Re: [ccp4bb] About Staraniso

hat is still so deeply ingrained in the collective worldview. With best wishes, Gerard. -- On Fri, Feb 16, 2024 at 09:59:59AM +0100, vincent Chaptal wrote: Hi Clemens and all, I've been following with a lot of interest of course, anisotropy has taken a lot of space in my membrane

Re: [ccp4bb] About Staraniso

https://www.globalphasing.com/autoproc/wiki/index.cgi?RunningAutoProcAtSynchrotrons [26]https://www.globalphasing.com/buster/ [27]https://staraniso.globalphasing.org/table1/ (e.g.https://staraniso.globalphasing.org/table1/ar/8ar7.html) [28]https://pdbj.org/mine/experi

Re: [ccp4bb] PAIREF, Anisotropy and STARANISO

A-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members ofwww.jiscmail.ac.uk/CCP4BB, a mailing list hosted bywww.jiscmail.ac.uk, terms & conditions are available athttps://www.jiscmail.ac.uk/policyandsecurity/ -- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Memb

Re: [ccp4bb] Anisotropy

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Re: [ccp4bb] Strange crystal packing in twined crystal

ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1> -- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnr

Re: [ccp4bb] what would be the best metric to asses the quality of a mtz file?

M. Peligro To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1> -- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membr

Re: [ccp4bb] when does non-isomorphism become a habit?

owing link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/ -- Vincent Chaptal,

Re: [ccp4bb] how to calculate the volume of a small molecule

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Re: [ccp4bb] cavities volume calculations

.2.31.47.01.32 coll...@cyceron.fr http://www.istct.cyceron.fr/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 -- Vincent Chaptal, PhD Director o

Re: [ccp4bb] Ideas for improving refinement with anisotopic data.

4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ -- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE

Re: [ccp4bb] Completeness question

e 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/ -- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 p

Re: [ccp4bb] Completeness question

t, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appic

[ccp4bb] supperpose "to the middle"?

here I can see the 2 lobes moving to the meeting point instead of just one half moving? Something like:  /\  ->  II  (instead of //) Thank you Best Vincent -- Vincent Chaptal, PhD MMSB -UMR5086 Drug Resistance and Membrane Proteins Laboratory 7 passage du Vercors 69007 LYON FRANCE +33

Re: [ccp4bb] Xray-dataset usable despite low completeness ?

is orthorhombic and the dataset was collected over 120° using fine slicing (0.1°). Best regards, Matthias Oebbeke -- Vincent Chaptal, PhD MMSB -UMR5086 Drug Resistance and Membrane Proteins Laboratory 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://mmsb.cnrs.fr/en

Re: [ccp4bb] Unusual dataset with high Rmerge and extremely low b-factors?

connection to country and community. ___ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- Vincent Chaptal, PhD MMSB -UMR5086 Drug Resistance and Membrane Proteins Laboratory 7 passage du Vercors 69

Re: [ccp4bb] challenges in structural biology

. -James Holton MAD Scientist To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- Vincent Chaptal, PhD MMSB -UMR5086 Drug Resistance and Membrane

Re: [ccp4bb] SA_flag vs PDB

SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- Vincent Chaptal, PhD MMSB -UMR5086 Drug Resistance and Membrane Proteins Laboratory 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://

Re: [ccp4bb] Sequence variability mapped on a PDB

) To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- Vincent Chaptal, PhD MMSB -UMR5086 Drug Resistance

Re: [ccp4bb] Thoughtful remark...

=CCP4BB=1 -- Vincent Chaptal, PhD MMSB -UMR5086 Drug Resistance and Membrane Proteins Laboratory 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://mmsb.cnrs.fr/en/ To unsubscribe from the CCP4BB list

Re: [ccp4bb] FW: complex multi-crystal averaging

Andy To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- Vincent Chaptal, PhD MMSB -UMR5086 Drug Resistance and Membrane Proteins Laboratory 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01

Re: [ccp4bb] help needed with a rabbit-head-shaped blob

Dear Deborah, Even though you mention differences between your two chains (it depends how much), I can't help thinking your  blob looks symmetric. Could there be a hidden two fold symmetry? BestVincent  Original message From: Deborah Harrus Date: 11/2/18 22:14 (GMT+01:00)

Re: [ccp4bb] preparing ellipsoidally truncated data for PDB deposition

l.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- Vincent Chaptal, PhD MMSB -UMR5086 Drug Resistan

Re: [ccp4bb] Compound with flexible conformation but nM Kd

rotein. Anything I have miss here that can increase the binding affinity without interacting with the target? Thanks. Kind regards, Wenhe -- Vincent Chaptal, PhD Institut de Biologie et Chimie des Protéines Drug Resistance and Membrane Proteins Laboratory 7 passage du Vercors 6

Re: [ccp4bb] A new capability on the STARANISO server: "PDBpeep"

nise more closely the protocols by which they collect diffraction data, or have such data collected on their behalf. We will be grateful to receive feedback about PDBpeep, just as we have been about the STARANISO server itself. With best wishes, The STARANISO developers. -- Vi

Re: [ccp4bb] looking for a link between diffraction resolution and order within the crystal

ou to make a general statement about what type of structural element is always ordered. I hope this helps. -Daniel Daniel M. Himmel, Ph. D. On Tue, Nov 28, 2017 at 9:44 AM, vincent Chaptal <vincent.chap...@ibcp.fr <mailto:vincent.chap...@ibcp.fr>> wrote: Hi, I've be

[ccp4bb] looking for a link between diffraction resolution and order within the crystal

to be ordered >3A: more and more order. Has this been described somewhere? I would appreciate any comments and reevaluation of this scale. Thank you in advance. All the best Vincent -- Vincent Chaptal, PhD Institut de Biologie et Chimie des Protéines Drug Resistance and Membrane Prote

Re: [ccp4bb] High R/Rfree after MR

the low resolution bin), perhaps some anisotropy is present. I have already refined 2 homologous structures at resolutions going from 3.2 to 3.8 and there were no problems (final R ~ 0.21/0.24). Any advice ? Thanks, GIA -- Vincent Chaptal, PhD Institut de Biologie et Chim

[ccp4bb] Staraniso - determination of anisotropic resolution limits and statistics

help and feedback. All the Best Vincent -- Vincent Chaptal, PhD Institut de Biologie et Chimie des Protéines Drug Resistance and Membrane Proteins Laboratory 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.ibcp.fr

Re: [ccp4bb] help needed to interpret a SRF

would be very interested if anyone can further my knowledge on this. All the best Vincent Eleanor Self Rotation Functions are a) hard to interpret and b) often misleading! On 31 May 2017 at 14:18, vincent Chaptal <vincent.chap...@ibcp.fr <mailto:vincent.chap...@ibcp.fr>> wrote:

[ccp4bb] help needed to interpret a SRF

to the crystal with additive where no peak stands out, which would lean towards a monomer in the ASU? Thank you for your help. Best Vincent -- Vincent Chaptal, PhD Institut de Biologie et Chimie des Protéines Drug Resistance and Membrane Proteins Laboratory 7 passage du Vercors 69007 LYON FRANCE +33

Re: [ccp4bb] off topic: pymol

and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany -- Vincent Chaptal, PhD Institut de Biologie et Chimie des Protéines Drug-resistance modulation and mechanism Laboratory 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 07 http

Re: [ccp4bb] off topic: related to Heavy atom screen

...@gmail.com mailto:email%3agangwar...@gmail.com -- Vincent Chaptal, PhD Institut de Biologie et Chimie des Protéines Drug-resistance modulation and mechanism Laboratory 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.ibcp.fr

Re: [ccp4bb] membrane protein and phase separation

(310)-983-3516 email pe...@mednet.ucla.edu mailto:pe...@mednet.ucla.edu -- Vincent Chaptal, PhD Institut de Biologie et Chimie des Protéines Drug-resistance modulation and mechanism Laboratory 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.ibcp.fr

[ccp4bb] relations between groups and subgroups?

Dear all, I am not sure I understand point groups and relations between groups and subgroups anymore, and would appreciate some guidance. I was under the impression that all point groups were related to an original P1 cell, and that by applying specific lattice symmetries, one could get

[ccp4bb] aimless, anisotropy, and resolution cutoff?

not [2] I can't seem to google up the aimless manual as readily as scala ... also, what consesquence would mosflm anisotropic resolution limits have on scaling (if aimless anisoscaling were true). -Bryan -- Vincent Chaptal, PhD Institut de Biologie et Chimie des Protéines Drug-resistance

[ccp4bb] MR and pseudo-translationnal-symmetry

to increase compleness and going for HA phasing, i was wondering if i could do something with what i have. thank you for your input. vincent -- Vincent Chaptal, PhD Institut de Biologie et Chimie des Protéines Drug-resistance modulation and mechanism Laboratory 7 passage du Vercors 69007 LYON FRANCE

Re: [ccp4bb] metal binds?

I would like to know, is there a way to check that heavy metal has bound to crystals before I take it to synchrotron which is far away? thanks Careina -- Vincent Chaptal, PhD Institut de Biologie et Chimie des Protéines Drug-resistance modulation and mechanism Laboratory 7 passage du

Re: [ccp4bb] Calculating Difference Maps Between an RCSB data set and an mtz (Different Ligand)

them 3) Use FFT to generate the diff map If I remember correctly, I think I am missing a scaling step somewhere. Any thoughts? Scott -- Scott D. Pegan, Ph.D. Assistant Professor Chemistry Biochemistry University of Denver Office: 303 871 2533 Fax: 303 871 2254 -- Vincent Chaptal

Re: [ccp4bb] problem in heavy metal soaking

in this crystallizing condition? Does AmSO4 interfere in heavy-metal soaking ? if yes, what's the reason? Thank you in advance. -- Vincent Chaptal Dept. of Physiology at UCLA http://www.physiology.ucla.edu/Labs/Abramson/index.html http://www.physiology.ucla.edu/Labs/Abramson/index.html/ Phone: 1-310

[ccp4bb] Protein + DNA volume calculation

Hi, I would like to measure the volume of a protein-DNA complex. I'm using VOIDOO but it only gives me the volume of the protein. Does anybody know of a software that allows calculation of DNA volume too? thanks a lot vincent -- Vincent Chaptal Dept. of Physiology at UCLA http

Re: [ccp4bb] Protein + DNA volume calculation (solved)

. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -- Vincent Chaptal Dept. of Physiology at UCLA http://www.physiology.ucla.edu/Labs/Abramson/index.html http://www.physiology.ucla.edu/Labs

Re: [ccp4bb] Buried surface area (BSA) vs. oligomeric interface

this strong interface formation. I am looking for some literature which provide guidelines to understand the relation of BSA or crystal contacts with oligomeric interfaces. Any suggestion is highly appreciated Thanks in advance Yogi -- Vincent Chaptal Dept. of Physiology at UCLA http

[ccp4bb] Postdoctoral position at UCLA on membrane protein structural biology

Posted on behalf of Dr. Jeff Abramson: A postdoctoral position is available in the laboratory of Dr. Jeff Abramson at the Department of Physiology, University of California Los Angeles (UCLA) for a highly motivated individual with a strong interest in structure and function of

Re: [ccp4bb] Difference Map images

Andy, on the practical point of view, you can create such images using Pymol and the command 'carve'. load composite_omit-ccp4.map, map-to-display, format=ccp4 isomesh mesh, map-to-display, 1.5, resi 45, carve=3 color blue, mesh this will display the map at 1.5 sigma, at 3 angstroms around the