Re: [ccp4bb] Crystallization of SARS-CoV-2 3CLpro and Mutants – Seeking Advice on Crystal Optimization

https://doi.org/10.1107/S1600576719006381 The crystallophore can be purchased from Mitegen/Molecular Dimensions/Polyvalan. Best of luck, Eric. Le 30/06/2025 à 09:17, Mohit Bhardwaj a écrit : Dear members, I am currently working on the crystallization of the main protease (3CLpro) of SARS-CoV

[ccp4bb] Reminder: EMBO SAXS/SANS practical course

)) -- Eric Girard Extremophiles and Large Macromolecular Assemblies (ELMA) group Institut de Biologie Structurale UMR 5075 CEA-CNRS-UGA-PSB 71 avenue des Martyrs CS 10090 38044 Grenoble Cedex 9 Phone: +33 (0)4 57 42 86 45 Fax: +33 (0)4 76 50 18 90 Web site: http://www.ibs.fr

[ccp4bb] EMBO SAXS/SANS practical course

meals. A limited number of EMBO travel grants are also available. Best regards, Frank Gabel (On behalf of the organizers: Anne Martel (ILL), Petra Pernot (ESRF), Mark Tully (ESRF) and Frank Gabel (ILL/IBS)) -- Eric Girard

Re: [ccp4bb] [ccpem] Making thioester bond in Chimera/ChimeraX

erax-us...@cgl.ucsf.edu <mailto:chimerax-us...@cgl.ucsf.edu>address: <https://rbvi.ucsf.edu/chimerax/docs/contact.html> I hope this helps, --Eric Eric Pettersen UCSF Computer Graphics Lab > From: Collaborative Computational Project in Electron cryo-Microscopy > m

[ccp4bb] Postodoc position in RNA biophysics & structural biology

ientists + 3 CNRS IR engineers, with complementary skills in molecular biology, biochemistry, biophysics, X-ray crystallography, NMR, cryoEM, Molecular Dynamics. Place: Institut de Biologie Moléculaire et Cellulaire - IBMC, Strasbourg (France) Lab "Architecture et Réactivité de l'A

Re: [ccp4bb] 3d stereo on windows 10/11

it's not very stable (very likely due to NVidia drivers updates, but maybe there are some other reasons). Eric > De: "Krishnan Raman" > À: "CCP4BB" > Envoyé: Vendredi 10 Février 2023 16:34:05 > Objet: [ccp4bb] 3d stereo on windows 10/11 > What is the

[ccp4bb] postdoc position - Toth Lab at the Institute for Bioscience and Biotechnology Research

qualifications -- *Eric A. Toth, Ph.D. * Research Assistant Professor Institute for Bioscience and Biotechnology Research 9600 Gudelsky Drive Rockville, MD 20850 Email: eat...@umd.edu Phone: x-240-314-6516 To unsubscribe from the

[ccp4bb] Postdoctoral Opportunity in Membrane Transporters (uOttawa)

environment. To apply, please send your CV and a letter of intent to Dr. Jyh-Yeuan (Eric) Lee: jyh-yeuan@uottawa.ca. Successful candidates will be notified for interviews, at which time reference letters or writing examples will be enquired for assessment. Application will remain open until the

Re: [ccp4bb] TWIN?

Maybe you have a bimolecular dimer when you expected a unimolecular hairpin? It’s happened before :) https://pubmed.ncbi.nlm.nih.gov/31584014/ Eric On Tue, Jun 8, 2021 at 10:15 AM Almudena Ponce Salvatierra < maps.fa...@gmail.com> wrote: > Hello everyone, > > I am working w

[ccp4bb] staff scientist position available at UAMS

publications, and a list of 3 references to: ejenem...@uams.edu https://external-uams.icims.com/jobs/73269/assistant-staff-scientist/job?hub=6 Best, Eric Eric J. Enemark Associate Professor University of Arkansas for Medical Sciences Department of Biochemistry and Molecular Biology 4301 W. Markham St

[ccp4bb] Two positions available at UAMS

al-fellow/job?hub=6 https://external-uams.icims.com/jobs/73187/research-associate-iii/job?hub=6 Best, Eric Eric J. Enemark Associate Professor University of Arkansas for Medical Sciences Department of Biochemistry and Molecular Biology 4301 W. Markham St., slot 516 Little Rock

Re: [ccp4bb] CCP4BB Digest - 13 Feb 2021 to 14 Feb 2021 (#2021-51)

"UNK" and this just needs to be > switched to something else. Has anyone else seen this? > Nick The PDB defines UNK as unknown amino acid. UNL is unknown ligand. N is unknown nucleic acid. --Eric Eric Pettersen UCSF Computer Graphics Lab ###

[ccp4bb] open Structural Biologist position at Rheos Medicines

. thank you and stay safe. Eric Larson eric.xt...@gmail.com 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 mem

[ccp4bb] Multiple positions available in the Fischerlab @Dana-Farber / Harvard Med

)crystal.harvard.edu <http://crystal.harvard.edu>* Best Eric To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

[ccp4bb] BDB rsync

hanks. :) Eric P.S. I've contacted Dr. Vriend, but I haven't heard back yet. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

[ccp4bb] Facility Staff position at UW-Madison

(erwrig...@wisc.edu) -- Eric J. Montemayor Associate Scientist Member of USNC/Cr Department of Biochemistry University of Wisconsin Madison 433 Babcock Dr. Room 145 Madison, WI 53706 To unsubscribe from the CCP4BB list

[ccp4bb] Postdoctoral position at UW-Madison

A postdoctoral position is immediately available in the laboratory of Professor Samuel Butcher at the University of Wisconsin-Madison. https://biochem.wisc.edu/faculty/butcher The Butcher laboratory is funded by the NIH to investigate the structure and function of RNA-protein complexes that regul

[ccp4bb] Computational cryo-EM faculty position at the Morgridge Institute for Research and UW-Madison

-ultrastructure-imaging-cluster-hire Bacteriology - http://jobs.hr.wisc.edu/cw/en-us/job/499304/assistant-professor For additional information, please contact Liz Wright (erwrig...@wisc.edu). -- Eric J. Montemayor Associate Scientist Department of Biochemistry University of Wisconsin Madison 433 Babcock

[ccp4bb] Cryo-EM virology faculty position at UW-Madison

cid-ultrastructure-imaging-cluster-hire> for the direct link to the post and application process. The deadline for receipt of applications is December 1, 2018. The position will remain open until filled. For more information, please contact Ann Palmenberg or Elizabeth Wright. -- Eric J.

[ccp4bb] Fwd: Crystallography job opportunities at HarkerBio in Buffalo, NY

positions. Please see the the job description below and submit your resume/CV along with a cover letter to care...@harkerbio.com. thank you. Eric *Scientist/Senior Scientist/Lead/Director: Structural Biology* *Summary* An opportunity to participate in (or, if sufficiently qualified, lead) our

Re: [ccp4bb] Off topic: Flourescence anisotropy measurement

is a significant signal change and measure the polarization every few minutes for an hour. You might find that you need to pre-incubate the samples for an extended time prior to taking measurements. With that said, my first suspicion is that you have lousy binding. Eric From: CCP4 bulletin

[ccp4bb] Emory University: Assistant/Associate Professor in Structural Biology (Tenure Track)

ica with BioQuantum and K2/K3 Upgrade dedicated to single particle studies. Warmest Regards, Eric Eric Ortlund, Ph.D. Associate Professor Director of Emory Integrated Lipidomics Core Department of Biochemistry Emory University School of Medicine 1510 Clifton Road, NE, Room G235 Atlanta, GA 3

Re: [ccp4bb] paired refinement

Thank you for all your comments! I think it would be great to have the "paired refinement" implemented in future updates of refinement programs. Coming back to my original questions: if I have overestimated the high resolution cutoff, what is the correct procedure to refine against lower resol

[ccp4bb] paired refinement

Hi all, I have a dataset processed in XDS to 2.3 A (based on CC1/2). I'm trying to do "paired refinement" to determine the optimal resolution cutoff. Here is what I get at different resolutions set in Phenix: Final Rfree/Rwork: 2.7—> 0.2498/0.2027 2.6—> 0.2519/0.2009 2.5—> 0.2567/0.2025 2.4 —>

[ccp4bb] Low Phaser RFZ

Hi all, Running Phaser using the apo protein as search model on a ~2.5 A dataset of a protein-DNA complex, I get a single solution but with low RFZ. The map looks reasonable but I was wondering why the RFZ is so low. Would this solution be acceptable? SOLU SET RFZ=3.2 TFZ=8.4 PAK=0 LLG=66

Re: [ccp4bb] Off topic -- Job post

Hi Xiaoshan, I am interested in applying, but do you think that an experienced protein-RNA crystallographer with a physical chemistry background would be given consideration? It so, I'll send a CV and cover letter through official channels. -- Eric J. Montemayor, Ph.D. Assistant Scie

Re: [ccp4bb] Demonstration for 2nd graders?

I like the sodium acetate crystallization from Dr. Shakhashiri’s Chemical Demonstrations. I prepare the supersaturated solution ahead of time, then seed it with crystals during class. It’s fast, simple, entertaining, and the flask gets warm, showing that heat is being released by the reaction.

[ccp4bb] Postdoctoral Position at the Institute for Bioscience and Biotechnology Research

ings/30999 Regards, Eric _ Eric A. Toth, Ph.D. Assistant Professor University of Maryland School of Medicine Department of Biochemistry and Molecular Biology Marlene and Stewart Greenebaum Cancer Center Section Leader, Structural Biology

Re: [ccp4bb] ATP library file in REFMAC - Part II

L On Aug 27, 2014 5:12 PM, "Santarsiero, Bernard D." wrote: > I appreciate all of the comments and suggestions on how to locate a better > CIF file for ATP. I adopted the suggestion of Boaz, and generated a new > ATP.cif file, and refined one of my structures. > > The validation server still uses

[ccp4bb] PhD-position in enzyme crystallography

CV and the contact data of two referees, should be sent directly to Prof. Plattner (dplattchemie.uni-freiburg.de). **** Eric Strittmatter Albert-Ludwigs-Universität Freiburg Institute of Organic Chemistry & Biochemistry Albertstraße 21, D-79104 Freiburg

Re: [ccp4bb] Kabat, insertion codes & refinement

on tags? "All sequences must start with 1"? (Not all antibodies are isolated from natural sources. Some are from human-designed libraries for example, so they are every bit as engineered as something with as His tag stuck on the end.) Cheers, Eric On Jun 16, 2014, at 7:23 AM, Ed

Re: [ccp4bb] Off topic: Homology modeling

r optimization that we gained more confidence in its accuracy. Cheers, Eric On May 22, 2014, at 3:48 PM, Theresa Hsu wrote: > Dear all > > I am working with a membrane protein without known structure. The closest > protein in PDB has 10% sequence identity/25% similarity to my

Re: [ccp4bb] Issue with Molecules per Asymmetric Unit for Molecular Replacement

Have you tried fixing the molecule that looks correct and searching for others? You might have greater than one but less than 9 molecules per ASU. When you do this, try imposing severe restraints on the packing function. This worked for me in Phaser with a difficult case. My anecdotal experience

[ccp4bb] OFF TOPIC - zebra printer labels for SBS format plates

. thanks in advance for your suggestions/advice. sincerely, Eric Eric Larson Structural Research Boehringer Ingelheim Pharmaceuticals Ridgefield, CT USA

Re: [ccp4bb] Validation reports for all X-ray structures in the PDB

Any chance validation reports will ever be made for obsoleted entries? Eric On Wed, Apr 16, 2014 at 1:01 PM, Gerard DVD Kleywegt wrote: > Hi all, > > You may not have noticed, but 19 March 2014 was VR Day - the day that new > style wwPDB validation reports for all X-ray structur

Re: [ccp4bb] sf_convert

of, and had misconceptions corrected. Pavel's right, though, and I should take my discussions off list before I accidentally offend any more developers with my inartful phrasing. ;) Eric

Re: [ccp4bb] sf_convert

ut to find cell and symmetry information that may be lacking in mmCIF structure factor files. I'm sure I could write a wrapper script of my own, but I was trying to avoid reinventing the wheel. Eric On Wed, Mar 26, 2014 at 5:51 AM, Tim Gruene wrote: > -BEGIN PGP SIGNED MESSAGE---

[ccp4bb] sf_convert

not found. export: Command not found. export: Command not found. if: Expression Syntax. Output File Name = 2hr0-sf.mtz : (MTZ format) No output file is produced. I recognize some of the output from ccp4-setup.sh, but I don't know what's going wrong. Ideas? Suggestions? Eric

Re: [ccp4bb] Stereo monitor

y!) but we were able to get the correct one by talking directly to HP. The card will drive the monitor at 144 Hz when stereo is disabled in the X server config file, but it drops to 120 Hz in stereo mode, which I assume is probably the maximum shutter speed on the 3D Vision Pro glasses. Ch

Re: [ccp4bb] Spots not getting indexed properly in protein-DNA complex

luck. _ Eric A. Toth, Ph.D. Assistant Professor Department of Biochemistry and Molecular Biology Marlene and Stewart Greenebaum Cancer Center University of Maryland School of Medicine 108 North Greene St. Baltimore, MD 21201 Email: et...@som.umaryland.edu<mailto:etoth...@umaryland.ed

Re: [ccp4bb] Of topic, trying to identify a reference for multiple crystal data collection

The table also appears in chapter 16 of this book: Sanderson, Mark R., and Jane Skelly, eds. *Macromolecular Crystallography: conventional and high-throughput methods*. Oxford University Press, 2007. Eric On Thu, Jul 18, 2013 at 11:29 PM, Edward Snell wrote: > Dear All, > > On a beaml

Re: [ccp4bb] Of topic, trying to identify a reference for multiple crystal data collection

This may be the publication you seek: Fry, Elizabeth E., Jonathan Grimes, and David I. Stuart. "Virus crystallography." *Molecular biotechnology* 12.1 (1999): 13-23. http://link.springer.com/article/10.1385/MB:12:1:13 Eric On Thu, Jul 18, 2013 at 11:29 PM, Edward Snell wrote:

Re: [ccp4bb] Why the name "aimless"

I've always thought "gormless" is a woefully underused word. Eric On Thu, May 2, 2013 at 11:53 AM, Mark van Raaij wrote: > i.e. the next program will be Graceless or Feckless? > > On 2 May 2013, at 12:10, Phil Evans wrote: > > > Reference: > > Gibbons

Re: [ccp4bb] delete subject

of problematic structures still sneak through peer review. Relaxing quality review standards that must be passed before a scientist gets to claim credit for a discovery is a step backwards IMO. Cheers, Eric On Mar 28, 2013, at 5:06 PM, Scott Pegan wrote: > Hey everyone, > > Both Mark

[ccp4bb] Professor Roger Fourme

beamline. As one of his student and colleague, it was a great privilege to work with him. Eric Girard. -- *** Eric Girard Extremophiles and Large Macromolecular Assemblies (ELMA) group Institut de Biologie Structurale J.-P. Ebel UMR 5075

Re: [ccp4bb] Boveral in SFCheck

When last I checked a few months ago, of the 12 implicated structures only 4 had been moved to the PDB's repository of obsolete structures. Eric On Fri, Dec 14, 2012 at 5:11 PM, Randy Read wrote: > Hi, > > It's hard to believe this has gone on so long, but the situation doe

Re: [ccp4bb] Boveral in SFCheck

I'm well aware of that. Since I'm looking for outliers in the PDB, avoiding 2HR0 is the opposite of what I want to be doing. ;) I only picked it for my example because it's one of a few IDs I have memorized. :) Eric On Fri, Dec 14, 2012 at 2:57 AM, Michael Hadders wrote: >

[ccp4bb] Boveral in SFCheck

no explanation for it in either the SFCheck manual or the original journal article. Perhaps I'm missing something obvious, but someone would really make my day if they could point me in the right direction. Thanks! :) Eric

Re: [ccp4bb] vitrification vs freezing

How about Latin? It already has a long and distinguished history of use in science. :) Eric On Fri, Nov 16, 2012 at 4:54 AM, Tim Gruene wrote: > -BEGIN PGP SIGNED MESSAGE- > Hash: SHA1 > > Hi James, > > I once heard that in (European) law French is the language of c

Re: [ccp4bb] Off-topic: Best Scripting Language

hat it will crash: [woz:~] bennette% cat pytest.py example_string = "10.3" number = int(example_string) [woz:~] bennette% /Library/Frameworks/Python.framework/Versions/2.6/bin/python pytest.py Traceback (most recent call last): File "pytest.py", line 2, in number = int(example_string) ValueError: invalid literal for int() with base 10: '10.3' That's brain dead. IMHO of course. Cheers, Eric

Re: [ccp4bb] Off-topic: Best Scripting Language

compatible with R and Python. Eric On Thu, Sep 13, 2012 at 2:21 PM, Jacob Keller < j-kell...@fsm.northwestern.edu> wrote: > It turns out that the syntax and semantics of all reasonable programming >> languages are very similar, or fall into only a few classes (e.g. C-like, >&g

Re: [ccp4bb] Off-topic: Best Scripting Language

Try R. :) http://www.r-project.org/ Eric On Wed, Sep 12, 2012 at 10:32 AM, Jacob Keller < j-kell...@fsm.northwestern.edu> wrote: > Dear List, > > since this probably comes up a lot in manipulation of pdb/reflection files > and so on, I was curious what people thought would be

Re: [ccp4bb] strict structure based alignment

in space. Be warned that Match->Align will be very slow for 10+ structures, but is fine for half a dozen or so. The generated alignment will be displayed in a window that will have a "File" menu where you can save the alignment to a variety of common formats. --Eric Eric Pettersen UCSF Computer Graphics Lab

Re: [ccp4bb] information received through the AFC: iycr2014

I'm guessing disorder is a major limiting factor on effective resolutions. ;) Eric On Thu, Jul 5, 2012 at 2:36 PM, Bernhard Rupp (Hofkristallrat a.D.) < hofkristall...@gmail.com> wrote: > **Ø **enjoy that the U.N.'s declaration of the International Year of > Crystallogr

Re: [ccp4bb] Tool for calculating RMSD

r rotation. www.cgl.ucsf.edu/chimera www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/measure.html --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Jun 22, 2012, at 4:00 PM, Jeremy Tame wrote: > Yes

Re: [ccp4bb] off-topic: Verify3D

ay be needed, but once everything compiles and runs properly, I'll let the list know (assuming anyone's interested). Thanks again. :) Eric On Fri, Jun 8, 2012 at 10:47 AM, Eric Williams wrote: > I recently acquired the source for Verify3D and have tried unsuccessfully > to compile it.

[ccp4bb] off-topic: Verify3D

u 11.04 in particular? Thanks. :) Eric Williams PhD candidate, Intelligent Systems Program University of Pittsburgh

Re: [ccp4bb] completeness in scala

In sports, maximal effort is considered to be 110%, so you're actually 9.9% short of getting everything you could out of that crystal at its resolution limit. All things considered, that's not bad. _ Eric A. Toth, Ph.D. Assistant

Re: [ccp4bb] Off topic about program for multiple protein sequence alignment

self. The bottom line is that no matter what method you use, you need to look at the alignment and, if possible, overlay the secondary structure for one or more of the homologs to make sure that gaps and insertions occur in sensible places (e.g. loops), signature sequences line up, etc. With best reg

[ccp4bb] Request for nominations

/content/pages/main-awards-prizes Please consider nominating an early career scientist!! Regards, Eric Montemayor

Re: [ccp4bb] very informative - Trends in Data Fabrication

to a hard drive 10 years ago have something that can still read an Irix EFS-formatted SCSI hard drive today and, if not, did they bother to move the data to some other storage medium? -Eric On Apr 5, 2012, at 9:08 AM, Roger Rowlett wrote: > FYI, every NSF grant proposal now must hav

Re: [ccp4bb] very informative - Trends in Data Fabrication

ave little to no utility..." -Amazon to some of its cloud customers following their major crash last year http://articles.businessinsider.com/2011-04-28/tech/29958976_1_amazon-customer-customers-data-data-loss -Eric On Apr 3, 2012, at 9:22 PM, Zhijie Li wrote: > Hi, > > Re

Re: [ccp4bb] Putting Text into Movies

rrent/docs/ContributedSoftware/2dlabels/2dlabels.html --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

Re: [ccp4bb] residuewise rmsd for multiple chain superposition

cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/matchalign/matchalign.html sequence aignment viewer: http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/multalignviewer/framemav.html --Eric Eric Pettersen http://www.cgl.ucsf.edu/h

Re: [ccp4bb] All-D World

now, his acolytes have attempted to hide the truth about the ribosome by referring to its work with the neutral, innocent-sounding phrase "translation". Don't be fooled, but instead pray for the development of the next generation of ribosome inhibitors, or at least dissolve the cur

Re: [ccp4bb] Freezing crystal

Hi Theresa, A good place to start when searching for suitable cryo conditions are the tables in these references: Garman, et al. J. Appl. Cryst. (1996). 29, 584-587. McFerrin, et al. J. Appl. Cryst. (2002). 35, 538-545. hope they help and good luck. Eric __ Eric Larson

Re: [ccp4bb] secondary structure output

ndary structure and if you then save a new PDB file (File->Save PDB) the saved file will have the appropriate HELIX/SHEET records. You can get Chimera from www.cgl.ucsf.edu/chimera . --Eric Eric Pettersen UCSF Computer Grap

[ccp4bb] job opening Application Scientist "Biological Crystallography"

[cid:image001.png@01CCC0A5.DB5D6690] To further strengthen the capacities of the application laboratories, Bruker (Karlsruhe, Germany) has an immediate opening for an Application Scientist "Biological Crystallography" (full-ti

Re: [ccp4bb] Software for showing crystal packing

do this. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/unitcell/unitcell.html --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

Re: [ccp4bb] [CCP4] identify a rotation centre: domain rotation

MatchMaker tool can match the smaller domains with having to delete part of the structure. --Eric On Nov 23, 2011, at 4:00 PM, WENHE ZHONG wrote: Dear members, I would like to have your ideas if there is any way to identify a rotation centre of domain in two different states using CCP4 or oth

Re: [ccp4bb] Superpositions: Deviation by Residue

ww.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/multalignviewer/multalignviewer.html#assessment --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

Re: [ccp4bb] Temperature Factor statistics

lator/calculator.html a tutorial focused on coloring by B-factor: www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/bfactor.html --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

Re: [ccp4bb] more Computer encryption matters

3 GHz core i7 iMac with the HDS722020ALA330 Hitachi drive. I believe this is the 870 series chip which does _not_ have the new AES instruction set on-chip. -Eric On Aug 18, 2011, at 5:50 PM, William G. Scott wrote: > OS X 10.7 enables you to do whole-drive encryption. > > Here is

Re: [ccp4bb] Computer encryption matters

t is using an older version. There is another workaround but it's kind of a hack. So I'd say problems are very rare, but if you run into strange behavior, don't rule out encryption as a possible cause. -Eric On Aug 17, 2011, at 3:13 PM, Jrh wrote: > Dear Colleagues, >

Re: [ccp4bb] COOT library

Thanks Huw. Unfortunately I have the same problem when using the new libraries. Maybe it has something to do with the pdb file (output from Phaser) I'm trying to refine. Do I have to rename the residues in the pdb file or is there another trick?

Re: [ccp4bb] COOT library

Thanks for the suggestions. I could solve the problem by using the setenv command to the coot directory,but I still cannot use the Real Space Refine Zone in Coot because the names are not compatible. I'm trying to build an RNA molecule by the way. Any suggestions? Eric

[ccp4bb] COOT library

Dear all, Is there a way to make COOT use it's own libraries and not the ones from ccp4 which is the default? I've tried using the command export COOT_REFMAC_LIB_DIR=//path/to/coot//share/coot/lib (mentioned elsewhere) but it doesn't work. Thanks Eric

Re: [ccp4bb] Another paper & structure retracted

errors or improve the structure, as reviewers do with papers. Guidelines could be given for a fair reviewing of the structure and depositors should be notified the name of the reviewer. Eric

[ccp4bb] MOLREP no output!

Dear all, I'm using MOLREP in CCP4 for MR. The problem is that it doesn't output a pdb file although the last contrast value written in the log file is 3.13! Are there certain criteria which have to be fulfilled before it gives a pdb file or is it a bug? Thanks for your help! Eric

Re: [ccp4bb] pdb_extact and refmac5.6

Hi Jan, Have you tried using the x.refmac file that is created instead of the log file. It is in cif format and may be in the "DepositFiles" directory. Hope you are well and talk to you later, Eric ==== Eric T. Larson, PhD Biomolecular Struct

Re: [ccp4bb] Concentrating a protein solution - subbu

rying in particular pH and precipitant concentration. best, Eric On Thu, 21 Jul 2011, ray-br...@att.net wrote: >What is the pI? Perhaps the protein will be more soluble close to this pH?  >You could increase the salt and/or add some glycerol or a >cofactor? >  >Normally cry

Re: [ccp4bb] Concentrating a protein solution - subbu

Some possible things to try: additive screen, include specific ligands, different temperature, different ratios of protein solution to crystallization solution, seeding, different crystallization methods (hanging vs. sitting drop, batch, diffusion,...), ... good luck,

Re: [ccp4bb] Off Topic: How to delete loops from a protein

. (http://www.ncbi.nlm.nih.gov/pubmed/19352432) good luck, Eric Eric T. Larson, PhD Biomolecular Structure Center Department of Biochemistry Box 357742 University of Washington Seattle, WA 98195 email: larso...@u.washington.edu On

Re: [ccp4bb] unusual sighting of a crystal structure

It would be even scarier if they used an NMR structure. -Eric On Jul 16, 2011, at 1:20 PM, Robbie Joosten wrote: > Hi Artem, > > Thank for that nice example of a protein structure used to pimp a movie. > Ribbon representations are always the scariest. > > Cheers, > Robbie

Re: [ccp4bb] Off topic - transformation problems

oops - I just caught that the empty pET20 did transform well so the other suggestions about toxicity are probably more accurate. On Thu, 14 Jul 2011, Eric Larson wrote: On Thu, 14 Jul 2011, Wonjin Bae wrote: Hi, all Recently, some bactrial source enzyme(sialidase) was subcloned pET20b and

Re: [ccp4bb] Off topic - transformation problems

know how to solve the this problems? Thanks a lot !! Genie, Eric T. Larson, PhD Biomolecular Structure Center Department of Biochemistry Box 357742 University of Washington Seattle, WA 98195 email: larso...@u.washington.edu

Re: [ccp4bb] Convert .cif to mtz

Hi Madhu, You don't need to use scala, d*trek can do the job as well. The easiest thing to do is to continue with d*trek to scale and merge your data and then input this scaled and merged file into Dtrek2mtz. Eric Eric T. Larson, PhD Biomolecular Stru

Re: [ccp4bb] Convert .cif to mtz

Madhu, I just noticed that your message said you "indexed and integrated" your data. Did you scale it with d*trek too (that needs to be done before using Dtrek2mtz) or are you looking to use the integrated d*trek reflections for subsequent scaling in ccp4 with scala? Eric On T

Re: [ccp4bb] Convert .cif to mtz

ml for more information. good luck, Eric ==== Eric T. Larson, PhD Biomolecular Structure Center Department of Biochemistry Box 357742 University of Washington Seattle, WA 98195 email: larso...@u.washington.edu On Fri, 24 Jun 2011, Mad

Re: [ccp4bb] Change cell parameter

Hi Zhiyi, This is very easily done using Pointless. From the gui, click "Match index to reference", enter your two mtz files and run. ERic ==== Eric T. Larson, PhD Biomolecular Structure Center Department of Biochemistry Box 357742 University of Washingt

Re: [ccp4bb] Defining an ellipse around a protein structure

://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-May/006407.html --Eric

Re: [ccp4bb] Low resolution refinement

thing you should explore. good luck, Eric Eric T. Larson, PhD Biomolecular Structure Center Department of Biochemistry Box 357742 University of Washington Seattle, WA 98195 email: larso...@u.washington.edu On Thu, 19 May 2011,

Re: [ccp4bb] mutation and minimization

o say that you shouldn't follow the protocol outlined by Saugata Hazra in another posting. It depends on your goals. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

Re: [ccp4bb] mutation and minimization

/docs/ContributedSoftware/rotamers/rotamers.html You can then use Chimera's Minimize Structure tool to minimize the side chain and/or the local environment or, if you're feeling frisky, the whole protein: http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/minimize/minimi

Re: [ccp4bb] Stereo solution with Nvidia '3D vision' or '3D vision pro'

didn't make any difference, still only 100 Hz. Are you using Windows or Linux? We're using the 64-bit Linux driver. -Eric On May 9, 2011, at 4:26 AM, Takaaki Fukami wrote: >> not seen a working 120 Hz stereo setup working on the Acer GD235 monitor. >> if you ask th

Re: [ccp4bb] Thermal Ellipsoids pic

lacks rastep's "cut-away quadrant" depiction but has all the other depictions. More info about Thermal Ellipsoids here: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/thermal/thermal.html about Chimera itself here: www.cgl.ucsf.edu/chimera --Eric

Re: [ccp4bb] Stereo solution with Nvidia '3D vision' or '3D vision pro'

ng at 120 and found that it is actually doing what people claim it can do. I find the 100 Hz LCD flicker annoying over long periods so I am still a neanderthal CRT user. My coworkers were convinced their LCD systems were running at 120, when they were actually only running at 100. I'm not

Re: [ccp4bb] Pymol questions

Hi Eric, On Wed, 4 May 2011, jlliu liu wrote: Hi All, I have two questions for Pymol. the pymol wiki is your friend (http://www.pymolwiki.org/index.php/Main_Page) as is the pymol users mailing list (http://sourceforge.net/mail/?group_id=4546). Follow the link to subscribe. 1. Can you

Re: [ccp4bb] Met auxotroph and aa-mix

Hi Eric, If you are trying to express your Se-Met protein, it is typically done in a defined media starting with a minimal media base so a mixture of amino acids, particularly those that are essential, is needed. You likely will not get very high yields of SeMet-labeled protein if you simply

Re: [ccp4bb] Comparing two proteins

nable here: http://www.cgl.ucsf.edu/chimera --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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