Re: [ccp4bb] ?lsqkab?

Charlie - can you point me to an example to test? Eleanor On 16 April 2018 at 23:57, Daniel M. Himmel, Ph. D. wrote: > Have you tried using the CNS script rmsd.inp? You can explicitly list > the atoms to superimpose and set "coord_fit=true;". > > -Daniel > > > On

Re: [ccp4bb] ?lsqkab?

Have you tried using the CNS script rmsd.inp? You can explicitly list the atoms to superimpose and set "coord_fit=true;". -Daniel On Mon, Apr 16, 2018 at 3:30 PM, Carter, Charlie wrote: > I think I’ve asked this question before and I was pointed in a number of >

[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] lsqkab

I noticed the same problem with more recent versions of CCP4 (up to and including 6.5.001) but failed to report it…. It seems that the problem occurs regardless of the atoms chosen for selection - main, side or all - and with both v2 and v3 PDB files. The 'LSQ Superpose’ in Coot can

Re: [ccp4bb] lsqkab

On 04/02/15 17:21, Robert Byrne wrote: The 'LSQ Superpose’ in Coot can superpose nucleic acids, but it is seemingly not possible to define non-contiguous selections. Admittedly there's no clicky-clicky interface, but you can do it and it's described in the manual.

[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

Re: [ccp4bb] lsqkab

Dear Charlie, could it be related to that furanose atoms now have primes (') instead of asterisks (*) in their names? Best, Tim On 02/04/2015 05:30 PM, Carter, Charlie wrote: I'm (still) using ccp4.6.1.1. Scripts that used to superimpose one tRNA on another now all return the error YOU

Re: [ccp4bb] lsqkab problem to be reported to developer

Can you send more details? the log file? the pdb On 30 May 2014 22:54, Carter, Charlie car...@med.unc.edu wrote: 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:

Re: [ccp4bb] lsqkab problem to be reported to developer

Charlie, Most probably this indicates a problem with your PDB file, either a format or things like misplaced or absent residue name etc. If you can send me your files and exact command that you run, I can have a look into this. In future, if you see a message like report to developer please

[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] LSQKAB

On 30/12/13 04:10, Doeke Hekstra wrote: Hi All, I would like to superimpose a query chain (moving frame) from a rather large PDB file (~50 chains) to a target frame specified by a chain in a reference PDB file. echo FIT RESIDUE CA 2 TO 63 CHAIN $CHAIN lsqkab.conf echo MATCH

Re: [ccp4bb] LSQKAB

Hi All, I would like to superimpose a query chain (moving frame) from a rather large PDB file (~50 chains) to a target frame specified by a chain in a reference PDB file. echo FIT RESIDUE CA 2 TO 63 CHAIN $CHAIN lsqkab.conf echo MATCH RESIDUE CA 2 TO 63 CHAIN A lsqkab.conf

[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 ***

[ccp4bb] השב: [ccp4bb] LSQKAB with trajectory files

regards, Boaz הודעה מקורית מאת Carter, Charlie car...@med.unc.edu תאריך: 03/11/2013 20:24 (GMT02:00) אל CCP4BB@JISCMAIL.AC.UK נושא [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

[ccp4bb] LSQKAB error: you have failed to find any atoms to fit

Dear All, I am trying to superpose 2 chains from the same pdb file. I have generated 2 separate pdb files, each with one chain, using PDBSET. When I run LSQKAB with the 2 generated files (on UBUNTU 10.04, ccp4 6.2) it fails to run. The 2 input files CONTAIN the columns for

[ccp4bb] LSQKAB error: you have failed to find any atoms to fit

Dear All, I am trying to superpose 2 chains from the same pdb file. I have generated 2 separate pdb files, each with one chain, using PDBSET. When I run LSQKAB with the 2 generated files (on UBUNTU 10.04, ccp4 6.2) it fails to run. The 2 input files CONTAIN the columns for

[ccp4bb] LSQKAB error: you have failed to find any atoms to fit

Dear All, I am trying to superpose 2 chains from the same pdb file. I have generated 2 separate pdb files, each with one chain, using PDBSET. When I run LSQKAB with the 2 generated files (on UBUNTU 10.04, ccp4 6.2) it fails to run. The 2 input files CONTAIN the columns for

[ccp4bb] LSQKAB error

Dear all, I am trying to compare several related structures using LSQKAB. In order to refine the superpositions, I'd like to use the option radius, to see the relative postion of certain residues within a given distance from a common point. The programme reads the commands OK: ALL

Re: [ccp4bb] LSQKAB error

the side effect of forcing the program to read in the XYZINF input file. Norman From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Anita Lewit-Bentley Sent: 16 March 2009 14:59 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] LSQKAB error Dear all, I am trying to compare several

Re: [ccp4bb] LSQKAB, version 6.0 vs version 6.1

Hi Dave, On Mon, Dec 22, 2008 at 02:58:31PM -0500, Borhani, David wrote: I think the LSQKAB change at Line 291(old)/Line 300(new) DOES introduce new and possibly incorrect logic. Very possible, but ... I haven't looked at all the code, but this one change does seem to substitute a check

Re: [ccp4bb] LSQKAB, version 6.0 vs version 6.1 - reposting (Sorry!)

Dear all, oops - due to some disk/network issues on my side, the final edits of my email got lost. Sorry for reposting this again (corrected): On Mon, Dec 22, 2008 at 02:58:31PM -0500, Borhani, David wrote: I think the LSQKAB change at Line 291(old)/Line 300(new) DOES introduce new and

Re: [ccp4bb] LSQKAB, version 6.0 vs version 6.1 - reposting (Sorry!)

atom name match. -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Clemens Vonrhein Sent: Tuesday, December 23, 2008 9:33 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] LSQKAB, version 6.0 vs version 6.1 - reposting (Sorry!) Dear all

Re: [ccp4bb] LSQKAB, version 6.0 vs version 6.1 - reposting (Sorry!)

Hi David, On Tue, Dec 23, 2008 at 10:31:28AM -0500, Borhani, David wrote: Hi Clemens, Thanks for all your tests; the scripts/keywords you used to run LSQKAB with these test systems would help to clarify what may be going right vs. going wrong. That was just a simple run with lsqkab

[ccp4bb] LSQKAB, version 6.0 vs version 6.1

Dear colleagues, While using LSQKAB I have encountered what it seems a different behavior between version 6.1 and 6.0. If I superpose two structures with LSQKAB version 6.1 (included in CCP4-6.1.0), residues with alternative conformations are not included for the calculations. This is an

Re: [ccp4bb] LSQKAB, version 6.0 vs version 6.1

Hi Tim, Not a stupid question at all. This is how I came to think that version 6.0 uses atoms with alternative conformations: If I do the same superposition (with a pdb file that contains alternative conformations) with LSQKAB version 6.0 and 6.1: 1) Version 6.0 reports 110 atoms to be

Re: [ccp4bb] LSQKAB, version 6.0 vs version 6.1

david.borh...@deshawresearch.com 212-478-0698 http://www.deshawresearch.com -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Kevin Cowtan Sent: Monday, December 22, 2008 11:39 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] LSQKAB, version 6.0 vs

[ccp4bb] lsqkab

Hi everybody, I wonder why in lsqkab, the glycine residues have a rms value for their side chains which are non null (the same calculation done with CNS give about the same results for the rms calculation, but with null value for the rms of glycine side chains). thanks a lot nathalie --