For the NMR structure ensemble, you could calculate root mean square fluctuations (RMSFs) and put them into the B factor column. This is a fairly common analysis within molecular dynamics software. You could also use the ProDy Python API to do this.
ProDy also has command line apps including one for writing out biomol assemblies, which could be added to the growing list too. Best wishes James > On May 27, 2021, at 00:03, CCP4BB automatic digest system > <lists...@jiscmail.ac.uk> wrote: > > There are 40 messages totaling 21155 lines in this issue. > > Topics of the day: > > 1. writing coordinates of full biomol into one (PDB) file (4) > 2. Postdoctoral position in structural biology of comammox in Vienna > 3. PhD position, University of Konstanz > 4. Fwd: Abstract submission deadline extended to 2 June - PSB Symposium > "Frontiers in Bioimaging", 1-2 July 2021 > 5. Unmodeled density (12) > 6. External: Re: [ccp4bb] Unmodeled density > 7. Analysis of NMR ensembles (19) > 8. Fully-funded PhD at the University of Liverpool > > ######################################################################## > > 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/ > > ---------------------------------------------------------------------- > > Date: Tue, 25 May 2021 16:58:49 -0700 > From: Pavel Afonine <pafon...@gmail.com> > Subject: Re: writing coordinates of full biomol into one (PDB) file > > Hi Frank, > > phenix.pdb.biomt_reconstruction command should do it. > > Pavel > >> On Tue, May 25, 2021 at 12:44 PM Frank von Delft < >> frank.vonde...@cmd.ox.ac.uk> wrote: >> >> Hello all - this presumably has a really simple solution: >> >> For a PDB file with a (correct) biomolecular assembly record (REMARK >> 350), what program do I use to generate and write out the coordinates of >> the biomolecular assembly (or one of them). >> >> Thanks >> Frank >> >> ######################################################################## >> >> 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/ >> > > ######################################################################## > > 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/ > > ------------------------------ > > Date: Wed, 26 May 2021 07:05:26 +0200 > From: Kristina Djinovic Carugo <kristina.djino...@univie.ac.at> > Subject: Postdoctoral position in structural biology of comammox in Vienna > > *Postdoctoral position in structural biology of comammox in Vienna* > > For 120 years, microbiologists had strongly assumed that nitrification > must be performed by two distinct groups of microorganisms > (‘nitrifiers’) in cooperation: the ammonia oxidizers and the nitrite > oxidizers, respectively. This scientific dogma broke in 2016, when > ‘complete ammonia oxidizers’ were discovered (1). In collaboration with > the research lab (Daims/Wagner) who discovered the comammox bacterium > Djinovic lab plans to structurally and biochemically characterize > selected enzymes of the comammox, with the aim to decipher the catalytic > mechanism and to identify those structural determinants of the substrate > affinity and specificity. > > *Qualifications and experience: *The applicants should hold a recent PhD > degree in a relevant field with a structural biology experience. Strong > background in molecular cloning, expression, and purification of protein > complexes is essential. Prior knowledge of crystallography and/or > single-particle electron microscopy is needed. Excellent spoken and > written English are required. > > Applications are accepted through *Vienna International Postdoctoral > Program (VIP^2 )*, details on the program which offers excellent > research environment,tructured training and career development program > are available here: > > https://training.vbc.ac.at/post-docs/vip2-post-doc-program/ > <https://training.vbc.ac.at/post-docs/vip2-post-doc-program/> > > *Deadline*: 15^th June 2021 > > For details in the project contact please contact: Kristina Djinovic > Carugo kristina.djino...@univie.ac.at > <mailto:kristina.djino...@univie.ac.at> > > 1.Daims, H., Lebedeva, E. V., Pjevac, P., Han, P., Herbold, C., > Albertsen, M., Jehmlich, N., Palatinszky, M., Vierheilig, J., Bulaev, > A., Kirkegaard, R. H., Von Bergen, M., Rattei, T., Bendinger, B., > Nielsen, P. H., and Wagner, M. (2015) Complete nitrification by > Nitrospira bacteria. /Nature/ *528*, 504-509; 10.1038/nature16461 > > -- > Department of Structural and Computational Biology > Max Perutz Labs > University of Vienna > Campus Vienna Biocenter 5 > A-1030 Vienna > Austria > > > e-mail: kristina.djino...@univie.ac.at > Phone: +43-1-4277-52203 > Phone: +43-1-4277-52201 (secretary) > Mobile A: +43-664-602 77-522 03 > Fax: +43-1-4277-9522 > > > ######################################################################## > > 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/ > > ------------------------------ > > Date: Wed, 26 May 2021 06:28:58 +0100 > From: Frank von Delft <frank.vonde...@cmd.ox.ac.uk> > Subject: Re: writing coordinates of full biomol into one (PDB) file > > Thanks for the quick responses! I was looking for a command-line tool > (should have said). Here's the list: > > 1. phenix.pdb.biomt_reconstruction > 2. Makemultimer.py: http://watcut.uwaterloo.ca/tools/makemultimer/docs > <http://watcut.uwaterloo.ca/tools/makemultimer/docs> > 3. Quat in pymol: https://pymolwiki.org/index.php/BiologicalUnit/Quat > <https://pymolwiki.org/index.php/BiologicalUnit/Quat> > 4. BiologicalUnit in pymol: > https://pymolwiki.org/index.php/BiologicalUnit > <https://pymolwiki.org/index.php/BiologicalUnit> > > (CCP4bb is amazing....) > > Frank > >> On 25/05/2021 20:44, Frank von Delft wrote: >> Hello all - this presumably has a really simple solution: >> >> For a PDB file with a (correct) biomolecular assembly record (REMARK >> 350), what program do I use to generate and write out the coordinates >> of the biomolecular assembly (or one of them). >> >> Thanks >> Frank >> >> ######################################################################## >> >> 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/ > > ######################################################################## > > 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/ > > ------------------------------ > > Date: Wed, 26 May 2021 09:10:17 +0200 > From: Marcin Wojdyr <woj...@gmail.com> > Subject: Re: writing coordinates of full biomol into one (PDB) file > > another one: > > gemmi convert --assembly=N input.pdb output.pdb > > >> On Wed, 26 May 2021 at 07:30, Frank von Delft >> <frank.vonde...@cmd.ox.ac.uk> wrote: >> >> Thanks for the quick responses! I was looking for a command-line tool >> (should have said). Here's the list: >> >> 1. phenix.pdb.biomt_reconstruction >> 2. Makemultimer.py: http://watcut.uwaterloo.ca/tools/makemultimer/docs >> <http://watcut.uwaterloo.ca/tools/makemultimer/docs> >> 3. Quat in pymol: https://pymolwiki.org/index.php/BiologicalUnit/Quat >> <https://pymolwiki.org/index.php/BiologicalUnit/Quat> >> 4. BiologicalUnit in pymol: >> https://pymolwiki.org/index.php/BiologicalUnit >> <https://pymolwiki.org/index.php/BiologicalUnit> >> >> (CCP4bb is amazing....) >> >> Frank >> >>> On 25/05/2021 20:44, Frank von Delft wrote: >>> Hello all - this presumably has a really simple solution: >>> >>> For a PDB file with a (correct) biomolecular assembly record (REMARK >>> 350), what program do I use to generate and write out the coordinates >>> of the biomolecular assembly (or one of them). >>> >>> Thanks >>> Frank >>> >>> ######################################################################## >>> >>> 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/ >> >> ######################################################################## >> >> 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/ > > ######################################################################## > > 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/ > > ------------------------------ > > Date: Wed, 26 May 2021 13:02:24 +0200 > From: Olga Mayans <olga.may...@uni-konstanz.de> > Subject: PhD position, University of Konstanz > > *PhD Position: molecular structural biology of muscle signalling* > > We have a vacancy for a PhD student to join our laboratory at the Department > of Biology, University of Konstanz, Germany. > > Our laboratory studies the molecular mechanisms underpinning the > architecture, stress response, adaptation and disease process of striated > muscle. The focus of this PhD project will be on understanding the assembly > and regulation of biomedically relevant, titin-based signalling nodes in the > sarcomere. We apply an integrative approach to structural biology that > combines a rich variety of biochemical, biophysical and structural > methodologies (with emphasis on X-ray crystallography). > > Qualifications > > Applicants should hold (or be in the process of acquiring) a Master's degree > in biochemistry, biophysics, life sciences or related discipline, and be > interested in learning both laboratory-based and computational analyses as > applicable to the study of molecular systems. A strong motivation to > understand and discover the molecular mechanisms that enable function in > living cells is required. Basic experience in molecular biology and/or > recombinant protein production is expected. Good command of written and > spoken English, the ability to work in a team, and good communication and > organizational skills are required. Some initial knowledge of a > structural/biophysical method would be of advantage. > > Application > > Applications should contain the following documents in PDF format: > > 1. Applicant's CV > 2. Copies of original degree transcripts displaying marks obtained > 2. *Short* statement of motivation for pursuing PhD studies in molecular > sciences > 3. Contact details of two referees > > Informal enquiries and application materials should be submitted by email to: > > olga.may...@uni-konstanz.de > > The position is now available and applications will be considered until the > position is filled. > > =================================== > Prof. Olga Mayans > Biophysics and Structural Biology > Dept of Biology > University of Konstanz > D-78457 Konstanz, > Germany > Tel: +49 7531 88-2212 > olga.may...@uni-konstanz.de > =================================== > > ######################################################################## > > 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/ > > ------------------------------ > > Date: Wed, 26 May 2021 11:55:44 +0000 > From: "Mooers, Blaine H.M. (HSC)" <blaine-moo...@ouhsc.edu> > Subject: Re: writing coordinates of full biomol into one (PDB) file > > If you have PyMOL installed, you can paste the bash function below into your > .bashrc file, enter 'source .bashrc', and then enter 'bu PDB-ID'. > All that you have to remember a month from now is 'bu'. > > Otherwise, you can replace the pymol command with one of the other commands > that have been suggested and replace the filename stem with $1. > > > bu() > { > echo "Write out the biological unit for a PDB file from PyMOL." > if [ $# -lt 1 ]; then > echo 1>&2 "$0: not enough arguments" > echo "Supply the PDB-ID." > echo "Example: bu 3nd4" > return 2 > elif [ $# -gt 1 ]; then > echo 1>&2 "$0: too many arguments" > echo "Supply the PDB-ID." > echo "Example: bu 3nd4" > fi > pymol -c -d "fetch $1,type=pdb1;set all_states,on;save $1bu.pdb,state=0" > } > > > Best regards, > > Blaine > > Blaine Mooers, Ph.D. > Associate Professor > Department of Biochemistry and Molecular Biology, College of Medicine > University of Oklahoma Health Sciences Center > ________________________________________ > From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Marcin Wojdyr > [woj...@gmail.com] > Sent: Wednesday, May 26, 2021 2:10 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: [EXTERNAL] Re: [ccp4bb] writing coordinates of full biomol into one > (PDB) file > > another one: > > gemmi convert --assembly=N input.pdb output.pdb > > >> On Wed, 26 May 2021 at 07:30, Frank von Delft >> <frank.vonde...@cmd.ox.ac.uk> wrote: >> >> Thanks for the quick responses! I was looking for a command-line tool >> (should have said). Here's the list: >> >> 1. phenix.pdb.biomt_reconstruction >> 2. >> https://urldefense.proofpoint.com/v2/url?u=http-3A__Makemultimer.py&d=DwIBaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=rhNY2JSSQ3mt4PoiF7pH9wntVmI3DY_o8a_vl6iStB8&s=wMMX-ub8O19NLtJDQdelGfFOni2RMO7EVgZG1XZ1Uu4&e= >> : >> https://urldefense.proofpoint.com/v2/url?u=http-3A__watcut.uwaterloo.ca_tools_makemultimer_docs&d=DwIBaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=rhNY2JSSQ3mt4PoiF7pH9wntVmI3DY_o8a_vl6iStB8&s=XQ41GNcbJlsckrDR76D9n7YD0eKVop24nJpUYi5pTPA&e= >> <https://urldefense.proofpoint.com/v2/url?u=http-3A__watcut.uwaterloo.ca_tools_makemultimer_docs&d=DwIBaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=rhNY2JSSQ3mt4PoiF7pH9wntVmI3DY_o8a_vl6iStB8&s=XQ41GNcbJlsckrDR76D9n7YD0eKVop24nJpUYi5pTPA&e= >> > >> 3. Quat in pymol: >> https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_BiologicalUnit_Quat&d=DwIBaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=rhNY2JSSQ3mt4PoiF7pH9wntVmI3DY_o8a_vl6iStB8&s=K4dJU4Mq8Mi4SgQB6UFnQcTzfnkCfius8_QsRmWs_ZQ&e= >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_BiologicalUnit_Quat&d=DwIBaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=rhNY2JSSQ3mt4PoiF7pH9wntVmI3DY_o8a_vl6iStB8&s=K4dJU4Mq8Mi4SgQB6UFnQcTzfnkCfius8_QsRmWs_ZQ&e= >> > >> 4. BiologicalUnit in pymol: >> https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_BiologicalUnit&d=DwIBaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=rhNY2JSSQ3mt4PoiF7pH9wntVmI3DY_o8a_vl6iStB8&s=yOPGY2fznON_wKdKHEXsGbfEj9dij-0NHHTuqHdH6tM&e= >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_BiologicalUnit&d=DwIBaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=rhNY2JSSQ3mt4PoiF7pH9wntVmI3DY_o8a_vl6iStB8&s=yOPGY2fznON_wKdKHEXsGbfEj9dij-0NHHTuqHdH6tM&e= >> > >> >> (CCP4bb is amazing....) >> >> Frank >> >>> On 25/05/2021 20:44, Frank von Delft wrote: >>> Hello all - this presumably has a really simple solution: >>> >>> For a PDB file with a (correct) biomolecular assembly record (REMARK >>> 350), what program do I use to generate and write out the coordinates >>> of the biomolecular assembly (or one of them). >>> >>> Thanks >>> Frank >>> >>> ######################################################################## >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1&d=DwIBaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=rhNY2JSSQ3mt4PoiF7pH9wntVmI3DY_o8a_vl6iStB8&s=Zc5y9vtC54wj1EQkTlPSy1gDJXFDHGKDWtpCUt0pGWs&e= >>> >>> This message was issued to members of >>> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.jiscmail.ac.uk_CCP4BB&d=DwIBaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=rhNY2JSSQ3mt4PoiF7pH9wntVmI3DY_o8a_vl6iStB8&s=3Td7Xm6df98q55Qfp858BRcgJ58KOFH7GgL3f0Ye0Hc&e= >>> , a >>> mailing list hosted by >>> 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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/ > > ------------------------------ > > Date: Wed, 26 May 2021 14:43:20 +0200 > From: Daouda Traore <trao...@ill.fr> > Subject: Fwd: Abstract submission deadline extended to 2 June - PSB Symposium > "Frontiers in Bioimaging", 1-2 July 2021 > > Dear all, > > Please note that the abstract submission deadline for the PSB Symposium > "Frontiers in Bioimaging" (1-2 July 2021) has been extended to > *Wednesday 2 June*. > > For further information: > https://www.esrf.fr/home/events/conferences/2021/psb-symposium-frontiers-in-bioimaging/call-for-abstracts-for-poster-and-oral-contributions.html > > <https://www.esrf.fr/home/events/conferences/2021/psb-symposium-frontiers-in-bioimaging/call-for-abstracts-for-poster-and-oral-contributions.html> > > Best regards, > > Florent > > On 2021-04-22 17:28, Florent Bernaudat wrote: > > Dear all, > > The Partnership for Structural Biology (PSB), an alliance of > research institutes (EMBL, ESRF, IBS and ILL) located in Grenoble, > France, is pleased to announce that the PSB Symposium "Frontiers in > Bioimaging" will take place on 1-2 July 2021. The meeting will be > held remotely on a virtual event platform over two afternoons, and > will include a series of invited and selected talks, interactive > virtual posters, and interactive virtual lounges. > > This is to announce that registration is now opened (*It's FREE.* > *Deadline on 27 June 2021*) and the programme is available. > > All participants are invited to submit an abstract for a poster > and/or an oral presentation (short talks of 10 minutes). *Submission > deadline on 2 June 2021*. The number of posters is limited to *50*, > and best poster prizes (*150 euros each*) will be awarded. > > For further information and to check out the exciting collection of > invited speakers: https://www.esrf.fr/psbsymposium2021 > <https://www.esrf.fr/psbsymposium2021> > > The aim and scope of this meeting is to highlight progress in 3D > imaging research that bridges the gap between the atomic and > cellular scales, with spatial resolutions spanning from subnanometer > to submicrometer range. Featured topics will include: cryo-electron > tomography, X-ray tomography, volume electron microscopy, image > analysis, super-resolution microscopy, and correlative approaches. > The applications of the above methods to address essential questions > in life sciences is of particular interest. > > Best regards, > > On behalf of the organising committee > > -- > > Florent Bernaudat, PhD > PSB Scientific Coordinator/Animator > > Partnership for Structural Biology > Carl-Ivar Brändén Building- office 018 > 71, Avenue des Martyrs, > CS 90181 > 38042 Grenoble cedex 9 > France > > http://www.psb-grenoble.eu <http://www.psb-grenoble.eu> > Phone: 33 (0) 476 20 94 08 > Fax: 33 (0) 476 20 94 00 > > > ######################################################################## > > 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/ > > ------------------------------ > > Date: Wed, 26 May 2021 14:08:44 +0100 > From: leo john <ljohn16012...@gmail.com> > Subject: Unmodeled density > > Hi Group > Can you please suggest what this unmodeled blob can be (see appended > picture)? > I have Malonate, Boric Acid and Peg in my condition, and crystals were > soaked in GOL. > > I have tried fitting PO4 and SO4 so far. > > Thank You > John > [image: image.png] > > ######################################################################## > > 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/ > > ------------------------------ > > Date: Wed, 26 May 2021 13:14:37 +0000 > From: "Pearce, N.M. (Nick)" <n.m.pea...@uu.nl> > Subject: Re: Unmodeled density > > Is it on a symmetry axis? If so it could be the superposition of two > molecules (a molecule and a copy of itself). > > On 26 May 2021, at 15:08, leo john > <ljohn16012...@gmail.com<mailto:ljohn16012...@gmail.com>> wrote: > > Hi Group > Can you please suggest what this unmodeled blob can be (see appended picture)? > I have Malonate, Boric Acid and Peg in my condition, and crystals were soaked > in GOL. > > I have tried fitting PO4 and SO4 so far. > > Thank You > John > <image.png> > > > > ________________________________ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > ######################################################################## > > 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/ > > ------------------------------ > > Date: Wed, 26 May 2021 14:20:34 +0100 > From: leo john <ljohn16012...@gmail.com> > Subject: Re: Unmodeled density > > Hi All: > > Thank You very much for the response and yes it is at symmetry axis. > Distance between the bigger blob and smaller ones is approx 1.45 Ang. > I have tried fitting BO3, BO4, but no luck? > > Thanks > John > > On Wed, May 26, 2021 at 2:14 PM Pearce, N.M. (Nick) <n.m.pea...@uu.nl> > wrote: > >> Is it on a symmetry axis? If so it could be the superposition of two >> molecules (a molecule and a copy of itself). >> >> On 26 May 2021, at 15:08, leo john <ljohn16012...@gmail.com> wrote: >> >> Hi Group >> Can you please suggest what this unmodeled blob can be (see appended >> picture)? >> I have Malonate, Boric Acid and Peg in my condition, and crystals were >> soaked in GOL. >> >> I have tried fitting PO4 and SO4 so far. >> >> Thank You >> John >> <image.png> >> >> >> >> ------------------------------ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> >> >> > > ######################################################################## > > 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/ > > ------------------------------ > > Date: Wed, 26 May 2021 06:21:17 -0700 > From: Dale Tronrud <de...@daletronrud.com> > Subject: Re: Unmodeled density > > Something to give context and scale would be helpful. Two views > would also be good. > > Dale Tronrud > >> On 5/26/2021 6:08 AM, leo john wrote: >> Hi Group >> Can you please suggest what this unmodeled blob can be (see appended >> picture)? >> I have Malonate, Boric Acid and Peg in my condition, and crystals were >> soaked in GOL. >> >> I have tried fitting PO4 and SO4 so far. >> >> Thank You >> John >> image.png >> >> >> >> ------------------------------------------------------------------------ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> >> > > ######################################################################## > > 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/ > > ------------------------------ > > Date: Wed, 26 May 2021 13:22:43 +0000 > From: Sandra Eltschkner <s.eltschk...@uva.nl> > Subject: Re: Unmodeled density > > How about [B(OH) > 4]− > > ________________________________ > From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Dale Tronrud > <de...@daletronrud.com> > Sent: Wednesday, May 26, 2021 3:21 PM > To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> > Subject: Re: [ccp4bb] Unmodeled density > > Something to give context and scale would be helpful. Two views > would also be good. > > Dale Tronrud > >> On 5/26/2021 6:08 AM, leo john wrote: >> Hi Group >> Can you please suggest what this unmodeled blob can be (see appended >> picture)? >> I have Malonate, Boric Acid and Peg in my condition, and crystals were >> soaked in GOL. >> >> I have tried fitting PO4 and SO4 so far. >> >> Thank You >> John >> image.png >> >> >> >> ------------------------------------------------------------------------ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=04%7C01%7Cs.eltschkner%40UVA.NL%7C10356849253843165b2f08d920492cb0%7Ca0f1cacd618c4403b94576fb3d6874e5%7C1%7C1%7C637576320916749017%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=AZYEEo20oeHc5K2YSligCv4KZG6lj0qzVltHY4%2FXdx0%3D&reserved=0 >> <https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=04%7C01%7Cs.eltschkner%40UVA.NL%7C10356849253843165b2f08d920492cb0%7Ca0f1cacd618c4403b94576fb3d6874e5%7C1%7C1%7C637576320916753983%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=IOr9UtVDFlSHPBRNernnvbPwp4FkeYvs0OTtT1K5gSg%3D&reserved=0> >> > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=04%7C01%7Cs.eltschkner%40UVA.NL%7C10356849253843165b2f08d920492cb0%7Ca0f1cacd618c4403b94576fb3d6874e5%7C1%7C1%7C637576320916753983%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=IOr9UtVDFlSHPBRNernnvbPwp4FkeYvs0OTtT1K5gSg%3D&reserved=0 > > This message was issued to members of > https://eur04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2FCCP4BB&data=04%7C01%7Cs.eltschkner%40UVA.NL%7C10356849253843165b2f08d920492cb0%7Ca0f1cacd618c4403b94576fb3d6874e5%7C1%7C1%7C637576320916753983%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=3lFPg4jWuCWDCGrIQvuOctJMDpgbtF%2BVL9NJ1ODocms%3D&reserved=0, > a mailing list hosted by > https://eur04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2F&data=04%7C01%7Cs.eltschkner%40UVA.NL%7C10356849253843165b2f08d920492cb0%7Ca0f1cacd618c4403b94576fb3d6874e5%7C1%7C1%7C637576320916753983%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=Y13y%2FtxE05ancY%2FlPMIh1vMGKrQLKfAuDEbQK0%2FtxIY%3D&reserved=0, > terms & conditions are available at > https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fpolicyandsecurity%2F&data=04%7C01%7Cs.eltschkner%40UVA.NL%7C10356849253843165b2f08d920492cb0%7Ca0f1cacd618c4403b94576fb3d6874e5%7C1%7C1%7C637576320916753983%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=U0eFEx29EjWBXwQHX7aXMUZ2a%2FpZwS%2F2syQUaXKPcGo%3D&reserved=0 > > ######################################################################## > > 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 > > ------------------------------ > > Date: Wed, 26 May 2021 16:47:30 +0300 > From: רז זריבץ <ra...@yahoo.com> > Subject: Re: Unmodeled density > > Its looks like a prefect symmetry axis/ I guess it may be combined from > two molecules. > >> On 26/05/2021 16:08, leo john wrote: >> Hi Group >> Can you please suggest what this unmodeled blob can be (see appended >> picture)? >> I have Malonate, Boric Acid and Peg in my condition, and crystals were >> soaked in GOL. >> >> I have tried fitting PO4 and SO4 so far. >> >> Thank You >> John >> image.png >> >> >> >> ------------------------------------------------------------------------ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> >> > -- > ---------------------------------------------------- > Raz Zarivach, Ph.D. > Department of Life Sciences and the NIBN > Ben-Gurion University of the Negev > POB 653, 84105, Beer-Sheva, Israel > > Home page: https://lifewp.bgu.ac.il/wp/zarivach/ > tel: +972-8-6461999 > fax: +972-8-6472970 > skype: zarivach zariv...@bgu.ac.il > ---------------------------------------------------- > > > ######################################################################## > > 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/ > > ------------------------------ > > Date: Wed, 26 May 2021 16:02:59 +0200 > From: "Mark J. van Raaij" <mjvanra...@cnb.csic.es> > Subject: Re: Unmodeled density > > the central blob looks too big for B or even for P or S. > Perhaps Zn, Cd? (although you didn’t add it, it might have been in the > protein buffer or dragged through the purification by the protein?) > > Mark J van Raaij > Dpto de Estructura de Macromoleculas > Centro Nacional de Biotecnologia - CSIC > calle Darwin 3 > E-28049 Madrid, Spain > Section Editor Acta Crystallographica F > https://journals.iucr.org/f/ > > >> On 26 May 2021, at 15:08, leo john <ljohn16012...@gmail.com> wrote: >> >> Hi Group >> Can you please suggest what this unmodeled blob can be (see appended >> picture)? >> I have Malonate, Boric Acid and Peg in my condition, and crystals were >> soaked in GOL. >> >> I have tried fitting PO4 and SO4 so far. >> >> Thank You >> John >> <image.png> >> >> >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> > > ######################################################################## > > 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/ > > ------------------------------ > > Date: Wed, 26 May 2021 16:06:11 +0200 > From: "Mark J. van Raaij" <mjvanra...@cnb.csic.es> > Subject: Re: Unmodeled density > > PS I’d model a metal and 4 waters and then measure the distances after > refinement. And then look at M Harding's ActaD papers and try to work out > which coordination configuration and distances work best. And, when you get > the chance, run an emission spectrum at the beamline to help identify the > putative heavy(ish) atom that was co-crystallised. > > Mark J van Raaij > Dpto de Estructura de Macromoleculas > Centro Nacional de Biotecnologia - CSIC > calle Darwin 3 > E-28049 Madrid, Spain > Section Editor Acta Crystallographica F > https://journals.iucr.org/f/ > > >> On 26 May 2021, at 15:08, leo john <ljohn16012...@gmail.com> wrote: >> >> Hi Group >> Can you please suggest what this unmodeled blob can be (see appended >> picture)? >> I have Malonate, Boric Acid and Peg in my condition, and crystals were >> soaked in GOL. >> >> I have tried fitting PO4 and SO4 so far. >> >> Thank You >> John >> <image.png> >> >> >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> > > ######################################################################## > > 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/ > > ------------------------------ > > Date: Wed, 26 May 2021 14:14:01 +0000 > From: Michel Fodje <michel.fo...@lightsource.ca> > Subject: Re: External: Re: [ccp4bb] Unmodeled density > > That looks like a magnessium hexahydrate. > > From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Pearce, N.M. > (Nick) > Sent: May 26, 2021 7:15 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: External: Re: [ccp4bb] Unmodeled density > > Is it on a symmetry axis? If so it could be the superposition of two > molecules (a molecule and a copy of itself). > > > On 26 May 2021, at 15:08, leo john > <ljohn16012...@gmail.com<mailto:ljohn16012...@gmail.com>> wrote: > > Hi Group > Can you please suggest what this unmodeled blob can be (see appended picture)? > I have Malonate, Boric Acid and Peg in my condition, and crystals were soaked > in GOL. > > I have tried fitting PO4 and SO4 so far. > > Thank You > John > <image.png> > > > ________________________________ > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > ________________________________ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > ######################################################################## > > 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/ > > ------------------------------ > > Date: Wed, 26 May 2021 16:14:36 +0200 > From: "Mark J. van Raaij" <mjvanra...@cnb.csic.es> > Subject: Re: Unmodeled density > > oh, 1.45 Å is a very short distance for metal coordination. > perchlorate has a Cl to O distance of that length > https://en.wikipedia.org/wiki/Perchlorate > > Mark J van Raaij > Dpto de Estructura de Macromoleculas > Centro Nacional de Biotecnologia - CSIC > calle Darwin 3 > E-28049 Madrid, Spain > Section Editor Acta Crystallographica F > https://journals.iucr.org/f/ > > >> On 26 May 2021, at 15:20, leo john <ljohn16012...@gmail.com> wrote: >> >> Hi All: >> >> Thank You very much for the response and yes it is at symmetry axis. >> Distance between the bigger blob and smaller ones is approx 1.45 Ang. >> I have tried fitting BO3, BO4, but no luck? >> >> Thanks >> John >> >> On Wed, May 26, 2021 at 2:14 PM Pearce, N.M. (Nick) <n.m.pea...@uu.nl >> <mailto:n.m.pea...@uu.nl>> wrote: >> Is it on a symmetry axis? If so it could be the superposition of two >> molecules (a molecule and a copy of itself). >> >>>> On 26 May 2021, at 15:08, leo john <ljohn16012...@gmail.com >>>> <mailto:ljohn16012...@gmail.com>> wrote: >>> >>> Hi Group >>> Can you please suggest what this unmodeled blob can be (see appended >>> picture)? >>> I have Malonate, Boric Acid and Peg in my condition, and crystals were >>> soaked in GOL. >>> >>> I have tried fitting PO4 and SO4 so far. >>> >>> Thank You >>> John >>> <image.png> >>> >>> >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> > > ######################################################################## > > 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/ > > ------------------------------ > > Date: Wed, 26 May 2021 15:32:16 +0100 > From: leo john <ljohn16012...@gmail.com> > Subject: Re: Unmodeled density > > Hi All > > Thank You very much for the responses. > > Based on suggestion regarding metal, I put 'Ca' and refined it, I got the > following density that I thought best represented by Imidazole. I added it > and removed 'Ca'. Again one round of refinement. > > [image: image.png] > > After another round of refinement, I got the following suggesting it is > wrongly placed (I think so). > > [image: image.png] > > I should have told earlier, but I did not: My data is of 1 Ang resolution. > If this is of any help to the community to suggest anything. > > Thank You > John > > > On Wed, May 26, 2021 at 3:14 PM Mark J. van Raaij <mjvanra...@cnb.csic.es> > wrote: > >> oh, 1.45 Å is a very short distance for metal coordination. >> perchlorate has a Cl to O distance of that length >> https://en.wikipedia.org/wiki/Perchlorate >> >> Mark J van Raaij >> Dpto de Estructura de Macromoleculas >> Centro Nacional de Biotecnologia - CSIC >> calle Darwin 3 >> E-28049 Madrid, Spain >> Section Editor Acta Crystallographica F >> https://journals.iucr.org/f/ >> >> >> On 26 May 2021, at 15:20, leo john <ljohn16012...@gmail.com> wrote: >> >> Hi All: >> >> Thank You very much for the response and yes it is at symmetry axis. >> Distance between the bigger blob and smaller ones is approx 1.45 Ang. >> I have tried fitting BO3, BO4, but no luck? >> >> Thanks >> John >> >> On Wed, May 26, 2021 at 2:14 PM Pearce, N.M. (Nick) <n.m.pea...@uu.nl> >> wrote: >> >>> Is it on a symmetry axis? If so it could be the superposition of two >>> molecules (a molecule and a copy of itself). >>> >>>> On 26 May 2021, at 15:08, leo john <ljohn16012...@gmail.com> wrote: >>> >>> Hi Group >>> Can you please suggest what this unmodeled blob can be (see appended >>> picture)? >>> I have Malonate, Boric Acid and Peg in my condition, and crystals were >>> soaked in GOL. >>> >>> I have tried fitting PO4 and SO4 so far. >>> >>> Thank You >>> John >>> <image.png> >>> >>> >>> >>> ------------------------------ >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>> >>> >>> >> ------------------------------ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> >> >> > > ######################################################################## > > 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/ > > ------------------------------ > > Date: Wed, 26 May 2021 10:32:50 -0400 > From: Roger Rowlett <rrowl...@colgate.edu> > Subject: Re: Unmodeled density > > Needs more context. What is the geometry around the central density? > (Tetrahedral?) What are the nearby polar interaction partners? Is this site > on a protein-protein interface? Or is it on the surface of the protein? > This information can provide some clues. Polyatomic ions like phosphate > usually look more blobby unless data is high resolution and the ion is > highly constrained by hydrogen bonding partners. Boron doesn't have much > scattering power, so I wouldn't expect the central blob in your density to > be a boron atom. > > Zinc(II) is a ubiquitous contaminant in many protein preps and should be a > consideration. Nickel(II) can also be present if the protein was purified > using nickel affinity chromatography. However, the typical tetrahedral > Zn-O/N or Ni-O/N bond distances are around 2.0 A. If the density is on a > symmetry axis, and alternate stable conformations are possible, then all > sorts of tricks can be played with the shape of the apparent density. > > _______________________________________ > Roger S. Rowlett > Gordon & Dorothy Kline Professor, Emeritus > Department of Chemistry > Colgate University > 13 Oak Drive > Hamilton, NY 13346 > > tel: (315)-723-7245 > email: rrowl...@colgate.edu > >> On Wed, May 26, 2021 at 9:09 AM leo john <ljohn16012...@gmail.com> wrote: >> >> Hi Group >> Can you please suggest what this unmodeled blob can be (see appended >> picture)? >> I have Malonate, Boric Acid and Peg in my condition, and crystals were >> soaked in GOL. >> >> I have tried fitting PO4 and SO4 so far. >> >> Thank You >> John >> [image: image.png] >> >> >> >> ------------------------------ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> > > ######################################################################## > > 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/ > > ------------------------------ > > Date: Wed, 26 May 2021 14:44:10 +0000 > From: "Fischmann, Thierry" <thierry.fischm...@merck.com> > Subject: Re: Unmodeled density > > Public > > If the large “blob” sits on a 2-fold crystallographic axis then its occupancy > is ½. > > So one possible interpretation is: > > * A cation present on the 2-fold axis, occupancy 0.5 > * Waters next to the cation position, also with occupancy 0.5, even if > they are not on the 2-fold: the water network / cation alternate in the > lattice. > > Thierry > > On 26 May 2021, at 15:20, leo john > <ljohn16012...@gmail.com<mailto:ljohn16012...@gmail.com>> wrote: > > Hi All: > > Thank You very much for the response and yes it is at symmetry axis. Distance > between the bigger blob and smaller ones is approx 1.45 Ang. > I have tried fitting BO3, BO4, but no luck? > > Thanks > John > > On Wed, May 26, 2021 at 2:14 PM Pearce, N.M. (Nick) > <n.m.pea...@uu.nl<mailto:n.m.pea...@uu.nl>> wrote: > Is it on a symmetry axis? If so it could be the superposition of two > molecules (a molecule and a copy of itself). > > > On 26 May 2021, at 15:08, leo john > <ljohn16012...@gmail.com<mailto:ljohn16012...@gmail.com>> wrote: > > Hi Group > Can you please suggest what this unmodeled blob can be (see appended picture)? > I have Malonate, Boric Acid and Peg in my condition, and crystals were soaked > in GOL. > > I have tried fitting PO4 and SO4 so far. > > Thank You > John > <image.png> > > > ________________________________ > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > ________________________________ > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > ________________________________ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > Notice: This e-mail message, together with any attachments, contains > information of Merck & Co., Inc. (2000 Galloping Hill Road, Kenilworth, > New Jersey, USA 07033), and/or its affiliates Direct contact information > for affiliates is available at > http://www.merck.com/contact/contacts.html) that may be confidential, > proprietary copyrighted and/or legally privileged. It is intended solely > for the use of the individual or entity named on this message. If you are > not the intended recipient, and have received this message in error, > please notify us immediately by reply e-mail and then delete it from > your system. > > > ######################################################################## > > 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/policyandsecu > > ------------------------------ > > Date: Wed, 26 May 2021 16:04:59 +0100 > From: Harry Powell - CCP4BB <hrp-ccp...@virginmedia.com> > Subject: Analysis of NMR ensembles > > Hi > > Given that there are plenty of people on this BB who are structural > biologists rather than “just” crystallographers, I thought someone here might > be able to help. > > If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of > structures that fit the NOEs, is there a tool available that will give me > some idea about the bits of the structure that do not vary much (“rigid”) and > the bits that are all over the place (“flexible”)? > > Would superpose or gesamt be a good tool for this? Ideally I’d like something > that could add a figure to the B columns in a PDB file so I could see > something in QTMG (or PyMol if forced…) or do other useful things with the > information. > > Harry > ######################################################################## > > 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/ > > ------------------------------ > > Date: Wed, 26 May 2021 11:21:47 -0400 > From: Jurgen Bosch <jxb...@case.edu> > Subject: Re: Analysis of NMR ensembles > > How about color by B-factor and look for the cold areas and hot areas? > Jürgen > >> On May 26, 2021, at 11:04 AM, Harry Powell - CCP4BB >> <0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: >> >> Hi >> >> Given that there are plenty of people on this BB who are structural >> biologists rather than “just” crystallographers, I thought someone here >> might be able to help. >> >> If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of >> structures that fit the NOEs, is there a tool available that will give me >> some idea about the bits of the structure that do not vary much (“rigid”) >> and the bits that are all over the place (“flexible”)? >> >> Would superpose or gesamt be a good tool for this? Ideally I’d like >> something that could add a figure to the B columns in a PDB file so I could >> see something in QTMG (or PyMol if forced…) or do other useful things with >> the information. >> >> Harry >> ######################################################################## >> >> 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/ > > ######################################################################## > > 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/ > > ------------------------------ > > Date: Wed, 26 May 2021 15:22:01 +0000 > From: "Rigden, Dan" <drig...@liverpool.ac.uk> > Subject: Fully-funded PhD at the University of Liverpool > > Please pass on this information to any plausible candidates you know. Thanks > > -------------------------------------------------------------------------------------------------------- > > Title: Efficient matching of protein structures to cryo-EM map segments > > Initial deadline: June 30th > > This project will develop creative methods and software to efficiently match > protein structures to cryo-EM map segments. The structures may be complexes, > chains or domains and may derive from experimental or computational studies. > The map segments may be derived with reference to map symmetry, by their > inferred secondary structure composition1 or using signals of supersecondary > motifs that they contain. The resulting software will eventually be > distributed as part of the CCP-EM suite. > > You will be based in Liverpool but will benefit from extensive collaboration > with the CCP-EM consortium. You will join a nurturing and productive group > with a strong track record in software development at the interface between > bioinformatics and structural biology. You will learn transferable skills in > computational science and programming, working in an area of biology relevant > to drug discovery and current health challenges. > > Requirements: You will have at least a good B.Sc. 2:1 in Biological or Life > Sciences, or possibly in a computational subject. An interest in programming, > especially with Python, is a requirement. > > Informal enquiries: drig...@liv.ac.uk. > > To apply: please send a CV and covering letter (plus references if available) > to drig...@liv.ac.uk > > Funding: This studentship is funded jointly by CCP-EM and the University of > Liverpool for 4 years. Funding covers tuition fees at the UK rate only, a > Research Training and Support Grant (RTSG) and stipend at the UKRI rate > (currently around £15,600 per year). Funds for travel and conference > attendance are also included. > > > -------------------------------------------------------------------------------------------------------- > > > Prof Daniel Rigden (He/Him) > Department of Biochemistry and Systems Biology > Institute of Systems, Molecular and Integrative Biology > Room 101, Biosciences Building > University of Liverpool > Crown St., Liverpool, L69 7ZB > > (+44) 151 795 4467 > www.liverpool.ac.uk/integrative-biology/staff/daniel-rigden/ > > > ######################################################################## > > 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/ > > ------------------------------ > > Date: Wed, 26 May 2021 16:28:20 +0100 > From: Harry Powell - CCP4BB <hrp-ccp...@virginmedia.com> > Subject: Re: Analysis of NMR ensembles > > Hi Jurgen > > NMR structures don’t appear to have B_factors, or at least not meaningful > ones (e.g. in 2kv5 they’re all 0.00…). > > thanks for the response, though > > Harry > >> On 26 May 2021, at 16:21, Jurgen Bosch <jxb...@case.edu> wrote: >> >> How about color by B-factor and look for the cold areas and hot areas? >> Jürgen >> >>>> On May 26, 2021, at 11:04 AM, Harry Powell - CCP4BB >>>> <0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: >>> >>> Hi >>> >>> Given that there are plenty of people on this BB who are structural >>> biologists rather than “just” crystallographers, I thought someone here >>> might be able to help. >>> >>> If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of >>> structures that fit the NOEs, is there a tool available that will give me >>> some idea about the bits of the structure that do not vary much (“rigid”) >>> and the bits that are all over the place (“flexible”)? >>> >>> Would superpose or gesamt be a good tool for this? Ideally I’d like >>> something that could add a figure to the B columns in a PDB file so I could >>> see something in QTMG (or PyMol if forced…) or do other useful things with >>> the information. >>> >>> Harry >>> ######################################################################## >>> >>> 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/ >> >> ######################################################################## >> >> 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/ > > ######################################################################## > > 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/ > > ------------------------------ > > Date: Wed, 26 May 2021 15:29:32 +0000 > From: "S. Mohanty" <bionm...@yahoo.com> > Subject: Re: Analysis of NMR ensembles > > Hi Harry, > The superpose/overlay of all the structures in PyMol should inform you the > rigid part of the protein as well as the flexible part. The rigid part would > have very low backbone RMSD or overlay tightly and the flexible part (loops, > N-term and C-term etc.) would not superpose tightly. If you check literature, > the dynamics of the protein may have been studied through NMR relaxation. > Smita > > On Wednesday, May 26, 2021, 10:05:05 AM CDT, Harry Powell - CCP4BB > <0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > > Hi > > Given that there are plenty of people on this BB who are structural > biologists rather than “just” crystallographers, I thought someone here might > be able to help. > > If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of > structures that fit the NOEs, is there a tool available that will give me > some idea about the bits of the structure that do not vary much (“rigid”) and > the bits that are all over the place (“flexible”)? > > Would superpose or gesamt be a good tool for this? Ideally I’d like something > that could add a figure to the B columns in a PDB file so I could see > something in QTMG (or PyMol if forced…) or do other useful things with the > information. > > Harry > ######################################################################## > > 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/ > > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > ------------------------------ > > Date: Wed, 26 May 2021 15:34:27 +0000 > From: Jon Cooper <jon.b.coo...@protonmail.com> > Subject: Re: Analysis of NMR ensembles > > The hard bit is to get the rmsd's into the B-factor column, but it shouldn't > stretch you too much, Harry ;- > > There is ProtSkin on the web which does something similar with sequence > alignments. > > Sent from ProtonMail mobile > > -------- Original Message -------- >> On 26 May 2021, 16:28, Harry Powell - CCP4BB wrote: >> >> Hi Jurgen >> >> NMR structures don’t appear to have B_factors, or at least not meaningful >> ones (e.g. in 2kv5 they’re all 0.00…). >> >> thanks for the response, though >> >> Harry >> >>>> On 26 May 2021, at 16:21, Jurgen Bosch <jxb...@case.edu> wrote: >>> >>> How about color by B-factor and look for the cold areas and hot areas? >>> Jürgen >>> >>>> On May 26, 2021, at 11:04 AM, Harry Powell - CCP4BB >>>> <0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: >>>> >>>> Hi >>>> >>>> Given that there are plenty of people on this BB who are structural >>>> biologists rather than “just” crystallographers, I thought someone here >>>> might be able to help. >>>> >>>> If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of >>>> structures that fit the NOEs, is there a tool available that will give me >>>> some idea about the bits of the structure that do not vary much (“rigid”) >>>> and the bits that are all over the place (“flexible”)? >>>> >>>> Would superpose or gesamt be a good tool for this? Ideally I’d like >>>> something that could add a figure to the B columns in a PDB file so I >>>> could see something in QTMG (or PyMol if forced…) or do other useful >>>> things with the information. >>>> >>>> Harry >>>> ######################################################################## >>>> >>>> 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/ >>> >>> ######################################################################## >>> >>> 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/ >> >> ######################################################################## >> >> 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/ > > ######################################################################## > > 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/policyandsecuri > > ------------------------------ > > Date: Wed, 26 May 2021 11:36:32 -0400 > From: Jurgen Bosch <jxb...@case.edu> > Subject: Re: Analysis of NMR ensembles > > I vaguely recall that using MUSTANG you will get the distance between > residues reflected in the b-value column and then you can color by B-value. > > https://lcb.infotech.monash.edu/mustang/mustang_psfb-final.pdf > <https://lcb.infotech.monash.edu/mustang/mustang_psfb-final.pdf> > > Jürgen > >> On May 26, 2021, at 11:28 AM, Harry Powell - CCP4BB >> <hrp-ccp...@virginmedia.com> wrote: >> >> Hi Jurgen >> >> NMR structures don’t appear to have B_factors, or at least not meaningful >> ones (e.g. in 2kv5 they’re all 0.00…). >> >> thanks for the response, though >> >> Harry >> >>>> On 26 May 2021, at 16:21, Jurgen Bosch <jxb...@case.edu> wrote: >>> >>> How about color by B-factor and look for the cold areas and hot areas? >>> Jürgen >>> >>>> On May 26, 2021, at 11:04 AM, Harry Powell - CCP4BB >>>> <0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: >>>> >>>> Hi >>>> >>>> Given that there are plenty of people on this BB who are structural >>>> biologists rather than “just” crystallographers, I thought someone here >>>> might be able to help. >>>> >>>> If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of >>>> structures that fit the NOEs, is there a tool available that will give me >>>> some idea about the bits of the structure that do not vary much (“rigid”) >>>> and the bits that are all over the place (“flexible”)? >>>> >>>> Would superpose or gesamt be a good tool for this? Ideally I’d like >>>> something that could add a figure to the B columns in a PDB file so I >>>> could see something in QTMG (or PyMol if forced…) or do other useful >>>> things with the information. >>>> >>>> Harry >>>> ######################################################################## >>>> >>>> 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/ >>> >>> ######################################################################## >>> >>> 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/ >> > > > ######################################################################## > > 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/ > > ------------------------------ > > Date: Wed, 26 May 2021 16:28:16 +0100 > From: Andrew Raine <andrew.ra...@mrc-mbu.cam.ac.uk> > Subject: Re: Analysis of NMR ensembles > > Hi Harry, > > (Oooh - after lurking on this list for probably 20 years, I can actually > comment on something...) > >> If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of >> structures that fit the NOEs, is there a tool available that will >> give me some idea about the bits of the structure that do not vary >> much (“rigid”) and the bits that are all over the place >> (“flexible”)? > I used to use a tool called "uwmn", originally written by Mike Hartshorn > when he was in York, and extended a bit by myself. > > This calculated a "mean interatomic distance matrix" over all the > structures in an ensemble, for the atoms selected on the command-line > and then projected it back into 3D (using PCA, or possibly PCoA - I > can't remember which) to make an "unweighted mean" structure. > > It then looped over all the individual structures to calculate a > least-squares fit to the mean structure, and populated the B-factor > field with each atom's deviation from the "mean" coordinate. > > To solve your problem, I would have first run it on the CA's of the > whole chain, and looked at the "B-factors" to see where the variability > was greatest, then iteratively excluded/included bits of backbone until > I thought I had a structurally-legitimate selection for the > not-so-variable regions. Convincing novices to check the ensemble > visually was an important part of this, I recall. > > I'd love to recommend you use Mike's/my code, but I'm not sure whether I > can find a copy, nor whether it will compile on a modern Linux. I'll > try to dig it out... > > Best regards, > > Andrew > > -- > Dr. Andrew Raine, Head of IT, MRC Mitochondrial Biology Unit, > Keith Peters Building, Biomedical Campus, Cambridge, CB2 0XY, UK > phone: +44 (0)1223 252830 web: www.mrc-mbu.cam.ac.uk > email: a...@mrc-mbu.cam.ac.uk > > ######################################################################## > > 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/ > > ------------------------------ > > Date: Wed, 26 May 2021 16:41:44 +0100 > From: Harry Powell - CCP4BB <hrp-ccp...@virginmedia.com> > Subject: Re: Analysis of NMR ensembles > > Hi Smita > > Yes, that’s the kind of analysis I had in mind. > > I have > 700 structures to “look” at so something that would say “these > residues overlay with a small RMSD so this bit is rigid, but these residues > don’t, so that part is flexible” ~700 times. > > Using an MG program of any kind would just be a sanity check that I’d use on > a very few structures (probably no more than ~20-30) to make sure I’m happy > with the results before automating the whole thing. > > Harry > >> On 26 May 2021, at 16:29, S. Mohanty <bionm...@yahoo.com> wrote: >> >> Hi Harry, >> >> The superpose/overlay of all the structures in PyMol should inform you the >> rigid part of the protein as well as the flexible part. The rigid part would >> have very low backbone RMSD or overlay tightly and the flexible part (loops, >> N-term and C-term etc.) would not superpose tightly. If you check >> literature, the dynamics of the protein may have been studied through NMR >> relaxation. >> >> Smita >> >> >> On Wednesday, May 26, 2021, 10:05:05 AM CDT, Harry Powell - CCP4BB >> <0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: >> >> >> Hi >> >> Given that there are plenty of people on this BB who are structural >> biologists rather than “just” crystallographers, I thought someone here >> might be able to help. >> >> If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of >> structures that fit the NOEs, is there a tool available that will give me >> some idea about the bits of the structure that do not vary much (“rigid”) >> and the bits that are all over the place (“flexible”)? >> >> Would superpose or gesamt be a good tool for this? Ideally I’d like >> something that could add a figure to the B columns in a PDB file so I could >> see something in QTMG (or PyMol if forced…) or do other useful things with >> the information. >> >> Harry >> >> ######################################################################## >> >> 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/ >> > > ######################################################################## > > 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/ > > ------------------------------ > > Date: Wed, 26 May 2021 17:45:57 +0200 > From: Cécile Breyton <cecile.brey...@ibs.fr> > Subject: Re: Analysis of NMR ensembles > > Hello, > > In my understanding of NMR, the loops and terminii that adopt very > different conformations in the structure ensemble rather reflect the > fact that for those residues, the number of constraints is lower, thus > the number of structures that fulfil the constraints is larger.... A > dynamics study of the protein will be much more informative. > > Cécile > >> Le 26/05/2021 à 17:29, S. Mohanty a écrit : >> Hi Harry, >> >> The superpose/overlay of all the structures in PyMol should inform you >> the rigid part of the protein as well as the flexible part. The rigid >> part would have very low backbone RMSD or overlay tightly and the >> flexible part (loops, N-term and C-term etc.) would not superpose >> tightly. If you check literature, the dynamics of the protein may have >> been studied through NMR relaxation. >> >> Smita >> >> >> On Wednesday, May 26, 2021, 10:05:05 AM CDT, Harry Powell - CCP4BB >> <0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: >> >> >> Hi >> >> Given that there are plenty of people on this BB who are structural >> biologists rather than “just” crystallographers, I thought someone >> here might be able to help. >> >> If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of >> structures that fit the NOEs, is there a tool available that will give >> me some idea about the bits of the structure that do not vary much >> (“rigid”) and the bits that are all over the place (“flexible”)? >> >> Would superpose or gesamt be a good tool for this? Ideally I’d like >> something that could add a figure to the B columns in a PDB file so I >> could see something in QTMG (or PyMol if forced…) or do other useful >> things with the information. >> >> Harry >> >> ######################################################################## >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> <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/ >> <https://www.jiscmail.ac.uk/policyandsecurity/> >> >> >> ------------------------------------------------------------------------ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> >> > > > ######################################################################## > > 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/ > > ------------------------------ > > Date: Wed, 26 May 2021 16:22:06 +0000 > From: Jon Cooper <jon.b.coo...@protonmail.com> > Subject: Re: Analysis of NMR ensembles > > Hello Harry, > > Looking at: > > http://www.mcgnmr.mcgill.ca/ProtSkin/ > > It says: "If your input is a plain file containing your scalar data to map, > such as heteronuclear NOE or chemical shift differences, ensure the first > column in your file contains residue numbers and the second column contains > the values to map, then click the Browse button to retrieve this file and > select "Plain list of scores" > > If you can get the residue number and rmsd data into columns in a file, it > should map them onto a pdb file for one monomer as pseudo-B-factors. > > HTH, Jon.C. > > Sent from ProtonMail mobile > > -------- Original Message -------- >> On 26 May 2021, 16:51, Harry Powell - CCP4BB wrote: >> >> Yes, Jon, but I was hoping I wasn’t the first person to ever want this… >> >> Harry >> >>>> On 26 May 2021, at 16:34, Jon Cooper >>>> <0000488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote: >>> >>> The hard bit is to get the rmsd's into the B-factor column, but it >>> shouldn't stretch you too much, Harry ;- >>> >>> There is ProtSkin on the web which does something similar with sequence >>> alignments. >>> >>> Sent from ProtonMail mobile >>> >>> >>> >>> -------- Original Message -------- >>>> On 26 May 2021, 16:28, Harry Powell - CCP4BB < >>>> 0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: >>> >>> Hi Jurgen >>> >>> NMR structures don’t appear to have B_factors, or at least not meaningful >>> ones (e.g. in 2kv5 they’re all 0.00…). >>> >>> thanks for the response, though >>> >>> Harry >>> >>>> On 26 May 2021, at 16:21, Jurgen Bosch <jxb...@case.edu> wrote: >>>> >>>> How about color by B-factor and look for the cold areas and hot areas? >>>> Jürgen >>>> >>>>> On May 26, 2021, at 11:04 AM, Harry Powell - CCP4BB >>>>> <0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: >>>>> >>>>> Hi >>>>> >>>>> Given that there are plenty of people on this BB who are structural >>>>> biologists rather than “just” crystallographers, I thought someone here >>>>> might be able to help. >>>>> >>>>> If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of >>>>> structures that fit the NOEs, is there a tool available that will give me >>>>> some idea about the bits of the structure that do not vary much (“rigid”) >>>>> and the bits that are all over the place (“flexible”)? >>>>> >>>>> Would superpose or gesamt be a good tool for this? Ideally I’d like >>>>> something that could add a figure to the B columns in a PDB file so I >>>>> could see something in QTMG (or PyMol if forced…) or do other useful >>>>> things with the information. >>>>> >>>>> Harry >>>>> ######################################################################## >>>>> >>>>> 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/ >>>> >>>> ######################################################################## >>>> >>>> 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/ >>> >>> ######################################################################## >>> >>> 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/ >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>> > > ######################################################################## > > 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/poli > > ------------------------------ > > Date: Wed, 26 May 2021 17:41:18 +0100 > From: Rasmus Fogh <rhf...@globalphasing.com> > Subject: Re: Analysis of NMR ensembles > > Hi, > > It has been a bit since I was in NMR, but I would propose CYRANGE > (http://www.bpc.uni-frankfurt.de/cyrange.html), based on the > recommendation of the PDB NMR Validation Task Force > (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3884077/). > > You can do both superposition and per-residue RMSD and find a way of > exporting the values to a PDB file somehow, in CcpNmr Analysis > (https://www.ccpn.ac.uk/), but that is a full NMR analysis package (even > if it is quite user-friendly ;-) ). > > All the best, > Rasmus > > >> On 26/05/2021 16:04, Harry Powell - CCP4BB wrote: >> Hi >> >> Given that there are plenty of people on this BB who are structural >> biologists rather than “just” crystallographers, I thought someone here >> might be able to help. >> >> If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of >> structures that fit the NOEs, is there a tool available that will give me >> some idea about the bits of the structure that do not vary much (“rigid”) >> and the bits that are all over the place (“flexible”)? >> >> Would superpose or gesamt be a good tool for this? Ideally I’d like >> something that could add a figure to the B columns in a PDB file so I could >> see something in QTMG (or PyMol if forced…) or do other useful things with >> the information. >> >> Harry >> ######################################################################## >> >> 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/ >> > > -- > Rasmus H. Fogh Tel.: +44 (0)1223 353033 > Global Phasing Ltd., Fax.: +44 (0)1223 366889 > Sheraton House, > Castle Park, > Cambridge CB3 0AX > United Kingdom > > ######################################################################## > > 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/ > > ------------------------------ > > Date: Wed, 26 May 2021 17:43:46 +0000 > From: Tristan Croll <ti...@cam.ac.uk> > Subject: Re: Analysis of NMR ensembles > > from chimerax.atomic import Residues, Atoms, selected_residues > from math import sqrt > import numpy > models = selected_residues(session).unique_structures > from chimerax.core.commands import run > > run(session, f'match {"|".join(["#"+m.id_string for m in models[1:]])} to > #{models[0].id_string}') > > for residues in zip(*[m.residues for m in models]): > residues = Residues(residues) > pas = Atoms(residues.principal_atoms) > if not len(pas): > residues.atoms.bfactors = 0 > continue > > coords = pas.scene_coords > avg = numpy.mean(coords, axis=0) > deviations = coords-avg > distances = numpy.linalg.norm(deviations, axis=0) > rms = sqrt(numpy.mean(distances**2)) > residues.atoms.bfactors = rms > > run(session, f'color bfactor sel') > > ######################################################################## > > 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 > > ------------------------------ > > Date: Wed, 26 May 2021 20:02:46 +0200 > From: Bernhard Rupp <hofkristall...@gmail.com> > Subject: Re: Analysis of NMR ensembles > > https://pubmed.ncbi.nlm.nih.gov/8744573/ > > Old but worked... > > Best br > >> On Wed, May 26, 2021, 19:43 Tristan Croll <ti...@cam.ac.uk> wrote: >> >> (sending properly this time, rather than just to Rasmus) >> >> I don't believe a "color by RMS" option is in ChimeraX right now (I'll >> suggest it to the developers), but this will align all models then set >> B-factors for each residue to the RMS CA deviation from the mean position. >> Could be extended fairly trivially to do all-atom RMS if you wanted to. >> Change the extension for the attached text file to .py, open your NMR >> ensemble in ChimeraX, select all the models (typically just "sel #1" should >> do the trick), then use File/Open and choose color_by_rms.py (or just "open >> color_by_rms.py" on the command line if it's in your working directory). As >> long as all models have the same set of residues, it should do the trick. >> Example image for 2kv5 attached. >> >> Have fun! >> >> -- Tristan >> ------------------------------ >> *From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Harry >> Powell - CCP4BB <0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> >> *Sent:* 26 May 2021 16:04 >> *To:* CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> >> *Subject:* [ccp4bb] Analysis of NMR ensembles >> >> Hi >> >> Given that there are plenty of people on this BB who are structural >> biologists rather than “just” crystallographers, I thought someone here >> might be able to help. >> >> If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of >> structures that fit the NOEs, is there a tool available that will give me >> some idea about the bits of the structure that do not vary much (“rigid”) >> and the bits that are all over the place (“flexible”)? >> >> Would superpose or gesamt be a good tool for this? Ideally I’d like >> something that could add a figure to the B columns in a PDB file so I could >> see something in QTMG (or PyMol if forced…) or do other useful things with >> the information. >> >> Harry >> ######################################################################## >> >> 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/ >> >> ------------------------------ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> > > ######################################################################## > > 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/ > > ------------------------------ > > Date: Wed, 26 May 2021 21:15:05 +0200 > From: Michal Jamroz <jam...@chem.uw.edu.pl> > Subject: Re: Analysis of NMR ensembles > > Dnia 2021-05-26, o godz. 16:04:59 > Harry Powell - CCP4BB > <0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> napisał(a): >> is there a tool available that will >> give me some idea about the bits of the structure that do not vary >> much (“rigid”) and the bits that are all over the place (“flexible”)? > > have a look on theseus https://theobald.brandeis.edu/theseus/ - that's > the tool you are looking for. > > if you would like to compare structures to those ensembles, you might > be interested in flexscore https://pubmed.ncbi.nlm.nih.gov/27307633/ > (autopromotionxD). > > have fun! > > ######################################################################## > > 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/ > > ------------------------------ > > Date: Wed, 26 May 2021 12:46:51 -0700 > From: Dale Tronrud <de...@daletronrud.com> > Subject: Re: Analysis of NMR ensembles > > I agree with Dr Breyton. The variability in an NMR ensemble does not > reflect "mobility" but simply "uncertainty" in conformation. The spread > in coordinates in some regions simply reflects the lack of experimental > data which could define a single conformation. There are many reasons > why these data are be absent and high mobility is only one. > > Dale Tronrud > >> On 5/26/2021 8:45 AM, Cécile Breyton wrote: >> Hello, >> >> In my understanding of NMR, the loops and terminii that adopt very >> different conformations in the structure ensemble rather reflect the >> fact that for those residues, the number of constraints is lower, thus >> the number of structures that fulfil the constraints is larger.... A >> dynamics study of the protein will be much more informative. >> >> Cécile >> >>> Le 26/05/2021 à 17:29, S. Mohanty a écrit : >>> Hi Harry, >>> >>> The superpose/overlay of all the structures in PyMol should inform you >>> the rigid part of the protein as well as the flexible part. The rigid >>> part would have very low backbone RMSD or overlay tightly and the >>> flexible part (loops, N-term and C-term etc.) would not superpose >>> tightly. If you check literature, the dynamics of the protein may have >>> been studied through NMR relaxation. >>> >>> Smita >>> >>> >>> On Wednesday, May 26, 2021, 10:05:05 AM CDT, Harry Powell - CCP4BB >>> <0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: >>> >>> >>> Hi >>> >>> Given that there are plenty of people on this BB who are structural >>> biologists rather than “just” crystallographers, I thought someone >>> here might be able to help. >>> >>> If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of >>> structures that fit the NOEs, is there a tool available that will give >>> me some idea about the bits of the structure that do not vary much >>> (“rigid”) and the bits that are all over the place (“flexible”)? >>> >>> Would superpose or gesamt be a good tool for this? Ideally I’d like >>> something that could add a figure to the B columns in a PDB file so I >>> could see something in QTMG (or PyMol if forced…) or do other useful >>> things with the information. >>> >>> Harry >>> >>> ######################################################################## >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>> <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/ >>> <https://www.jiscmail.ac.uk/policyandsecurity/> >>> >>> >>> ------------------------------------------------------------------------ >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> >>> >> >> >> ------------------------------------------------------------------------ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> >> > > ######################################################################## > > 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/ > > ------------------------------ > > Date: Wed, 26 May 2021 20:06:23 +0000 > From: Boaz Shaanan <bshaa...@bgu.ac.il> > Subject: Re: Analysis of NMR ensembles > > Hi Dale and Cecil, > > This is quite a circular argument, isn't it? Deficient NOE's for some regions > (e.g. loops) arise from their flexibility, hence they are not as well > resolved as other (e.g. internal ) regions for which the number of NOE is > large. So they are flexible by all accounts and, not surprisingly, align > usually with high B-factor regions in the corresponding crystal structures. > In cases where such flexible regions are held by crystal contacts the > situations would likely be different. > > Cheers, > > Boaz > > > > > Boaz Shaanan, Ph.D. > Dept. of Life Sciences > Ben-Gurion University of the Negev > Beer-Sheva 84105 > Israel > > E-mail: bshaa...@bgu.ac.il > Phone: 972-8-647-2220 > Fax: 972-8-647-2992 or 972-8-646-1710 > > > > > ________________________________ > From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Dale Tronrud > <de...@daletronrud.com> > Sent: Wednesday, May 26, 2021 10:46 PM > To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> > Subject: Re: [ccp4bb] Analysis of NMR ensembles > > I agree with Dr Breyton. The variability in an NMR ensemble does not > reflect "mobility" but simply "uncertainty" in conformation. The spread > in coordinates in some regions simply reflects the lack of experimental > data which could define a single conformation. There are many reasons > why these data are be absent and high mobility is only one. > > Dale Tronrud > >> On 5/26/2021 8:45 AM, Cécile Breyton wrote: >> Hello, >> >> In my understanding of NMR, the loops and terminii that adopt very >> different conformations in the structure ensemble rather reflect the >> fact that for those residues, the number of constraints is lower, thus >> the number of structures that fulfil the constraints is larger.... A >> dynamics study of the protein will be much more informative. >> >> Cécile >> >>> Le 26/05/2021 à 17:29, S. Mohanty a écrit : >>> Hi Harry, >>> >>> The superpose/overlay of all the structures in PyMol should inform you >>> the rigid part of the protein as well as the flexible part. The rigid >>> part would have very low backbone RMSD or overlay tightly and the >>> flexible part (loops, N-term and C-term etc.) would not superpose >>> tightly. If you check literature, the dynamics of the protein may have >>> been studied through NMR relaxation. >>> >>> Smita >>> >>> >>> On Wednesday, May 26, 2021, 10:05:05 AM CDT, Harry Powell - CCP4BB >>> <0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: >>> >>> >>> Hi >>> >>> Given that there are plenty of people on this BB who are structural >>> biologists rather than “just” crystallographers, I thought someone >>> here might be able to help. >>> >>> If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of >>> structures that fit the NOEs, is there a tool available that will give >>> me some idea about the bits of the structure that do not vary much >>> (“rigid”) and the bits that are all over the place (“flexible”)? >>> >>> Would superpose or gesamt be a good tool for this? Ideally I’d like >>> something that could add a figure to the B columns in a PDB file so I >>> could see something in QTMG (or PyMol if forced…) or do other useful >>> things with the information. >>> >>> Harry >>> >>> ######################################################################## >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>> <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<http://www.jiscmail.ac.uk/CCP4BB>, a >>> mailing list hosted by www.jiscmail.ac.uk<http://www.jiscmail.ac.uk>, terms >>> & conditions are >>> available at https://www.jiscmail.ac.uk/policyandsecurity/ >>> <https://www.jiscmail.ac.uk/policyandsecurity/> >>> >>> >>> ------------------------------------------------------------------------ >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> >>> >> >> >> ------------------------------------------------------------------------ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> >> > > ######################################################################## > > 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<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list > hosted by www.jiscmail.ac.uk<http://www.jiscmail.ac.uk>, terms & conditions > are available at https://www.jiscmail.ac.uk/policyandsecurity/ > > ######################################################################## > > 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 ava > > ------------------------------ > > Date: Wed, 26 May 2021 14:06:06 -0700 > From: Dale Tronrud <de...@daletronrud.com> > Subject: Re: Analysis of NMR ensembles > > Dear Boaz, > > We are likely in agreement. "Deficient NOE's for some regions (e.g. > loops) arise from their flexibility, ..." This makes it sound like you > agree that these deficiencies in other regions may be caused by > properties other than flexibility. > > As an extreme example, the N-terminal region of a protein may have a > broad distribution in the ensemble model either because this region > experiences many conformations in solution, or because this peptide was > cleaved from the protein at some earlier time and its absence was not > recognized by the experimentalist. > > Dale Tronrud > >> On 5/26/2021 1:06 PM, Boaz Shaanan wrote: >> Hi Dale and Cecil, >> >> This is quite a circular argument, isn't it? Deficient NOE's for some >> regions (e.g. loops) arise from their flexibility, hence they are not as >> well resolved as other (e.g. internal ) regions for which the number of >> NOE is large. So they are flexible by all accounts and, not >> surprisingly, align usually with high B-factor regions in the >> corresponding crystal structures. In cases where such flexible regions >> are held by crystal contacts the situations would likely be different. >> >> Cheers, >> >> Boaz >> >> >> /Boaz Shaanan, Ph.D. >> Dept. of Life Sciences >> Ben-Gurion University of the Negev >> Beer-Sheva 84105 >> Israel >> >> E-mail: bshaa...@bgu.ac.il >> Phone: 972-8-647-2220 >> Fax: 972-8-647-2992 or 972-8-646-1710 / >> // >> // >> / >> >> / >> ------------------------------------------------------------------------ >> *From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Dale >> Tronrud <de...@daletronrud.com> >> *Sent:* Wednesday, May 26, 2021 10:46 PM >> *To:* CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> >> *Subject:* Re: [ccp4bb] Analysis of NMR ensembles >> I agree with Dr Breyton. The variability in an NMR ensemble does not >> reflect "mobility" but simply "uncertainty" in conformation. The spread >> in coordinates in some regions simply reflects the lack of experimental >> data which could define a single conformation. There are many reasons >> why these data are be absent and high mobility is only one. >> >> Dale Tronrud >> >>> On 5/26/2021 8:45 AM, Cécile Breyton wrote: >>> Hello, >>> >>> In my understanding of NMR, the loops and terminii that adopt very >>> different conformations in the structure ensemble rather reflect the >>> fact that for those residues, the number of constraints is lower, thus >>> the number of structures that fulfil the constraints is larger.... A >>> dynamics study of the protein will be much more informative. >>> >>> Cécile >>> >>> Le 26/05/2021 à 17:29, S. Mohanty a écrit : >>>> Hi Harry, >>>> >>>> The superpose/overlay of all the structures in PyMol should inform you >>>> the rigid part of the protein as well as the flexible part. The rigid >>>> part would have very low backbone RMSD or overlay tightly and the >>>> flexible part (loops, N-term and C-term etc.) would not superpose >>>> tightly. If you check literature, the dynamics of the protein may have >>>> been studied through NMR relaxation. >>>> >>>> Smita >>>> >>>> >>>> On Wednesday, May 26, 2021, 10:05:05 AM CDT, Harry Powell - CCP4BB >>>> <0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: >>>> >>>> >>>> Hi >>>> >>>> Given that there are plenty of people on this BB who are structural >>>> biologists rather than “just” crystallographers, I thought someone >>>> here might be able to help. >>>> >>>> If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of >>>> structures that fit the NOEs, is there a tool available that will give >>>> me some idea about the bits of the structure that do not vary much >>>> (“rigid”) and the bits that are all over the place (“flexible”)? >>>> >>>> Would superpose or gesamt be a good tool for this? Ideally I’d like >>>> something that could add a figure to the B columns in a PDB file so I >>>> could see something in QTMG (or PyMol if forced…) or do other useful >>>> things with the information. >>>> >>>> Harry >>>> >>>> ######################################################################## >>>> >>>> To unsubscribe from the CCP4BB list, click the following link: >>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> >>>> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> <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 >>>> <http://www.jiscmail.ac.uk/CCP4BB>, a >>>> mailing list hosted by www.jiscmail.ac.uk <http://www.jiscmail.ac.uk>, >>>> terms & conditions are >>>> available at https://www.jiscmail.ac.uk/policyandsecurity/ >> <https://www.jiscmail.ac.uk/policyandsecurity/> >>>> <https://www.jiscmail.ac.uk/policyandsecurity/ >> <https://www.jiscmail.ac.uk/policyandsecurity/>> >>>> >>>> >>>> ------------------------------------------------------------------------ >>>> >>>> To unsubscribe from the CCP4BB list, click the following link: >>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> >>>> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1>> >>>> >>> >>> >>> ------------------------------------------------------------------------ >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> >>> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1>> >>> >> >> ######################################################################## >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> <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 >> <http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by >> www.jiscmail.ac.uk <http://www.jiscmail.ac.uk>, terms & conditions are >> available at https://www.jiscmail.ac.uk/policyandsecurity/ >> <https://www.jiscmail.ac.uk/policyandsecurity/> > > ######################################################################## > > 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/ > > ------------------------------ > > Date: Wed, 26 May 2021 23:38:19 +0200 > From: "Mark J. van Raaij" <mjvanra...@cnb.csic.es> > Subject: Re: Analysis of NMR ensembles > > Dear Dale, > Aren’t NMR spectroscopists, in contrast to us crystallographers, not in the > lucky situation though that they should have noticed the absence of terminal > residues during the assignment phase though? I.e. they would usually have > peaks for the protons of those residues in the 1D, TOCSY, COSY spectra, even > though NOEs may be absent. > I agree with you that other reasons than flexibility could cause absence of > NOE’s, although I think that for well-determined NMR ensembles in almost all > cases it is indeed flexibility / multiple conformations. If not enough > restraints have been input, you might get artificial “flexible” regions, and > obtaining more NOEs, secondary structure restraints, measuring orientational > restraints should shore these up. > (Assuming that in the previous assignent phase all protons peaks could be > properly assigned of course). > Mark > > Mark J van Raaij > Dpto de Estructura de Macromoleculas > Centro Nacional de Biotecnologia - CSIC > calle Darwin 3 > E-28049 Madrid, Spain > Section Editor Acta Crystallographica F > https://journals.iucr.org/f/ > > >> On 26 May 2021, at 23:06, Dale Tronrud <de...@daletronrud.com> wrote: >> >> Dear Boaz, >> >> We are likely in agreement. "Deficient NOE's for some regions (e.g. loops) >> arise from their flexibility, ..." This makes it sound like you agree that >> these deficiencies in other regions may be caused by properties other than >> flexibility. >> >> As an extreme example, the N-terminal region of a protein may have a broad >> distribution in the ensemble model either because this region experiences >> many conformations in solution, or because this peptide was cleaved from the >> protein at some earlier time and its absence was not recognized by the >> experimentalist. >> >> Dale Tronrud >> >>> On 5/26/2021 1:06 PM, Boaz Shaanan wrote: >>> Hi Dale and Cecil, >>> This is quite a circular argument, isn't it? Deficient NOE's for some >>> regions (e.g. loops) arise from their flexibility, hence they are not as >>> well resolved as other (e.g. internal ) regions for which the number of NOE >>> is large. So they are flexible by all accounts and, not surprisingly, align >>> usually with high B-factor regions in the corresponding crystal structures. >>> In cases where such flexible regions are held by crystal contacts the >>> situations would likely be different. >>> Cheers, >>> Boaz >>> /Boaz Shaanan, Ph.D. >>> Dept. of Life Sciences >>> Ben-Gurion University of the Negev >>> Beer-Sheva 84105 >>> Israel >>> E-mail: bshaa...@bgu.ac.il >>> Phone: 972-8-647-2220 >>> Fax: 972-8-647-2992 or 972-8-646-1710 / >>> // >>> // >>> / >>> / >>> ------------------------------------------------------------------------ >>> *From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Dale >>> Tronrud <de...@daletronrud.com> >>> *Sent:* Wednesday, May 26, 2021 10:46 PM >>> *To:* CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> >>> *Subject:* Re: [ccp4bb] Analysis of NMR ensembles >>> I agree with Dr Breyton. The variability in an NMR ensemble does not >>> reflect "mobility" but simply "uncertainty" in conformation. The spread >>> in coordinates in some regions simply reflects the lack of experimental >>> data which could define a single conformation. There are many reasons >>> why these data are be absent and high mobility is only one. >>> Dale Tronrud >>> On 5/26/2021 8:45 AM, Cécile Breyton wrote: >>>> Hello, >>>> In my understanding of NMR, the loops and terminii that adopt very >>>> different conformations in the structure ensemble rather reflect the fact >>>> that for those residues, the number of constraints is lower, thus the >>>> number of structures that fulfil the constraints is larger.... A dynamics >>>> study of the protein will be much more informative. >>>> Cécile >>>> Le 26/05/2021 à 17:29, S. Mohanty a écrit : >>>>> Hi Harry, >>>>> >>>>> The superpose/overlay of all the structures in PyMol should inform you >>>>> the rigid part of the protein as well as the flexible part. The rigid >>>>> part would have very low backbone RMSD or overlay tightly and the >>>>> flexible part (loops, N-term and C-term etc.) would not superpose >>>>> tightly. If you check literature, the dynamics of the protein may have >>>>> been studied through NMR relaxation. >>>>> >>>>> Smita >>>>> >>>>> >>>>> On Wednesday, May 26, 2021, 10:05:05 AM CDT, Harry Powell - CCP4BB >>>>> <0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: >>>>> >>>>> >>>>> Hi >>>>> >>>>> Given that there are plenty of people on this BB who are structural >>>>> biologists rather than “just” crystallographers, I thought someone here >>>>> might be able to help. >>>>> >>>>> If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of >>>>> structures that fit the NOEs, is there a tool available that will give me >>>>> some idea about the bits of the structure that do not vary much (“rigid”) >>>>> and the bits that are all over the place (“flexible”)? >>>>> >>>>> Would superpose or gesamt be a good tool for this? Ideally I’d like >>>>> something that could add a figure to the B columns in a PDB file so I >>>>> could see something in QTMG (or PyMol if forced…) or do other useful >>>>> things with the information. >>>>> >>>>> Harry >>>>> >>>>> ######################################################################## >>>>> >>>>> To unsubscribe from the CCP4BB list, click the following link: >>>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> >>>>> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>> <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 >>>>> <http://www.jiscmail.ac.uk/CCP4BB>, a >>>>> mailing list hosted by www.jiscmail.ac.uk <http://www.jiscmail.ac.uk>, >>>>> terms & conditions are >>>>> available at https://www.jiscmail.ac.uk/policyandsecurity/ >>> <https://www.jiscmail.ac.uk/policyandsecurity/> >>>>> <https://www.jiscmail.ac.uk/policyandsecurity/ >>> <https://www.jiscmail.ac.uk/policyandsecurity/>> >>>>> >>>>> >>>>> ------------------------------------------------------------------------ >>>>> >>>>> To unsubscribe from the CCP4BB list, click the following link: >>>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> >>>>> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1>> >>>>> >>>> ------------------------------------------------------------------------ >>>> To unsubscribe from the CCP4BB list, click the following link: >>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> >>>> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1>> >>> ######################################################################## >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>> <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 >>> <http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by >>> www.jiscmail.ac.uk <http://www.jiscmail.ac.uk>, terms & conditions are >>> available at https://www.jiscmail.ac.uk/policyandsecurity/ >>> <https://www.jiscmail.ac.uk/policyandsecurity/> >> >> ######################################################################## >> >> 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/ > > ######################################################################## > > 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/ > > ------------------------------ > > Date: Wed, 26 May 2021 15:23:46 -0700 > From: Dale Tronrud <de...@daletronrud.com> > Subject: Re: Analysis of NMR ensembles > > You are much more knowledgeable than me about the details of > structure determination via resonance spectroscopy. I was attempting to > come up with a toy example that showed that there are reasons for the > absence of cross-peaks other than flexibility. I accept that the > misinterpretation I proposed would be difficult for a careful > experimenter to make. > > I do get uncomfortable when I'm told that A implies B in a well > executed experiment but I have no way of knowing if the model I'm > looking at was constructed via a "well executed experiment". Am I right > that the PDB still has no validation slider for the quality of the fit > of an NMR model to its data? > > I know, via existence proofs, that there are crystallographic models > in the PDB that fit their data poorly or are simply unjustified by the > experimental results. Does this never happen with NMR? How can I know > that the model I'm looking at in the PDB was created using all the > powerful techniques you describe, and that those techniques were > correctly performed? > > Only with knowledge of those details can I say that the model I'm > looking at is one of your "well-determined NMR ensembles" and I can > trust that the variability in the ensemble reflects the structural > variability. > > Dale Tronrud > >> On 5/26/2021 2:38 PM, Mark J. van Raaij wrote: >> Dear Dale, >> Aren’t NMR spectroscopists, in contrast to us crystallographers, not in the >> lucky situation though that they should have noticed the absence of terminal >> residues during the assignment phase though? I.e. they would usually have >> peaks for the protons of those residues in the 1D, TOCSY, COSY spectra, even >> though NOEs may be absent. >> I agree with you that other reasons than flexibility could cause absence of >> NOE’s, although I think that for well-determined NMR ensembles in almost all >> cases it is indeed flexibility / multiple conformations. If not enough >> restraints have been input, you might get artificial “flexible” regions, and >> obtaining more NOEs, secondary structure restraints, measuring orientational >> restraints should shore these up. >> (Assuming that in the previous assignent phase all protons peaks could be >> properly assigned of course). >> Mark >> >> Mark J van Raaij >> Dpto de Estructura de Macromoleculas >> Centro Nacional de Biotecnologia - CSIC >> calle Darwin 3 >> E-28049 Madrid, Spain >> Section Editor Acta Crystallographica F >> https://journals.iucr.org/f/ >> >> >>>> On 26 May 2021, at 23:06, Dale Tronrud <de...@daletronrud.com> wrote: >>> >>> Dear Boaz, >>> >>> We are likely in agreement. "Deficient NOE's for some regions (e.g. >>> loops) arise from their flexibility, ..." This makes it sound like you >>> agree that these deficiencies in other regions may be caused by properties >>> other than flexibility. >>> >>> As an extreme example, the N-terminal region of a protein may have a >>> broad distribution in the ensemble model either because this region >>> experiences many conformations in solution, or because this peptide was >>> cleaved from the protein at some earlier time and its absence was not >>> recognized by the experimentalist. >>> >>> Dale Tronrud >>> >>> On 5/26/2021 1:06 PM, Boaz Shaanan wrote: >>>> Hi Dale and Cecil, >>>> This is quite a circular argument, isn't it? Deficient NOE's for some >>>> regions (e.g. loops) arise from their flexibility, hence they are not as >>>> well resolved as other (e.g. internal ) regions for which the number of >>>> NOE is large. So they are flexible by all accounts and, not surprisingly, >>>> align usually with high B-factor regions in the corresponding crystal >>>> structures. In cases where such flexible regions are held by crystal >>>> contacts the situations would likely be different. >>>> Cheers, >>>> Boaz >>>> /Boaz Shaanan, Ph.D. >>>> Dept. of Life Sciences >>>> Ben-Gurion University of the Negev >>>> Beer-Sheva 84105 >>>> Israel >>>> E-mail: bshaa...@bgu.ac.il >>>> Phone: 972-8-647-2220 >>>> Fax: 972-8-647-2992 or 972-8-646-1710 / >>>> // >>>> // >>>> / >>>> / >>>> ------------------------------------------------------------------------ >>>> *From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Dale >>>> Tronrud <de...@daletronrud.com> >>>> *Sent:* Wednesday, May 26, 2021 10:46 PM >>>> *To:* CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> >>>> *Subject:* Re: [ccp4bb] Analysis of NMR ensembles >>>> I agree with Dr Breyton. The variability in an NMR ensemble does not >>>> reflect "mobility" but simply "uncertainty" in conformation. The spread >>>> in coordinates in some regions simply reflects the lack of experimental >>>> data which could define a single conformation. There are many reasons >>>> why these data are be absent and high mobility is only one. >>>> Dale Tronrud >>>> On 5/26/2021 8:45 AM, Cécile Breyton wrote: >>>>> Hello, >>>>> In my understanding of NMR, the loops and terminii that adopt very >>>>> different conformations in the structure ensemble rather reflect the fact >>>>> that for those residues, the number of constraints is lower, thus the >>>>> number of structures that fulfil the constraints is larger.... A dynamics >>>>> study of the protein will be much more informative. >>>>> Cécile >>>>> Le 26/05/2021 à 17:29, S. Mohanty a écrit : >>>>>> Hi Harry, >>>>>> >>>>>> The superpose/overlay of all the structures in PyMol should inform you >>>>>> the rigid part of the protein as well as the flexible part. The rigid >>>>>> part would have very low backbone RMSD or overlay tightly and the >>>>>> flexible part (loops, N-term and C-term etc.) would not superpose >>>>>> tightly. If you check literature, the dynamics of the protein may have >>>>>> been studied through NMR relaxation. >>>>>> >>>>>> Smita >>>>>> >>>>>> >>>>>> On Wednesday, May 26, 2021, 10:05:05 AM CDT, Harry Powell - CCP4BB >>>>>> <0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: >>>>>> >>>>>> >>>>>> Hi >>>>>> >>>>>> Given that there are plenty of people on this BB who are structural >>>>>> biologists rather than “just” crystallographers, I thought someone here >>>>>> might be able to help. >>>>>> >>>>>> If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of >>>>>> structures that fit the NOEs, is there a tool available that will give >>>>>> me some idea about the bits of the structure that do not vary much >>>>>> (“rigid”) and the bits that are all over the place (“flexible”)? >>>>>> >>>>>> Would superpose or gesamt be a good tool for this? Ideally I’d like >>>>>> something that could add a figure to the B columns in a PDB file so I >>>>>> could see something in QTMG (or PyMol if forced…) or do other useful >>>>>> things with the information. >>>>>> >>>>>> Harry >>>>>> >>>>>> ######################################################################## >>>>>> >>>>>> To unsubscribe from the CCP4BB list, click the following link: >>>>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>>> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> >>>>>> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>>> <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 >>>>>> <http://www.jiscmail.ac.uk/CCP4BB>, a >>>>>> mailing list hosted by www.jiscmail.ac.uk <http://www.jiscmail.ac.uk>, >>>>>> terms & conditions are >>>>>> available at https://www.jiscmail.ac.uk/policyandsecurity/ >>>> <https://www.jiscmail.ac.uk/policyandsecurity/> >>>>>> <https://www.jiscmail.ac.uk/policyandsecurity/ >>>> <https://www.jiscmail.ac.uk/policyandsecurity/>> >>>>>> >>>>>> >>>>>> ------------------------------------------------------------------------ >>>>>> >>>>>> To unsubscribe from the CCP4BB list, click the following link: >>>>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>>> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> >>>>>> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>>> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1>> >>>>>> >>>>> ------------------------------------------------------------------------ >>>>> To unsubscribe from the CCP4BB list, click the following link: >>>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>>> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> >>>>> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>>> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1>> >>>> ######################################################################## >>>> To unsubscribe from the CCP4BB list, click the following link: >>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>>> <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 >>>> <http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by >>>> www.jiscmail.ac.uk <http://www.jiscmail.ac.uk>, terms & conditions are >>>> available at https://www.jiscmail.ac.uk/policyandsecurity/ >>>> <https://www.jiscmail.ac.uk/policyandsecurity/> >>> >>> ######################################################################## >>> >>> 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/ >> >> ######################################################################## >> >> 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/ >> > > ######################################################################## > > 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/ > > ------------------------------ > > End of CCP4BB Digest - 25 May 2021 to 26 May 2021 (#2021-147) > ************************************************************* ######################################################################## 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/
