... I guess it might be related to the executables of VINA since the local path was empty I tried to put there the full path to vina (which works well from the terminal on my mac) /usr/local/bin/vina and it gaved me 5 docking solutions BINGO!! :-) one question: how I could remove only protein's Hydrogen atoms using Chimera's command line (keeping them on the ligand)??? ср, 5 янв. 2022 г. в 09:30, Enrico Martinez <jmsstarlight@gmail.com>:

Thank you very much, Eric! I actually tried to remove all hydrogens from the protein and ligand and in that case there was an error related to prepare_ligand4.py

then I removed hydrogens only from the protein (keeping them for the ligand) and got new error: Service 'local:' is unavailable. See Reply Log for more details. Wrote test.receptor.pdb into /Users/gleb/Desktop/docking_tuto adding gasteiger charges to peptide 'Deleting non-standard residues: from test.receptor Wrote test.ligand.pdb into /Users/gleb/Desktop/docking_tuto Traceback from web application request: Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/share/WebServices/appWebService.py", line 48, in _initApp self.backend = Backend(service, url) File "/Applications/Chimera.app/Contents/Resources/share/WebServices/opal_local.py", line 59, in __init__ % self.exePath) UserError: "" is not an executable Service 'local:' is unavailable. See Reply Log for more details.

вт, 4 янв. 2022 г. в 19:20, Eric Pettersen <pett@cgl.ucsf.edu>:

...

Hi, Autodock Vina is getting tripped up by hydrogen names it doesn't expect. Try this: delete all hydrogens with the command (Favorites→Command Line) "del H". Then under "Receptor options" in the AutoDock Vina panel change "Add hydrogens in Chimera" to "false".

--Eric

Eric Pettersen UCSF Computer Graphics Lab

...

On Jan 4, 2022, at 7:27 AM, Enrico Martinez via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Dear Chimera Users, First Happy New Year to you and your families!

I am trying to perform protein-ligand docking using UCSF Chimera 1.16v installed on my iMAC Big Sur. Using the pdb of the receptor and mol2 of the ligand (that I have already tested with VINA 1.2.3!) I got the following error: Model 1 (receptor.pdb) appears to be a protein without secondary structure assignments. Automatically computing assignments using 'ksdssp' and parameter values: energy cutoff -0.5 minimum helix length 3 minimum strand length 3 Use command 'help ksdssp' for more information. No SEQRES records for receptor.pdb (#1) chain A; guessing terminii instead Chain-initial residues that are actual N terminii: #1 SER 1.A Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: Chain-final residues that are not actual C terminii: #1 THR 304.A 278 hydrogen bonds Removing spurious proton from 'C' of #1 THR 304.A Hydrogens added Wrote test.receptor.pdb into /Users/gleb/Desktop/docking_tuto adding gasteiger charges to peptide Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/share/vina/ws.py", line 395, in prepareReceptor execfile(scriptPath, d) File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/AutoDockTools/Utilities24/prepare_receptor4.py", line 172, in <module> delete_single_nonstd_residues=delete_single_nonstd_residues) File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/AutoDockTools/MoleculePreparation.py", line 533, in __init__ version=version, delete_single_nonstd_residues=delete_single_nonstd_residues) File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/AutoDockTools/MoleculePreparation.py", line 140, in __init__ self.addCharges(mol, charges_to_add) File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/AutoDockTools/MoleculePreparation.py", line 226, in addCharges chargeCalculator.addCharges(mol.allAtoms) File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/MolKit/chargeCalculator.py", line 80, in addCharges babel.assignHybridization(atoms) File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/PyBabel/atomTypes.py", line 127, in assignHybridization a.babel_atomic_number = self.get_atomic_number(a.babel_type) File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/PyBabel/atomTypes.py", line 103, in get_atomic_number (name,_name) ) ValueError: Could not find atomic number for Hn Hn Receptor preparation for AutoDock Vina failed; please look in Reply Log to see error messages.cannot prepare receptor for AutoDock Vina; please look in Reply Log and/or run Chimera with --debug flag to see errors.

So here are my questions: 1) May this error be related to the version of OSX installed on my imac (I can not run MGL tools on the Big Sur for instance) ??

2) Alternatively may I use the ADT scripts integrated in the Chimera like prepare_receptor4.py for my scripting purposes (outside of the UCSF Chimera) on the same iMAC machine ?

Many thanks in advance! Cheers Enrico _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

Hi, I've been trying out ChimeraX v. 1.3 vs. Chimera v. 1.15 on the same computer and notice that the publication presets for Chimera (Preset publication 1) look to my eye far superior to the preset publication setting for ChimeraX. This is really noticeable when comparing side by side at 400% enlargement. The attached tif file was created from powerpoint at 300 dpi comparing the same set of pdbs superimposed using Matchmaker from similar vantage points (but colored differently) and saved as tiff files or copied using screenshots. To my eye, the screenshot of the Chimera image is better than the ChimeraX tiff and the Chimera tiff is the best of all. The alpha helices in ChimeraX look washed out and the shading is less defined. Is there any way to get comparable images to the Chimera preset publication 1 in ChimeraX? Also, although these images are from the same pdb sources, it seems that the backbone ribbon is much more jagged in ChimeraX. Is there more smoothing in the algorithm for Chimera? Not that it matters that much, but I'd just like to know. Thanks, Ralph Loring Associate Professor of Pharmacology Department of Pharmaceutical Sciences 166 TF Northeastern University 360 Huntington Avenue Boston, MA 02115 USA 617-373-3216 office 617-373-8886 fax r.loring@northeastern.edu On Wed, Jan 5, 2022 at 12:13 PM Elaine Meng via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:

You can remove hydrogens from the protein part only using Chimera (or ChimeraX) command:

delete H & protein

That would not include the water, however. You could also do this to remove water hydrogens:

delete H & solvent

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

...

On Jan 5, 2022, at 12:50 AM, Enrico Martinez via Chimera-users < chimera-users@cgl.ucsf.edu> wrote: [...] one question: how I could remove only protein's Hydrogen atoms using Chimera's command line (keeping them on the ligand)???

_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

Ralph, It looks like the Chimera 'publication 1' preset turns off depth cueing, while the ChimeraX 'publication' preset does not change depth cueing (it looks like it's turned on in these images). Depth cueing could be contributing to the washed-out look of features that are farther from the screen. You can turn it off in ChimeraX with lighting depthCue false It might also have something to do with lighting intensity. I'm not sure how Chimera and ChimeraX differ in that regard. The Chimera models also look more reflective. You can try running material shiny to see if that looks better. https://www.cgl.ucsf.edu/chimerax/docs/user/commands/lighting.html https://www.cgl.ucsf.edu/chimerax/docs/user/commands/material.html Best, Tony ________________________________ From: ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu> on behalf of Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Sent: Wednesday, January 5, 2022 1:17 PM To: Ralph Loring <rhloring@gmail.com> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu>; chimera-users@cgl.ucsf.edu List <chimera-users@cgl.ucsf.edu> Subject: [chimerax-users] pub preset: Chimera vs. ChimeraX silhouettes [EXTERNAL SENDER - PROCEED CAUTIOUSLY] Hi Ralph, It looks like the difference between the pub presets of Chimera and ChimeraX is all in the silhouette edges (black outlines), and that what you want is for them to be thicker and drawn in more places. These are the silhouette linewidth and depthJump parameters, which can be controlled in the ChimeraX "graphics silhouettes" command: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#silhouettes> E.g. to make them fatter in ChimeraX graphics silhouettes width 3 ....and drawn in more places graphics silhouettes depthJump 0.01 As I understand it, the reason the preset can't make these exactly 1-to-1 between the two programs in all situations is that it depends on the graphics windowsize, the size of the image that you save, and depth (Z-range) of the data that is shown, since depth jump is a fraction of that rather than a specific distance. So if you had a smaller protein it would be better about drawing the silhouettes around individual parts of the ribbon. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Jan 5, 2022, at 9:56 AM, Ralph Loring <rhloring@gmail.com> wrote:

Hi, I've been trying out ChimeraX v. 1.3 vs. Chimera v. 1.15 on the same computer and notice that the publication presets for Chimera (Preset publication 1) look to my eye far superior to the preset publication setting for ChimeraX. This is really noticeable when comparing side by side at 400% enlargement. The attached tif file was created from powerpoint at 300 dpi comparing the same set of pdbs superimposed using Matchmaker from similar vantage points (but colored differently) and saved as tiff files or copied using screenshots. To my eye, the screenshot of the Chimera image is better than the ChimeraX tiff and the Chimera tiff is the best of all. The alpha helices in ChimeraX look washed out and the shading is less defined. Is there any way to get comparable images to the Chimera preset publication 1 in ChimeraX? Also, although these images are from the same pdb sources, it seems that the backbone ribbon is much more jagged in ChimeraX. Is there more smoothing in the algorithm for Chimera? Not that it matters that much, but I'd just like to know. Thanks, Ralph Loring Associate Professor of Pharmacology Department of Pharmaceutical Sciences 166 TF Northeastern University 360 Huntington Avenue Boston, MA 02115 USA 617-373-3216 office 617-373-8886 fax r.loring@northeastern.edu

_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users

Hi, I'm updating protein problems for the upcoming semester and translating the instructions from Chimera to ChimeraX. I can't find the Ramachandran plot in ChimeraX. Is there an add-in that I'm missing? I don't see it mentioned in the guide and can't find it in the help section. If it's not there, is there a reason it was dropped? The students find it instructive. Thanks, Ralph Ralph H. Loring Associate Professor of Pharmacology Department of Pharmaceutical Sciences 166 TF Northeastern University 360 Huntington Avenue Boston, MA 02115 USA 617-373-3216 office 617-373-8886 fax r.loring@northeastern.edu On Wed, Jan 5, 2022 at 12:56 PM Ralph Loring <rhloring@gmail.com> wrote:

Hi, I've been trying out ChimeraX v. 1.3 vs. Chimera v. 1.15 on the same computer and notice that the publication presets for Chimera (Preset publication 1) look to my eye far superior to the preset publication setting for ChimeraX. This is really noticeable when comparing side by side at 400% enlargement. The attached tif file was created from powerpoint at 300 dpi comparing the same set of pdbs superimposed using Matchmaker from similar vantage points (but colored differently) and saved as tiff files or copied using screenshots. To my eye, the screenshot of the Chimera image is better than the ChimeraX tiff and the Chimera tiff is the best of all. The alpha helices in ChimeraX look washed out and the shading is less defined. Is there any way to get comparable images to the Chimera preset publication 1 in ChimeraX? Also, although these images are from the same pdb sources, it seems that the backbone ribbon is much more jagged in ChimeraX. Is there more smoothing in the algorithm for Chimera? Not that it matters that much, but I'd just like to know. Thanks, Ralph Loring Associate Professor of Pharmacology Department of Pharmaceutical Sciences 166 TF Northeastern University 360 Huntington Avenue Boston, MA 02115 USA 617-373-3216 office 617-373-8886 fax r.loring@northeastern.edu

On Wed, Jan 5, 2022 at 12:13 PM Elaine Meng via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:

...

You can remove hydrogens from the protein part only using Chimera (or ChimeraX) command:

delete H & protein

That would not include the water, however. You could also do this to remove water hydrogens:

delete H & solvent

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

...

On Jan 5, 2022, at 12:50 AM, Enrico Martinez via Chimera-users < chimera-users@cgl.ucsf.edu> wrote: [...] one question: how I could remove only protein's Hydrogen atoms using Chimera's command line (keeping them on the ligand)???

_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

Hi all, Yep - ISOLDE certainly does have a Ramachandran plot (a rather pretty one, I like to think!). See https://isolde.cimr.cam.ac.uk/static/isolde/doc/tools/gui/validate.html#the-.... Best regards, Tristan ________________________________ From: ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu> on behalf of Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Sent: 12 January 2022 16:50 To: Ralph Loring <rhloring@gmail.com> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu>; chimera-users@cgl.ucsf.edu List <chimera-users@cgl.ucsf.edu> Subject: [chimerax-users] Ramachandran Map in ChimeraX? Hi Ralph, A missing tool (something in Chimera but not ChimeraX) should not be interpreted as intentionally chosen to be dropped... instead we may not have had time yet to add it. It's certainly fine to ask on this mailing list, and good for us to hear which features users are most eager to have in ChimeraX. Since ChimeraX is built using entirely different frameworks than Chimera, tools need to be reimplemented mostly from scratch rather than simply copied and slotted in. We have somewhat limited manpower. Consider that Chimera tools were added over 15-20 years! As for Ramachandran maps specifically, there may be something like that in the ISOLDE plugin. ISOLDE is generally for rather advanced users building atomic structures into cryoEM density, but I can investigate whether it could simply be used to show a Ramachandran map for protein structures and how difficult that might be for somebody at the student level. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Jan 12, 2022, at 5:41 AM, Ralph Loring <rhloring@gmail.com> wrote:

Hi, I'm updating protein problems for the upcoming semester and translating the instructions from Chimera to ChimeraX. I can't find the Ramachandran plot in ChimeraX. Is there an add-in that I'm missing? I don't see it mentioned in the guide and can't find it in the help section. If it's not there, is there a reason it was dropped? The students find it instructive. Thanks, Ralph

Ralph H. Loring Associate Professor of Pharmacology Department of Pharmaceutical Sciences 166 TF Northeastern University 360 Huntington Avenue Boston, MA 02115 USA 617-373-3216 office 617-373-8886 fax r.loring@northeastern.edu

_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users

No problem! For the record, ISOLDE adds another ~200 MB - but the installation is fairly trivial via the ChimeraX ToolShed (Tools/More Tools in the menu). -- Tristan ________________________________ From: Ralph Loring <rhloring@gmail.com> Sent: 12 January 2022 17:17 To: Tristan Croll <tic20@cam.ac.uk> Cc: Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu>; Elaine Meng <meng@cgl.ucsf.edu>; chimera-users@cgl.ucsf.edu List <chimera-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Ramachandran Map in ChimeraX? Thanks Tristan! Unfortunately, the students tell me that the 1 GB size of ChimeraX is about what their laptops can handle, so I'm reluctant to require them to install another program to do a small part of a larger exercise. Hopefully ChimeraX will have a Ramachandran plot at some point in the future, but I'll have other things for the students to do this year. Ralph On Wed, Jan 12, 2022 at 11:55 AM Tristan Croll <tic20@cam.ac.uk<mailto:tic20@cam.ac.uk>> wrote: Hi all, Yep - ISOLDE certainly does have a Ramachandran plot (a rather pretty one, I like to think!). See https://isolde.cimr.cam.ac.uk/static/isolde/doc/tools/gui/validate.html#the-.... Best regards, Tristan ________________________________ From: ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu<mailto:chimerax-users-bounces@cgl.ucsf.edu>> on behalf of Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> Sent: 12 January 2022 16:50 To: Ralph Loring <rhloring@gmail.com<mailto:rhloring@gmail.com>> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>>; chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> List <chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> Subject: [chimerax-users] Ramachandran Map in ChimeraX? Hi Ralph, A missing tool (something in Chimera but not ChimeraX) should not be interpreted as intentionally chosen to be dropped... instead we may not have had time yet to add it. It's certainly fine to ask on this mailing list, and good for us to hear which features users are most eager to have in ChimeraX. Since ChimeraX is built using entirely different frameworks than Chimera, tools need to be reimplemented mostly from scratch rather than simply copied and slotted in. We have somewhat limited manpower. Consider that Chimera tools were added over 15-20 years! As for Ramachandran maps specifically, there may be something like that in the ISOLDE plugin. ISOLDE is generally for rather advanced users building atomic structures into cryoEM density, but I can investigate whether it could simply be used to show a Ramachandran map for protein structures and how difficult that might be for somebody at the student level. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Jan 12, 2022, at 5:41 AM, Ralph Loring <rhloring@gmail.com<mailto:rhloring@gmail.com>> wrote:

Hi, I'm updating protein problems for the upcoming semester and translating the instructions from Chimera to ChimeraX. I can't find the Ramachandran plot in ChimeraX. Is there an add-in that I'm missing? I don't see it mentioned in the guide and can't find it in the help section. If it's not there, is there a reason it was dropped? The students find it instructive. Thanks, Ralph

Ralph H. Loring Associate Professor of Pharmacology Department of Pharmaceutical Sciences 166 TF Northeastern University 360 Huntington Avenue Boston, MA 02115 USA 617-373-3216 office 617-373-8886 fax r.loring@northeastern.edu<mailto:r.loring@northeastern.edu>

_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users