Re: [COOT] map-molecule-chooser-gui

thing... F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

Re: [COOT] Recover Accidentally-Deleted Coordinates

It might be in your coot-backup directory. ( which is located in either in the PWD you used to start coot or COOT_BACKUP_DIR ) Another question: When is an entry in coot-backup triggered? F On Nov 30, 2011, at 11:35 AM, Jacob Keller wrote: Dear Coot List, I just did a bit of work on

Re: [COOT] Coot for OSX 10.6

Hi Phil I have 0.7-pre-1-3633 (in a .deb format). Let me know if this interests you. F On Oct 31, 2011, at 6:11 AM, Phil Evans wrote: As I understand it, Bill Scott now only builds Coot for OSX 10.7: is that right? At least his recent stand-alone builds don't seem to work with 10.6 Is

Re: [COOT] Adding nucleotide to RNA chain fails with ERROR:: nucleotide_to_nucleotide() unassigned type

a C, add a terminal nucleotide, and then mutate it back to a C. - Kevin On 10/24/2011 11:09 AM, Francis E Reyes wrote: This seems to still be a problem for me. Adding a nucleotide to the 5' end it works fine, but adding to the 3' end gives me the following error: ERROR

Re: [COOT] Adding nucleotide to RNA chain fails with ERROR:: nucleotide_to_nucleotide() unassigned type

This seems to still be a problem for me. Adding a nucleotide to the 5' end it works fine, but adding to the 3' end gives me the following error: ERROR:: nucleotide_to_nucleotide() unassigned type mol_base_is_pyrimidine: -1 mol_base_is_purine: -1 std_base_is_pyrimidine: 0 std_base_is_purine:

Re: [COOT] Adding nucleotide to RNA chain fails with ERROR:: nucleotide_to_nucleotide() unassigned type

Oops this occurs with svn 3633. I know this isn't the 'latest' but the 'latest' is having trouble compiling in SL for now... and it doesn't seem (from the svn logs) that much has changed with regard to this issue. F On Oct 24, 2011, at 9:09 AM, Francis E Reyes wrote: This seems to still

[COOT] XML-RPC interface?

Hi cooters Is there an xml-rpc interface for coot? Is it documented (somewhere)? I would love an example of loading maps/pdbs . Thanks! F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

[COOT] Clear on screen labels?

I've made a mess and I've got lots of labels on my coot view (via shift left click on atom). I shift left click on the same atom to remove the label, but how do I remove all the labels at once? Thanks! F - Francis E. Reyes M.Sc. 215 UCB University

[COOT] Incorrect atom labels when building ideal RNA helices.

. F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

Re: [COOT] Incorrect atom labels when building ideal RNA helices.

are inconsistent with the internal monomer library. F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

Re: [COOT] Red Hat Enterprise Linux 6 (RHEL 6) compability issue

. - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

Re: [COOT] Red Hat Enterprise Linux 6 (RHEL 6) compability issue

- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

Re: [COOT] Automatic renaming of RNA residues?

Excellent. Thanks for the toggle. F On Feb 25, 2011, at 10:29 AM, Paul Emsley wrote: On 23/02/11 22:40, Francis E Reyes wrote: Hi all I think I may be losing my mind, but it seems that COOT is renaming my A 's to Ar upon loading the pdb.. Am I losing my mind? F

[COOT] Copy NCS chain issues..

Hi all I can toggle between NCS using the 'o' key, but when I try to Extensions - NCS - Copy NCS Chain and input the chain ID of the chain I want to copy to its NCS mate, I get nothing? F - Francis E. Reyes M.Sc. 215 UCB University of Colorado

[COOT] Just like you can press escape on a real space refine to stop...

- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

[COOT] set resolution when opening .mtz's and calculating maps?

Hi all I'm wondering if there's a way to specify the low/high resolution cut off when opening/calculating a map. Thanks! F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2

[COOT] change names of maps?

Hi All maybe a feature request or maybe it's already implemented. Can we change the names of loaded maps to whatever we want? I tried to do it under display manager but it wouldn't let me. Running Coot 0.6.2-pre (rev 3186). F - Francis E

Re: [COOT] Coot installation on PowerPC...

.0.9.8.dylib Referenced from: /sw/lib/libssh2.1.dylib Reason: image not found /sw/bin/coot: line 6: 55673 Trace/BPT trap /sw/bin/coot- real $@ I think the package you need is openssl098. FR - Francis E. Reyes M.Sc. 215 UCB University

Re: [COOT] I wish I could lose weight like this (OS X 10.6)

Does it influence load times ? (compressing programs at least) Disk space is cheap, and I don't like waiting :) FR On Sep 20, 2009, at 12:10 PM, William G. Scott wrote: Hi Folks: On OS X, 10.6, I have been playing around with hfsCompression. I can decrease the size of /sw/share/coot

[COOT] click on residue get geometry analysis?

Is there a shortcut for this? I'm looking for something similar to the analysis you obtain after a real space refine. Thanks FR - Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2

[COOT] regularize zone fits to density?

Hi all With the regularize zone button, does it fit it to the density and idealizes the residue or just the latter? Thanks FR - Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2

[COOT] Stop real space refine tools with a keystroke?

Is there anyway to do this? Sometimes (err I mean a lot of times) I'm building into a low res map, trying to real space refine or regularize several residues in a stretch and Coot gets stuck (still iterating but not moving the atoms on screen anymore). Can I press escape or something to

[COOT] stereochemical violations in real space refinement?

Hi all, Just tried to submit a PDB and it seems that LEU is not correctly positioned (CG/CD1,CD2). I real space refined this residue, does the real space refinement take into account stereochemical considerations? Thanks FR - Francis Reyes M.Sc.

Re: [COOT] stereochemical violations in real space refinement?

Actually i just checked my structure with the Validate - Incorrect Chiral Volumes. It seems to check out OK, but the PDB doesn't like it? Anyone? thanks FR On Mar 5, 2009, at 4:25 PM, Francis E Reyes wrote: Hi all, Just tried to submit a PDB and it seems that LEU is not correctly

[COOT] NCS Map averaging problems

Hi all This is my first time building with NCS and I wanted to take a look at the NCS averaged maps option in coot. However, I can't seem to get coot to make it. I simply loaded my molecule and then my 2fofc and fofc maps then went to Calculate - NCS Maps, selected my model and then the

[COOT] An annoying coot crash.

All Perhaps this bug / crash has finally pushed my buttons, but my hesitation to report it due to the fact that's it seems sporadic. I can track it down to clicking outside of the main coot window onto an external panel (e.g. mutate residue, any of the refine tools). Coot freezes then