[ccp4bb] trouble running optimize in pymol under Mac OSX

I want to use the optimize command in pymol to refine the configurations of a series of aminoacyl-adenylates complexed with an enzyme active site. My macPro laptob runs OSX Big Sur 11.2.3 and my pymol is the open source build of V. 2.4.0. After some difficulties, I managed to install an

Re: [ccp4bb] new PDB file format

I fell for this momentarily, hence compliments to James. I was fooled by the absolutely sensible intro. Charlie > On Apr 1, 2023, at 12:34 AM, James Holton wrote: > > Anyone who has ever had to lecture a student for writing their unit cell > lengths to dozens of decimal places is going to

[ccp4bb] Alexey Vagin

I never met Alexei Vagin and it has been some time since I’ve done much crystallography. Nonetheless, this news saddens me because of the oversize reputation I knew he had built. His name became legendary even to me quite early on. I appreciate knowing that his personality was as generous as

Re: [ccp4bb] Another folding AI

https://utw10426.utweb.utexas.edu/Topics/Models/Text.html though of course there are many other sources Still all good fun to discuss. Colin From: Carter, Charlie mailto:car...@med.unc.edu>> Sent: 06 November 2022 21:19 To: Nave, Colin (DLSLtd,RAL,LSCI) mailto:colin.n...@diamond.ac.uk&

Re: [ccp4bb] Another folding AI

Colin, A former graduate student of mine alerted me to Box GEP, Hunter WG, Hunter JS. 1978. Statistics for Experimenters. New York: Wiley Interscience in ~1984. I bought a new copy then and have very likely spent more time inside that book than any other over the years since then. So I’m

[ccp4bb] Fwd: [ccp4bb] Another folding AI

Begin forwarded message: From: "charles w carter, jr" mailto:cwcar...@ad.unc.edu>> Subject: Re: [ccp4bb] Another folding AI Date: November 5, 2022 at 12:13:04 PM EDT To: "Nave, Colin (DLSLtd,RAL,LSCI)" mailto:colin.n...@diamond.ac.uk>> As notable a scientist as Maxwell was, he also has been

[ccp4bb] Open Position

We are searching for a post-doctoral associate with expertise in analytical chemistry and chemical biology and interest in a project entitled “Translatomics of Ribosome-Free Coded Peptide Bond Formation”.

Re: [ccp4bb] superimposition of 3D structures with the DNA part only

In my experience, lsqkab wouldn’t orient nucleic acid atoms, and I think Eleanor once told me I needed a different alternative for nucleic acids. If this is no longer true, I’m happy to learn of it. Charlie On Apr 28, 2020, at 6:40 AM, benjamin bax mailto:ben.d.v@gmail.com>> wrote: HI

[ccp4bb] Fwd: [ccp4bb] CCP4BB vs COVID19

Begin forwarded message: From: "charles w carter, jr" mailto:cwcar...@ad.unc.edu>> Subject: Re: [ccp4bb] CCP4BB vs COVID19 Date: March 21, 2020 at 8:07:53 AM EDT To: James Holton mailto:jmhol...@lbl.gov>> Brilliant post, James. Thanks so much! I also find what you describe interesting,

[ccp4bb] Fwd: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2

Begin forwarded message: From: "charles w carter, jr" mailto:cwcar...@ad.unc.edu>> Subject: Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2 Date: July 19, 2019 at 1:32:53 PM EDT To: Patrick Loll mailto:pjl...@gmail.com>> Hi Pat, I, too have fallen into this rabbit hole while Mark

Re: [ccp4bb] 2019 New Year’s resolutions of a cryo-EM newbie

I, for one, was very happy to see Marin’s remark, which pointed something everyone is shoving under the rug. By far the most significant source for information to US citizens is FOX news, which is pay rolled to brainwash as many as they reach. Even public television and NPR have been hammered

[ccp4bb] Fwd: [ccp4bb] VERY old mtz file..

Begin forwarded message: From: "charles w carter, jr" mailto:cwcar...@ad.unc.edu>> Subject: Re: [ccp4bb] VERY old mtz file.. Date: November 14, 2018 at 10:16:23 AM EST To: Eleanor Dodson mailto:eleanor.dod...@york.ac.uk>> I’ve found this thread to be most interesting and out of near

[ccp4bb] Does Saturn furnish an ultra large water crystal?

https://cosmosmagazine.com/space/saturn-s-hexagon-may-tower-to-the-stratosphere Does this arise from a phenomenon related to snowflakes? http://www.iceandclimate.nbi.ku.dk/research/flowofice/ice_crystal_structure/ To

Re: [ccp4bb] unexpected errors in LSQKAB

around.. e On 10 September 2018 at 12:15, Carter, Charlie mailto:car...@med.unc.edu>> wrote: Eleanor, I’ll check into the tRNA TER cards. I have probably experienced difficulties with them before, so that may solve one of the problems, but not, I think, the other. Here are two pdb

[ccp4bb] ?lsqkab?

I think I’ve asked this question before and I was pointed in a number of unsuitable (for various reasons, including lack of access to the programs like ccot) directions. Why can one not use lsqkab to superimpose the nucleic acid portions of protein RNA complexes? I’m asking now because I’ve

Re: [ccp4bb] biological molecule?

the RCSB PDB website and looked up a random structure. You can > still download the biological unit in pdb format from the download files > pulldown > > J > > -Original Message- > From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Carter, Charlie >

[ccp4bb] biological molecule?

I knew this would happen one day. I loathed the cif versions of the coordinates, but fortunately, I’ve never had to use a .cif file. Now, the pdb no longer offers anything but… I cannot find in the .cif file where the instructions are to generate the biological molecule from the asymmetric

[ccp4bb] Stand-alone programs

This is a strange question, even from me. I’ve an undergraduate working on a project that requires superimposing large numbers of pdb files. I would like to have him use lsqkab but he is rather unsophisticated in a computational sense. He is already using various other programs, e.g. Pymol,

[ccp4bb] Thanks!

Bill, I followed Abraham Szöke’s work from a distance, but never met him. I knew he was imaginative, and that he made original contributions to density modification. I was much moved to read your appreciation of him. Many thanks, Charlie

[ccp4bb] Fwd: Please read, and sign

Begin forwarded message: From: Myron Liptzin > Subject: Please read, and sign Date: November 15, 2016 at 12:37:50 PM EST To: Raymond Dooley >, Myron Liptzin >,

Re: [ccp4bb] Two SGs in one droplet?

An arcane, but quite interesting and ultimately functionally relevant discussion of this problem can be found here: L. Kuyper and C. W. Carter, Jr., Resolving Crystal Polymorphisms by finding "Stationary Points" from Quantitative Analysis of Crystal Growth Response Surfaces, Journal of Crystal

[ccp4bb] pdbset

I'm trying to generate an oligomer using pdbset with the script attached below. The rotated molecules appear to be oriented properly, but they cannot be viewed correctly in PYMOL because the cartoon option fails to connect many of the residues. What am I doing wrong? Thanks, Charlie pdbset

[ccp4bb] lsqkab

I'm (still) using ccp4.6.1.1. Scripts that used to superimpose one tRNA on another now all return the error YOU HAVE FAILED TO FIND ANY ATOMS TO FIT I've looked high and low for a reason for this and failed. The pdb files themselves look normal and behave well in PYMOL. They have CRYST1

[ccp4bb] Selenium in AreaImol

I want to have a quantitative estimate for the accessible solvent area for a Selenocysteine residue in a tripeptide, gly-Sec-gly. AreaImol doesn't recognize Selenium, at least in the version I'm using (6.1.1). The online documentation for Areaimol doesn't include the text Selenium. Do newer

[ccp4bb] lsqkab problem to be reported to developer

This is a bizarre problem. I'm trying to superimpose multiple conformations of the same protein using segments I expect not to change. LSQKAB bails with this error each time: *** RWBROOK error: point code unitfunction ***1 -1022MMDB_F_Atom *** file :

Re: [ccp4bb] SOS from last century!

for Raster3D and also for Povray, in case this might be an option for you. That way you can easily include maps in the rendered file. Regards, Tim On 05/06/2014 07:15 PM, Carter, Charlie wrote: I need help with a problem whose dimensions I perceive, but cannot surmount. It appears

[ccp4bb] SOS from last century!

I need help with a problem whose dimensions I perceive, but cannot surmount. It appears to be very important for me to re-make an illustration I made long ago using molscript. For various reasons, I cannot think of a way to do this with Pymol. I want to highlight active site residues by

[ccp4bb] LSQKAB with trajectory files

I've just tried to use LSQKAB to transform an entire trajectory file that is a pdb file with ENDMDL cards between models to a new orientation for the purpose of making use of work with the new orientation. LSQKAB returns with an error: *** RWBROOK error: point code unitfunction ***

Re: [ccp4bb] Who invented PDB format?

While I cannot be sure about the format, the original PDB was the creation of Edgar Meyer, Walter Hamilton, and Helen Berman. Hamilton was at Brookhaven, which held the database until 1994. It passed to the Rutgers consortium in 1998. It is likely that the format, which hasn't changed

[ccp4bb] Mg++ interactions

Begin forwarded message: Date: November 28, 2012 8:18:37 AM EST To: William G. Scott wgsc...@ucsc.edumailto:wgsc...@ucsc.edu Subject: Re: [ccp4bb] Mg++ interactions Bill, I cannot answer your question, except to comment that in many, if not all Class I aminoacyl-tRNA synthetases, Mg++ is

[ccp4bb] Fwd: [ccp4bb] PNAS on fraud

Begin forwarded message: Date: October 19, 2012 4:40:35 AM EDT To: Randy Read rj...@cam.ac.ukmailto:rj...@cam.ac.uk Subject: Re: [ccp4bb] PNAS on fraud This thread has been quite interesting to me. I've had a long interest in scientific fraud, which I've generally held to be victimless. While

Re: [ccp4bb] PNAS on fraud

: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Carter, Charlie Sent: 19 October 2012 13:09 To: ccp4bb Subject: [ccp4bb] Fwd: [ccp4bb] PNAS on fraud Begin forwarded message: Date: October 19, 2012 4:40:35 AM EDT To: Randy Read rj...@cam.ac.ukmailto:rj...@cam.ac.uk Subject: Re

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

A similar remark was made to me by David Blow, while he was on sabbatical at UNC in the 1980s, working with the UNC Computer Science Department and in a moment of intense frustration with the overpowering ignorance of fortran and the enthusiasm for Unix exhibited by that department. Charlie

[ccp4bb] Fwd: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?

Begin forwarded message: Date: June 6, 2012 3:05:16 PM EDT To: aaleshin aales...@burnham.orgmailto:aales...@burnham.org Subject: Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique? There are four such papers in Methods in Enzymology, Vols 368 and 374: David

[ccp4bb] Fwd: [ccp4bb] quasispecies

Begin forwarded message: Date: January 24, 2012 7:16:42 PM EST To: Bart Hazes bha...@ualberta.camailto:bha...@ualberta.ca Subject: Re: [ccp4bb] quasispecies This remark brings to mind a paper published recently by Ariel Fernandez and Mike Lynch: Nature 474:502, 2011: Non-adaptive Origins of