in the
beginning of his/her career. I am tempted to favour, at this point of time
of my career, the suggestion to part not only with the PDB but even with
raw data at the time of submission. However, considering the non ideal
systems that we have to deal with, I would expect the community to put a
rider to stop the rarest of rare 'reviewer' misconducts, even though it
can only be a costly affair to a handful!
-Sankar
On Fri, Apr 20, 2012 at 10:38 PM, Ed Pozharski wrote:
> Manoj,
>
> while reviewer-bashing is my favorite pastime too (recent gem: "studying
> transcription factors will not advance our understanding of mechanistic
> enzymology"), you should remember that they are unpaid individuals who
> volunteer their time to help you to improve your paper (or so the idea
> goes). It is also important to recognize that the editor accepts the
> paper, not the reviewer (who acts in advisory capacity).
>
> A much better alternative to your draconian list was already mentioned -
> "I'll give you my data if you tell me who you are". Works for me.
>
> Cheers,
>
> Ed.
>
> On Fri, 2012-04-20 at 11:07 -0400, Manoj Tiwari wrote:
> > 1) The reviewer should be given at most 24-48 hours of time to give
> > comments after receiving the data.
> >
> > 2) (S)he should declare to the editor that the paper is going to be
> > accepted if everything with the data/model is okay. The reviewer
> > should also send comments to author on what does (s)he intend to
> > examine in the structure.
> >
> > 3) After going through the model/data, the reviewer's comment should
> > be exclusively based on the structure or its correlation with the
> > experimental data.
> >
> > 4) If reviewer finds any mistake which can not be corrected or which
> > changes the theme of the paper and the reviewer rejects the paper, the
> > responsibility should lie on author. But certainly the editor or a
> > team decided by editor should ensure that when the paper is rejected
> > at this stage, the reason for rejection is valid and the mistakes can
> > not be rectified. Editor should also ensure that authors are given
> > sufficient opportunity to correct the mistake if possible.
> >
> >
>
> --
> I don't know why the sacrifice thing didn't work.
> Science behind it seemed so solid.
>Julian, King of Lemurs
>
Re: [ccp4bb] Another paper & structure retracted
The reviewers who wish to get access to raw data should reveal their identity by signing the report! -Sankar On Thu, Aug 11, 2011 at 10:28 AM, Ethan Merritt wrote: > On Wednesday, 10 August 2011, Nian Huang wrote: > > I Agree with the idea of adding crystallographer reviewers. > > But accessing to data is not feasible unless there is a good way > > to protect authors. > > Disagree. > The data supporting a paper's claims should always be made available > to the reviewers. How else can you be assured of a valid review? > > The only exception to this I can think of would be human subjects/ > privacy issues, but that must be a rarity in crystallographic papers. > >Ethan > > > For > > example, the editor should agree to publish the paper swiftly in advance > > before the data become accessible to reviewers. > > In any case, the flaw of this structure is very clear in the table. > > > > Nian > > > > > > > > On Wed, Aug 10, 2011 at 5:25 PM, Filip Van Petegem < > > filip.vanpete...@gmail.com> wrote: > > > > > Just another example of where it would have been good for the reviewers > to > > > get access to the data during the review process... and where at least > one > > > of the reviewers *should* be a protein crystallographer... > > > > > > Filip Van Petegem > > > > > > On Wed, Aug 10, 2011 at 2:01 PM, David Schuller > wrote: > > > > > >> Time to fuel up the gossip engines for the approaching weekend: > > >> > > >> > > >> http://www.sciencedirect.com/science/article/pii/S096921260800186X > > >> > > >> RETRACTED: Structure of the Parathyroid Hormone Receptor C Terminus > Bound > > >> to the G-Protein Dimer Gβ1γ2 > > >> Structure, Volume 16, Issue 7< > http://www.sciencedirect.com/science?_ob=PublicationURL&_tockey=%23TOC%236269%232008%23999839992%23693753%23FLA%23&_cdi=6269&_pubType=J&view=c&_auth=y&_acct=C22719&_version=1&_urlVersion=0&_userid=492137&md5=9dc4b8953d3fa243dc98e395b6ac590d > >, > > >> 9 July 2008, Pages 1086-1094 > > >> Structure 2QNS withdrawn. > > >> > > >> -- > > >> > === > > >> All Things Serve the Beam > > >> > === > > >>David J. Schuller > > >>modern man in a post-modern world > > >>MacCHESS, Cornell University > > >>schul...@cornell.edu > > >> > > >> > > > > > > > > > -- > > > Filip Van Petegem, PhD > > > Assistant Professor > > > The University of British Columbia > > > Dept. of Biochemistry and Molecular Biology > > > 2350 Health Sciences Mall - Rm 2.356 > > > Vancouver, V6T 1Z3 > > > > > > phone: +1 604 827 4267 > > > email: filip.vanpete...@gmail.com > > > http://crg.ubc.ca/VanPetegem/ > > > > > >
[ccp4bb] Phenix - Ligand search
Dear All Greetings I was searching for a ligand present in the active site of my protein using Ligand Search in "PHENIX" but i stuck in between with an error : A Python error was detected. This may be a problem with the program settings, an error in your data, or a bug; click "OK" to send a bug report to the PHENIX developers. AttributeError : ligand_identification instance has no attribute 'connections' Traceback: File "/home/programs/linux/phenix-1.6.1-357/cctbx_project/libtbx/thread_utils.py", line 137, in run return_value = self._target(self._args, self._kwargs, self._c) File "/home/programs/linux/phenix-1.6.1-357/cctbx_project/libtbx/runtime_utils.py", line 55, in __call__ result = self.target() File "/home/programs/linux/phenix-1.6.1-357/phenix/phenix/command_line/ligand_identification.py", line 1769, in __call__ identify_ligands = ligand_identification(args=list(self.args), quiet=False) File "/home/programs/linux/phenix-1.6.1-357/phenix/phenix/command_line/ligand_identification.py", line 308, in __init__ ligand_identification.Run(self, params) File "/home/programs/linux/phenix-1.6.1-357/phenix/phenix/command_line/ligand_identification.py", line 1454, in Run return self.connections['STOP '] I am not able to identify the problem? Please let me know if some one can identify the problem, i don't know whether it is a bug or problem in my files. Thanks for your suggestions in advance. Rajan -- Current Address: Rajan Vyas Research Scholar Deptt. of Biotechnology Panjab University Chandigarh, India 160014Mob. +919417374197 Fax: +91-172-2625254
[ccp4bb] Lots of noise in structure
Dear All, Happy New Year I am working with a 2.06 Ang resolution structure in F432 space group and further using REFMAC (also tried Phenix) program for refinement of my model. Every thing in the structure seems good, R factor/ R free= 18.59/20.77 but the structure is too noisy (blobs of difference Fourier with red as well as green density). As such electron density is looking good for the protein part. Is there any parameter which i had to check. Thanking you in advance Rajan -- Current Address: Rajan Vyas Research Scholar Deptt. of Biotechnology Panjab University Chandigarh, India 160014Mob. +919417374197 Fax: +91-172-2625254
[ccp4bb] unknown density
Dear all, i am working on a structure of M.tb, solved at 2.18 A. In my structure there is a density near to the active site and we modelled it as a malonate (C3 O4 H2) molecule acorrding to the density, which was not used in any of our buffer except we used 10 mM DTT, 1.6 M Ammonium sulphate, 100 mM citric acid. Is their any possible way to check for unknown densities or can any one suggest me for any possible compound which can be similar to the malonate or can be formed from above mentioned solutions (byproduct). Thanks Rajan -- Current Address: Rajan Vyas Research Scholar Deptt. of Biotechnology Panjab University Chandigarh, India 160014Mob. +919417374197 Fax: +91-172-2625254
[ccp4bb] Review on Membrane Protein Purification and Crystallization
Hi All, Is there a good review or special issue of a journal dedicated to the problems associated with membrane protein purification and crystallization? Key points of focus would be on overcoming the solubility problem, stability and techniques of crystallization. Thanks, Rajan
[ccp4bb] Summary: Ordering a cDNA library
This was long overdue. The sources that some have suggested are as follows: 1. Origene 2. Imagenes However, after some searching I found the following two as a good source of human cDNA 1. Openbiosystems 2. ATCC On Fri, Dec 19, 2008 at 7:55 AM, Guenter Fritz < guenter.fr...@uni-konstanz.de> wrote: > Rajan, > have a look at http://www.imagenes-bio.de. I guess there are more > suppliers. Please send a summary to the board. > Good luck, > Guenter > > > Rajan Pillai wrote: > >> Hi All, >> >> Apologies for a non-CCP4 question. I want to clone a couple of proteins of >> human and mouse origin. Can anyone tell me where from I can order Human and >> mouse (brain/liver) cDNA library? Any suggestions are welcome. >> >> Thanks, >> >> Rajan >> > > -- > *** > > Priv.Doz.Dr. Guenter Fritz > Fachbereich Biologie > Sektion Naturwissenschaften > Universitaet Konstanz > http://www.biologie.uni-konstanz.de/fritz > > Universitaetsstrasse 10 > Postfach M665 > D-78457 Konstanz > > e-mail: guenter.fr...@uni-konstanz.de > > Tel. Office: +49-(0)7531 88 3205 Tel. Lab : +49-(0)7531 88 3687 > Fax: +49-(0)7531 88 2966 >
[ccp4bb] Ordering a cDNA library
Hi All, Apologies for a non-CCP4 question. I want to clone a couple of proteins of human and mouse origin. Can anyone tell me where from I can order Human and mouse (brain/liver) cDNA library? Any suggestions are welcome. Thanks, Rajan
Re: [ccp4bb] generating omit maps
Hi What about the SFcheck omit map calculation in 'Map and Mask utilities' module in CCP4? R.Sreekanth On Wed, 10 Dec 2008 Kathleen Frey wrote : >Hi Everyone, > >Can anyone tell me a relatively easy way to generate an omit density map for >a ligand? I know that CNS can do this, but I was wondering if there's a CCP4 >related program to generate omit maps. > >Thanks, >Kathleen
Re: [ccp4bb] Clarification of MOLREP logfile
Hi All, In the portion of the MOREP logfile where it lists the RF peaks, what does Rf and Rf/sigma mean? Is Rf - peak height and Rf/sigma - peak heights measured as deviations from mean? Looking into the CCP4 tutorial on MOLREP (http://www.ccp4.ac.uk/dist/examples/tutorial/html/mr-tutorial.html) this is mentioned as R factor. Please explain. Rajan. >
[ccp4bb] Clarification of MOLREP logfile
Hi All, In the portion of the MOREP logfile where it lists the RF peaks, what does Rf and Rf/sigma mean? Is Rf - peak height and Rf/sigma - peak heights measured as deviations from mean? Looking into the CCP4 tutorial on MOLREP (http://www.ccp4.ac.uk/dist/examples/tutorial/html/mr-tutorial.html) this is mentioned as R factor. Please explain. Rajan.
[ccp4bb] Resolution limit for Molecular Replacement
Hi All, I read some literature for phasing by molecular replacement performed with reflections upto 3.5 Angstroms. Can anybody tell me why? I would prefer deleting low resolutions so as to reduce contribution from the solvent that might affect RF search and obtaining a solution. Your responses to this question would also be highly appreciated. Thanks, Rajan
[ccp4bb] Rotation Function of MOLREP
Hi All, I want to plot the rotation function that MOLREP uses. I cannot find any output of rotation function in the logfile or in moIrep.doc. I want to locate the peaks of the rotation function, that are shortlisted as solutions, which would help me in understanding the following problem. My protein is a tetramer with 222 point group symmetry. In I4(1) space group Molrep gives two molecules in the asymmetric unit with top two RF peak heights 10 sigma and 6 sigma. The final solution is obtained from these two peaks after TF search. Moreover in case of another protein with the same tetrameric assembly and quite the same unit cell parameters, but in space group I4(1)22, Molrep gives 1 molecule in the asymmetric unit; however, in this case the peaks from the RF are 14 and 12 sigmas and the solution is obtained from the first peak after TF search. In the input file I did not mention the number of monomers to be searched. It detects that based on Matthews coefficient. I am a bit confused as to why in space group I4(1) the RF values are so different. I would have expected them to be closer in values as they are dimer. And also, in case of I4(1)22, the RF values also should be closer. I was wondering if plotting the RF can help in understanding the relation of the peaks and their values based on their location. I believe MOLREP calculates RF over the whole unit cell, instead of the asymmetric unit. Thanks, Rajan
Re: [ccp4bb] Ratio of Number of Reflections to Number of restrained Parameters
The question was well crafted. It behooves on part of the respondent to understand the question or clarify before answering. On Fri, Aug 29, 2008 at 2:24 PM, Ian Tickle <[EMAIL PROTECTED] > wrote: > > Agreed - but it wasn't entirely clear from the original question that > this was the purpose of the calculation. Assuming that is the case then > it surely behoves subscribers as far as possible to ask the right > questions, or at least explain their reasons for needing to perform the > calculation: it should not be assumed that others will understand what > you meant to say, as opposed to what you did say! > >
[ccp4bb] Ratio of Number of Reflections to Number of restrained Parameters
Hi All, I was wondering if there is any program that calculates the ratio of number of reflections (observation) to number of restrained parameters. If not then how it can be calculated. The number of reflections is it number of unique reflections or number of the total reflections? Thanks, Rajan
[ccp4bb] Ligand Binding
Hi All, I want to confirm the binding of the substrate in the active site of the enzyme by soaking crystals of the apo-protein with the substrate. I generated a Fobs_lig - Fobs_apo difference electron density map. Inspection of the map did not show the characteristic electron density of the substrate. However, the difference electron density map (1Fo - 1Fc) generated after restrained refinement reveals the characteristic electron density of the substrate. I am scaling Fobs of both the ligand bound and apo proteins and using the phi_c from the apo to calculate Fobs_lig - Fobs_apo difference map. Can this problem arise due to loss of isomorphism in the crystals after soaking with the substrate? The c-axis dimension increased by ~10 angstroms after soaking while the a and b axises increased by less than an angstrom. Moreover, I need to do a full blown MR instead of rigid body replacement with the apo protein. Thanks, Rajan.
[ccp4bb] Phased Anomalous Difference Map
Hi All, Can anyone tell me how I calculate a phased anomalous difference map? I want to confirm such as the presence of Cl or S ion in an unknown electron density. Rajan.
[ccp4bb] Calculating volume of Ligands
Hi All, Can anyone tell me any program that calculates voume of a ligand? Moreover, is there also any program that can calculate the volume of a ligand from its coordinates? Thanks, Rajan.
[ccp4bb] Measuring the volume and surface area of an active site
Hi All, Can anyone tell me if there is any program available that can measure the surface area and volume of the active site of a protein? Thanks, Rajan.
