- Chimera-users - RBVI Mailing Lists

Double chain IDs
by Albert WEIXLBAUMER 08 Aug '19

08 Aug '19

Dear Chimera developers, My apologies if this question has been asked before but I was not able to find an answer so far. I am dealing with PDB files that contain too many individual chains and as such need two-character chain IDs. Ideally I do not want to split the PDB-files (to be able and work with single-character chain IDs). In addition, the PDB-file also contains more than 100,000 atoms and thus uses alphanumeric atom numbers. It seems Chimera is not aware of the two-character chain IDs because selecting a certain chain in the GUI shows only single character chain IDs and it leads to the selection of the two distinct chains (e.g. chain AA and chain BA are both treated as chain A). Is there a workaround? I’ve also noticed that saving such a PDB-file in Chimera changes all ATOM records to HETATM - I don’t know if this is related to the double-character chain IDs or alphanumeric atom numbers but this causes problems downstream because it’s very difficult to change this back to ATOM records without also affecting true HETATM entries. Thank you for your help! Best regards, Albert -- Albert Weixlbaumer Centre for Integrative Biology Department of Integrated Structural Biology Institute of Genetics and Molecular and Cellular Biology IGBMC - UMR 7104 - U 1258 1, rue Laurent Fries BP 10142 67404 ILLKIRCH CEDEX FRANCE Phone: +33 3 6948 5103 Email: Albert.Weixlbaumer(a)igbmc.fr<mailto:Albert.Weixlbaumer@igbmc.fr> OpenPGP KeyID: 0x7F644168

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Making PDBs with over 10,000 atoms
by Ryan Harlich 07 Aug '19

07 Aug '19

Hi Chimera, I am trying to make a PDB with over 10,000 atoms. Currently we have this marked as a limitation to our project. I am researching to see if there is a way around this. Our current idea is to make the next 10,000 atoms another chain. Although when I apply this to a sample I get a break point between chain A and chain B. I do want them connected and to be different chains. So: 9,998.A 9,999.A 0.B 1.B connect. In addition, I would need helices and sheets to span over these two chains. So helix or sheet would start at 9,998.A and end at 1.B. Best, Ryan Harlich Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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Superimpose protein chains
by Peter Snyder 07 Aug '19

07 Aug '19

How can I superimpose two (or three) chains from a single structure (ie two homologous subunits that form a multimeric protein)? Thank you Pete

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Is "volume #0 voxelSize 1" a isosurface display changes
by Ryan Harlich 06 Aug '19

06 Aug '19

Hi Chimera, Is "volume #0 voxelSize 1" a isosurface display changes? So if I volume save this would it save this change? Best, Ryan Harlich Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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Morphing, ligands, and secondary structure
by Yan Kung 06 Aug '19

06 Aug '19

Hi Chimera, I’m a new-ish user, and I’ve found that morphing structures is usually very straightforward and easy to use. But I’m now running into an issue with morphing and ligands (and secondary structure). I’d like to make a single morph composed of states A-B-C-B-A (so 4 movements between 5 states). These movements are: (1) A-B: domain opens, (2) B-C: a ligand flies out, (3) C-B: the same ligand flies back in, and (4) B-A: domain closes. First problem: the ligand does not appear in the resulting morph, a problem suggested by the documentation, which I have tried (and failed) to solve using the tips I found in archived posts from this mailing list. Also, because the ligand has to fly in and out, I can’t simply superimpose the ligand from any of the individual states over the morph. So I tried a workaround: make each movement a separate morph. This works for movements 2 and 3 (where the ligand flies out and in). But the ligand still does not appear in movements 1 and 4 (where the ligand remains in place and the domain moves). I’m not sure why the ligand’s appearance would depend on whether it flies in/out, or whether a domain moves… But it seems to. Moreover, a second problem emerges that has to do with secondary structure and is difficult to explain. (Essentially: a few protein regions are on the border between helices and loops such that they appear as helices in some states but as loops in others, and vice versa. If possible, I’d like the secondary structure to remain constant across all states, or else it’s distracting. Even still, I’ve tried to embrace this and use ksdssp to show the helices/loop switching back and forth, but this is distracting as they flicker between helices and loops, each region at its own separate frame. Specifying ksdssp only in certain frames to minimize the flickering doesn’t work either, as different regions switch back and forth at different times.) The only solution I can think of that would maintain the same secondary structure throughout is to just make a single morph of all movements (and not use ksdssp). But this puts me back where I started! Any ideas? (Separately, I realize that I could make a simpler morph of just A-B-C, then record it as “roundtrip”, i.e. forward and backwards, to achieve the same thing as A-B-C-B-A. But this doesn’t solve the problems above.) Thanks very much, Yan -- Yan Kung Assistant Professor Department of Chemistry Bryn Mawr College http://www.brynmawr.edu/people/yan-kung Follow: @KungLab<https://twitter.com/KungLab>

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Nvidia 3D Vision on a large display
by Tom Goddard 02 Aug '19

02 Aug '19

Krish Raman asked what kind of large displays might work with Nvidia 3D Vision stereo glasses with Chimera. Hi Krish, I believe any display capable of a high refresh rate, at least 120 Hz (even 100Hz would do) will be able to show stereo with Nvidia 3D vision. Conventional 60 Hz displays could only show stereo at 30 Hz in each eye (since the display first shows the left eye, then shows the right eye in sequence), and 30 Hz is too slow causing flicker. Video gaming displays are usually advertised as 144 Hz and I believe any of those would work. It is hard to find big displays at 144 Hz, but here is an example, 49 inch ultra wide Samsung CHG90 https://www.amazon.com/Samsung-49-Inch-Curved-Monitor-LC49HG90DMNXZA/dp/B07… <https://www.amazon.com/Samsung-49-Inch-Curved-Monitor-LC49HG90DMNXZA/dp/B07…> If one person is using this sitting at a desk it is very wide and would probably give very nice immersive stereo because of the width. It is not ideal for your use with an audience standing further back because of its extreme 32:0 aspect ratio. You could look for a video gaming TV, such as these https://www.tomsguide.com/us/best-4k-gaming-tv,review-4837.html <https://www.tomsguide.com/us/best-4k-gaming-tv,review-4837.html> Keep in mind your Nvidia 3DVision system may not work with any of these. I would strongly recommend testing at a store with your 3DVision before buying. Stereo is an an extremely obscure niche product and there is no telling if it will work without testing. Another option is to use a high refresh rate projector. That is what we use at my lab -- (ours is a $50,000 Christie, so I don't recommend it). Also I am sure you are aware that Nvidia discontinued support for 3D Vision and it will not work with any Nvidia drivers released after April 2019. So the 3D Vision system is going to be dead soon. Tom

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crash on using Preset Publication 2
by Dieter Blaas 02 Aug '19

02 Aug '19

Hi, I have been using the Publication Preset 2 for making figures of a number of pdb structures without problems. However, I now have a pdb that shows up well in Chimera and does not have any obvious problems. However, when trying rendering it with the Preset Publication 2 (and only with this one) Chimera crashes with the error message below: *** stack smashing detected +++: /home/blaas/.local/UCSF-Chimera64-1.10.2/bin/python2.7 terminated Since I have prepared the other figures with this setting I'd like using it as well for the next figure but how? Thanks a lot, best regards, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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Chimera Viewdock Bug
by Sacco, Michael 02 Aug '19

02 Aug '19

Hello all, I would like to report a bug. When using Chimera in dual monitor mode on windows OS and loading the viewdock module, Chimera becomes unresponsive. However, when the second monitor is unplugged, it functions normally. I have confirmed this on multiple computers. After force closing Chimera a pop-up appears with the message "Chimera exited abnormally; the exit code was: 1.". Thanks everyone! Michael

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OBJ files are exported too small and won't open on other programs.
by Josh Moon 01 Aug '19

01 Aug '19

Hello! I am a relatively new and inexperienced user of Chimera. I am having a difficult time working with obj files. The Scenes I'm exporting as obj's end up having a very small file size (67 bytes in one case) and are being processed very quickly. The resulting file won't open successfully on any program that should understand an obj. Stl's are fine. Conversely, when I try to open an obj file into Chimera, it asks me to manually "Designate the File Type" as though it doesn't know what to do with it. Can someone please suggest what features I'm missing so that I can successfully export an OBJ? I'm also interested in how best to handle color information. Thank you! Josh ----------------------------------------- Josh Moon, Ph.D. (he/him/his) Educational Technology Specialist Kalamazoo College (269) 337-7415

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inquire about molecular docking
by Mohamed Hegazy 31 Jul '19

31 Jul '19

Hey , My name is Mohamed Hegazy, beginner in molecular docking , recently I performed a molecular docking procedure using chimera and I found that the initial structure of the ligand differs from the minimized one , and the binding score for a ligand would change during my different runs. The binding score you obtain from my docking cannot be a constant number. Sent from Mail for Windows 10 Mohamed Said Hegazy --- This email has been checked for viruses by Avast antivirus software. https://www.avast.com/antivirus

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AreaSAS Issue
by Rucco,Dominic J 31 Jul '19

31 Jul '19

Hello, I'll start by saying your software has helped me visualize protein structure for quite some time and overall has been easy to use! I do have a question however: I was recently using the "render by attribute" feature to display areaSAS measurements but have run into an issue. I can no longer select this attribute from the dropdown menu. I noticed this when I attempted to render it on the protein mCherry (PDB 2H5Q). Even when I have gone back to other PDB entries I know have worked for areaSAS rendering, it doesn't appear as an option anymore. The only time I can get it to appear is when I load a session that already has the rendering performed on the protein. Any help would be appreciated, thank you, Dominic Dominic Rucco | Ph.D. Candidate George and Josephine Butler Polymer Research Laboratory Center for Macromolecular Science and Engineering Department of Chemistry University of Florida Leigh Hall 314 | PO Box 117200 | Gainesville, FL 32611-7200 drucco(a)ufl.edu<mailto:drucco@ufl.edu> | www.savin.chem.ufl.edu<http://savin.chem.ufl.edu/>

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--nogui gets permission denied when fetching pdb id
by Ryan Harlich 30 Jul '19

30 Jul '19

Hi Chimera, I am trying to run a script with the –nogui option and run command “open 1a1x” and I get permission denied. It works with the GUI so I am not sure why it is not working with –nogui. Best, Ryan Harlich Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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Minimization with sulfur atom
by sara20＠mail.ustc.edu.cn 30 Jul '19

30 Jul '19

Dear users I have complex structure with ligand having sulfur atom in it. I am trying to minimize it but it fails giving the following error: (LIG) /home/usr/.local/UCSF-Chimera64-1.12/bin/amber16/bin/antechamber: Fatal Error! (LIG) Cannot properly run "/home/usr/.local/UCSF-Chimera64-1.12/bin/amber16/bin/sqm -O -i sqm.in -o sqm.out". I assume it's because of sulfur atom in ligand because I tried running it with out sulfur and it worked fine. I checked MMKT Atom database for sulfur file and it's already there: name = 'sulphur' symbol = 'S' mass = [(31.97207070, 95.02), (32.97145843, 0.75), (33.96786665, 4.21), (35.9670806, 0.02)] color = 'yellow' vdW_radius = 0.18 b_coherent = 2.847*fm b_incoherent = 0.188*fm b_coherent_deut = 2.847*fm b_incoherent_deut = 0.188*fm Any help would be highly appreciated. Thanks Sara

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Applying session parameters to another pdb file.
by David Sáez 29 Jul '19

29 Jul '19

Dear Chimera experts, I have saved a session of Chimera showing the perfect angle and size for the molecules of interest. Now I would like to apply the same parameters to visualize another (but similar, only differnet coordinates) pdb file. Is there a way to do that? Thanks in advance. David

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Editing sequences within Chimera
by Joshua Plank 26 Jul '19

26 Jul '19

Hi, I am wondering if it is possible to edit the amino acid sequence somehow? I have a .pdb file of the protein I'm interested in, but would like to change two of the amino acids to something else. Is this possible? thanks, Josh -- *Joshua Plank* *PhD Student* *Department of Electrical and Computer Engineering* *University of California, Riverside* *email: jplan002(a)ucr.edu <jplan002(a)ucr.edu>* *phone: 505-977-9919*

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Measuring the distance between residues and a surface
by Stanley, Julian A 25 Jul '19

25 Jul '19

Hello! I'm fairly new to Chimera, so if you're able to point me towards any resources that can help me answer questions like this one independently in the future, please do! Here's the question: I would like to measure the distance between the ends arginine and lysine residues and a surface, using Chimera's python modules. Typically, I would load my .pdb file, generate a surface, and then use the "measure distance" command and parse the output from the Reply Log. This approach works fine, except since "measure distance" prints to the reply log, I need to run my script in GUI mode. If possible, I'd prefer to run everything from the command line only. I thought that I might be able to do this with the distance() command, but I can't figure out how to pass a surface to that command. Does anyone have any tips/advice? In summary, what I usually do: ``` from chimera import runCommand as rc # load the file rc("open " + pdbFile) # Generate a surface rc("select protein") rc("split") rc("surface allComponents false") rc("~select") # Measure distance between arg and lys and the surface rc("select #0") rc("~select #0:@") rc("measure distance :arg@cd|:lys@ce selection multiple true show true") ``` And then I parse out the distances from the Reply Log. What I would prefer to do: It would be better to have the output to go to STDOUT when I run the script. I imagine that I'd use something like the `distance()` command, of the premade scripts (like here: http://plato.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scripts/atomdist.py) but they are designed to measure the distance between atoms or residues, not between residues and a surface. Thanks for your help! Sincerely, Julian

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Modeller Restraints
by Danilo Boškovic 24 Jul '19

24 Jul '19

Dear all, how do i add restraints specific to my templates that i use for comparative modelling in chimera? Specifically what are the names assigned to those templates? Do i need the names to specify the template residues that i want to restrain? Are the names same as in the tab when i choose the templates for the run? Thanks, D. B.

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Re: [Chimera-users] Cannot resample to voxel size of 1
by Tom Goddard 22 Jul '19

22 Jul '19

It sounds like you just want to resample a map at a new grid spacing. Chimera does not have such a feature. The vop resample command is intended make the grids of two different maps match each other. Tom > On Jul 22, 2019, at 1:54 PM, Ryan Harlich <ryanharlich(a)hotmail.com> wrote: > > Hi Tom, > > I need the voxel size to be 1, so subdivideSurface and subdivisionLevel options won’t work. Also, vop new won’t work because I need it to have the same bounding box as the input surface. > > Best, > Ryan Harlich > > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10 > > From: Tom Goddard <goddard(a)sonic.net> > Sent: Monday, July 22, 2019 1:49:38 PM > To: Ryan Harlich <ryanharlich(a)hotmail.com> > Cc: chimera-users(a)cgl.ucsf.edu BB <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Cannot resample to voxel size of 1 > > Hi Ryan, > > Resampling only works on the grid of another map as you can see from the documentation so "vop new" allows you to make that map. If you just want to make the mesh of a surface depiction of a map finer then look at the volume command subdivideSurface and subdivisionLevel options. > > https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#dispsurf <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.…> > > Tom > > >> On Jul 22, 2019, at 12:03 PM, Ryan Harlich <ryanharlich(a)hotmail.com <mailto:ryanharlich@hotmail.com>> wrote: >> >> Hi Elaine, >> >> I think you missed the point. I am trying to take an existing surface and resample it to a grid Spacing of 1. I am not sure I see the point of making a new map. >> >> Best, >> Ryan Harlich >> >> Sent from Mail <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgo.micros…> for Windows 10 >> >> From: Elaine Meng <meng(a)cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> >> Sent: Monday, July 22, 2019 11:59:06 AM >> To: Ryan Harlich <ryanharlich(a)hotmail.com <mailto:ryanharlich@hotmail.com>> >> Cc: chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> BB <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> >> Subject: Re: [Chimera-users] Cannot resample to voxel size of 1 >> >> Hi Ryan, >> You can make a new map of whatever grid spacing you want without any atoms using “vop new”: >> <https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.u… <https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.u…>> >> >> I hope this helps, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. >> UCSF Chimera(X) team >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> > On Jul 22, 2019, at 11:33 AM, Ryan Harlich <ryanharlich(a)hotmail.com <mailto:ryanharlich@hotmail.com>> wrote: >> > >> > Hi Chimera Bug Team, >> > >> > I am unable to resample surface to a grid spacing of 1 to be 1 voxel. >> > >> > Currently I do this: >> > 'molmap #2 6 gridSpacing 1\n' >> > 'vop resample #3 onGrid #2.1\n' >> > >> > But this requires me to have a pdb structure. I would like to do this without a pdb structure. >> > >> > Another alternative is I could automatically without GUI interface make a 3 atom pdb structure with python script that is the size of the surface’s boundary box. Although there is no way to get surface’s boundary box x,y,z. >> > >> > Any help would be much appreciated. Option 1 would be a much better approach. >> > >> > Best, >> > Ryan Harlich >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fplato.cgl.…>

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Cannot resample to voxel size of 1
by Ryan Harlich 22 Jul '19

22 Jul '19

Hi Chimera Bug Team, I am unable to resample surface to a grid spacing of 1 to be 1 voxel. Currently I do this: 'molmap #2 6 gridSpacing 1\n' 'vop resample #3 onGrid #2.1\n' But this requires me to have a pdb structure. I would like to do this without a pdb structure. Another alternative is I could automatically without GUI interface make a 3 atom pdb structure with python script that is the size of the surface’s boundary box. Although there is no way to get surface’s boundary box x,y,z. Any help would be much appreciated. Option 1 would be a much better approach. Best, Ryan Harlich Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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same volume data values over the entire volume
by Dieter Blaas 22 Jul '19

22 Jul '19

Hi, Trying to color a volume according to "volume data" I get the same numerical values for all colors and a speckled appearance. When using "volume data gradient norm" I get the expected colors, i.e. strong local changes of the volume data are red and spots where there is essentially no change are in blue. How is this possible? If I understand correctly, "volume data gradient norm" colors according to the first derivative of "volume data" or is this wrong? Do I need something like a normalization? Thanks a lot for explanations, best, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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Fitting the structure into the map after changing origin
by Ahmad Khalifa 22 Jul '19

22 Jul '19

Is there a shortcut way of transforming the model to fit the map after I change, center or reset the origin? Best regards.

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RMSD Chimera
by Ishita Gupta 22 Jul '19

22 Jul '19

Hi, I have a few questions in mind regarding rmsd calculation in chimera: 1. Does the matchmaker tool calculate c alpha? 2. Do we consider RMSD of pruned atoms or the total atoms while reporting? 3. If we use structural comparison match align tool then rmsd is based on multiple sequence alignment? And it also gives C alpha? 4. If we calculate rmsd from multi align viewer by clicking on the structure and then match. What these rmsd values denote? Please elaborate on these points. Thanks Ishita

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Measurement similarity protein structure
by Nail Besli 18 Jul '19

18 Jul '19

Hi I superimposed two proteins in chimera with winch algorithms( blossom62) and p250. The result is the same. Why is the result same for both two proteins, although I tried two different algorithm settings? I am using the chimera's MatchMaker tool. The only thing different is the sequence alignment score. I attached the result file. kind regards

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what laptop configuration should I get for using Chimera and ChimeraX with very large volumes?
by Ilona Nudelman 18 Jul '19

18 Jul '19

Hi, I'm looking for an upgrade to my PC laptop (Windows) and wanted to ask if anyone has any advice on the configuration needed to run Chimera and ChimeraX with very large volumes and lots of heavy pdb's docked in. I am looking for a mobile workstation type laptop but I don't want to spend too much money - maybe 2,500-3,500$. Within these confines what memory, GPU, processor etc. would you recommend? Thanks! Ilona

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how to obtain information regarding complexes
by Quadir, Farhan (MU-Student) 18 Jul '19

18 Jul '19

Hello, I am relatively new to chimera. I am stuck with a problem of how to perform the following from a pdb file which contains multiple chains: 1. I would like to find regions which are 5.0 Angstroms or less between selected chains. 2. After obtaining that I would like to get from (1) a list of the residues and their positions in the chain that are interacting with each other inter-chainwise. Regards, Farhan Quadir PhD Student and Graduate Research Assistant Bioinformatics, Data Mining and Machine Learning (DBM) Lab 304 Engineering Building 1 Electrical Engineering and Computer Science (EECS) Department University of Missouri, Columbia, MO 65201, USA Email: fqg7h(a)mail.missouri.edu Phone (Cell): 573-846-4047

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Finding dimensions of density map
by Ryan Harlich 16 Jul '19

16 Jul '19

Hi Chimera, I want to plot 8 voxels (atoms) in a pdb such that they are the slightly greater than the greatest bounding box of two mrc density maps. In order to do that I need the dimensions of both mrc density maps or there eight greatest corners. How would I go about doing this; that is, getting the 8 corners of the mrc density maps? Is there a command to help this process? Best, Ryan Harlich Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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energy minimization
by sara20＠mail.ustc.edu.cn 16 Jul '19

16 Jul '19

Dear I am trying to minimize a structure with HEME cofactor. I added heme frcmod and prep files from Amber parameter database in parm and prep folders respectively.I minimized the structure at different steps of steepest descent from 100 to 1000.But in all the structures FE of heme is not well aligned with HEME structure (it is pointed out of structure).I tried with both all atom and united atom frcmod and prep files but the results are same.Please find attached the minimized structure. Kindly tell me where am I wrong. Any help would be appreciated. Thank you Regards Sara

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visualizing distance restraints using Chimera
by Matthew Fountain 16 Jul '19

16 Jul '19

Is there any way to import a list of distance restraints and have Chimera display them based on the restraint violation. -- Matthew Fountain Professor and Chair Fredonia State University of New York Chemistry and Biochemistry Department

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Export morph confirmation scene to 3D Studio Max
by Edel Fenix 16 Jul '19

16 Jul '19

Hi, I just discovered Chimera and love the morph confirmation function! Amazing! I would like to export a full morph confirmation scene with surface render from Chimera with all frames in a format that I can import in 3D Studio Max as a complete animation. I can import individual OBJ but not what I am looking for with higher number of frames. I've tried all formats Chimera can natively export as but I can not open any of them in 3D Studio Max. Has anyone done this? Didn't find a relevant prior post when I searched. Is there a way to export formats multiple times to achieve this? Deeply appreciate any help in finding a solution. Best regards, Edel

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command lines to replace "joint models"
by wangdj7＠mail.ustc.edu.cn 15 Jul '19

15 Jul '19

Dear Chimera developers, I'm so sorry to interrupt you. I have to run Chimera in Linux,but there is no command line of "joint modeles".I need to get 2 modified amino acids or peptides together and not creating crashes.In windows,"joint models" is my best choice,it's very convient and perfect.But in Linux,I tried some command line,such as "combine","bond",but it can't automatically repositioning the models and the structure was not right. So,could you please tell me how to use command lines to replace "joint models" function? Thanks in advance Best Regards Daojiong Wang

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Parse error Chimera
by Dorfner, Maja 15 Jul '19

15 Jul '19

To whom it may concern, Using Swissmodel, I have constructed a model based on an original PDB file. NAP is part of this model. The docking works when the option of either "Ignore chains of non-standart residues" or "Ignore all non-standart residues" is chosen as false. The Problem is that in the PDBQT file of the receptor shows that NAP was not considered during the docking, making the Substrate float either within the NAP or to far from it. The docking worked fine with the original PDB file but not with the newly modeled one. Could the problem be that the NAP is a separate chain? I have already tried to erase the H before using AutoDock Vina. Here is the Reply log: Running AutoDock Vina for PmWT.pdb failed; see Reply Log for more information Application stderr ----- Parse error on line 3578 in file "receptor.pdbqt": ATOM syntax incorrect: "Ho" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive. ----- Application stdout ----- ################################################################# # If you used AutoDock Vina in your work, please cite: # # # # O. Trott, A. J. Olson, # # AutoDock Vina: improving the speed and accuracy of docking # # with a new scoring function, efficient optimization and # # multithreading, Journal of Computational Chemistry 31 (2010) # # 455-461 # # # # DOI 10.1002/jcc.21334 # # # # Please see http://vina.scripps.edu for more information. # ################################################################# Detected 4 CPUs Reading input ... ----- Thank you for your patience. Sincerely, Maja Dorfner

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Surface render error in MD movie for morph conformation
by Edel Fenix 15 Jul '19

15 Jul '19

Everything works at the basic level and has produced very useful data and animations. I am most grateful for these tools and your help. The BIG problem I have is that for some frames no surface is rendered at all. Other parts "magically" disappear and reappear during the transformation. *What I would want to do:* 1. There are missing structures/regions in need of repairs in the PDB files I work with (see attached screenshot example). The files are for the same protein but different regions missing in different models and they differ some, ideally they shouldn't. I am using Chimera and Modeller to repair these with loops/refinement. Ideally I would want to match/alter the proteins so the gaps connect correctly and their amino acid structure is the same for all models. I feel like this may be the/one cause for the surface errors when rendering? I've tried using modeller both locally and the web service so I have verified installation, integration and function. Must I generate multiple drafts and manually review and select the one best corresponding or is there a way to get it performed for all models loaded of the same protein? Further, if I want them to have the same genetic makeup, can I somehow use one as reference to alter the others? 2. Align the protein snapshots from the configurational change using matchmaker (works great!). 3. Use morph conformation to generate an animation of the configurational change with surface rendered. Works sort of, with errors for some frames where no surface is rendered at all or regions magically appearing/disappearing. 4. Solve the surface error I get, see attached error message :( If I use split copying from the example page, the model looks nothing like it should look like and more like boiling gruel. I am not experienced with Chimera but I feel like if I ensure the files have no gaps and are structurally identical with the same amino acid makeup it may work as is? *The problems with existing suggested solutions:* The link below present 4 possible solutions linked from the error message. Solution 1 looks nothing like what I want when rendered in my test. Solution 2 does not solve the issue of disappearing structures magically appearing again. I am not sure of the cause but could be because the models have different structure/missing parts. If repaired and matched across all protein models in the animation might work? If so, might not even give an error message? Looks viable but does not solve the problem. Solution 3 is not viable as I am looking to render the surface in details, not "overall" look for large structures. Solution 4 is not applicable as I do not want CPK. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html Any help would be greatly appreciated, Edel [image: Screenshot 2019-07-15 at 12.05.12.png] [image: Screenshot 2019-07-15 at 14.30.00.png] )

2 2

Integer Values instead of Floats in Render by Attribute
by Daniil Prigozhin 11 Jul '19

11 Jul '19

Hello, I am using the latest nightly build and in the Render/Select by attribute window the values in the Value box (defining the color scheme) are reported as integers and accept only integer input, when in fact the Attribute that I defined is a float, and shows up as a float. This does not happen with "native" attributes, only with the newly defined one. Is it a problem with the defattr function not determining/passing the data type correctly? I am pasting the top of the attribute deffinition file below. Many thanks, - Daniil attribute: shannonEntropy match mode: 1-to-1 recipient: residues #0:1.L 0.865 #0:2.L 0.743

3 2

Issue regarding Chimera-Vina
by Prabuddha Bhattacharya 11 Jul '19

11 Jul '19

Dear Sir, I am a beginner in the field of molecular docking. However, I started doing it using Chimera Vina. UCSF Chimera 1.13rc provides the interface while AutoDock Vina does the docking part. For a couple of cases I have found that inspite of keeping all the parameters same, the best obtained dock scores are coming different for each individual job-run. Is it so because it is a stocastic method? With such different dock scores, what should I do? I will be extremely grateful of you can kindly address this issue. Thanking you in advance, Best regards -- *Prabuddha Bhattacharya *

2 1

Structure overlay
by Chakraborty, Joydeep 10 Jul '19

10 Jul '19

Dear all, I am trying to overlay two structures. 1. Wild type enzyme and 2. A mutant, with a single point mutation on the wild type. However, somehow when I am opening the structures, both are overlapping automatically and showing as one structure. I need to have two separate strands overlay, so I can show the change in the active site pocket. I was hoping if anyone could shed some light on this issue. Thanks, Joydeep.

2 1

Volumes comparison
by Dmitry A. Semchonok 09 Jul '19

09 Jul '19

Dear colleagues, How to compare 2 volumes in Chimera by cross-correlation? Thank you. Sincerely, Dmitry

3 5

Associate Scientist/Scientist Position in Protein Engineering
by Andrew Waight 07 Jul '19

07 Jul '19

Dear Chimera Users We are seeking a fresh phD graduate or postdoc with a structural, biophysics or computational background to join our group. This is an excellent opportunity for anyone looking to break into the extremely desirable field of antibody engineering for immuno-oncology. The position entails the design, cloning, purification and in vitro testing of multispecific antibody type molecules. The training involves in silico design (including MD analysis) molecular biology, HEK and CHO expression, Antibody purification and biophysical analysis including SEC, MALS, DLS, RP, Mass Spec, Kinetic analysis (Octet) Binning, Humanization, and *in vitro* validation including FACs analysis, immune cell activation and cancer cell line killing assays. Although experience is not necessary, we expect interview candidates to have researched the above topics thoroughly and to express and explicit interest in the field of protein engineering for immuno-oncology. If interested, please see the link below and feel free to contact me personally with any questions. So sorry to the rest of Chimera-users for the spam. https://www.linkedin.com/jobs/view/1358848339/

1 0

Question regarding RR Distance Maps
by Meysam T. Chorsi 03 Jul '19

03 Jul '19

Hello, I need to use Chimera to determine the distance map, but for some reason the output matrix is not symmetric. I used other software as well, they all giving a symmetric matrix which makes sense to me. Could you please let me know how can I fix this? Thank you Sincerely, Meysam -- *Meysam T. Chorsi* *University of Connecticut * *191 Auditorium Road, Storrs, CT 06269, USA*

2 1

Cylinder coloring extension
by Thomas Marcellino 03 Jul '19

03 Jul '19

Dear Chimera Team, I am aiming to color a stucture according to the B factor and represent it as a cylinder (pipes and planks) is there any possibility to apply different colors within the same cylinder or assign the coloring scheme to the cylinder representation in the same way as doing it with surface ? Looking forward to an answer, Thank you for your time reading my suggestion. Thomas M

2 1

Creating a smooth disk
by Henrique C. S. Junior 02 Jul '19

02 Jul '19

Dear list, I'd like to create a disk that didn't show lines in the surface depending on the orientation angle (see the image attached). Right now I can clearly see that the circle is formed by several triangles, so I'd like to smooth things up. I can actually get rid of the triangles by disabling the silhouette of the plane, but I'd like to keep it to show where the plane ends. Thanks in advance -- *Henrique C. S. Junior*

2 2

Volume save after volume changes
by Ryan Harlich 01 Jul '19

01 Jul '19

Hi Chimera, I am having problems saving changes of volume. Here is my script: 1. open C:\Users\ Desktop\density.map 2. volume #0 level 1.0 3. sel #0 4. volume sel save C:\Users\ Desktop\density2.mrc This does not save the change at line 2. How can I go about to save the change? Best, Ryan Harlich Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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Saving .pdb file in location of .mrc file
by Ryan Harlich 27 Jun '19

27 Jun '19

Hi Chimera, I am having a bit of difficulty figuring out how to move the location of a map and save it in that location. I am able to move it but when I save and reopen it is back to where it is. I see I can use molmap and use onGrid to achieve this but this overwrites gridSpacing 1 which is crucial as I need to set the resolution to 1. So the problem is when I save a molmap with gridSpacing after performing move cofr and reopen it, it is not in the location of my .mrc. If I use onGrid I cannot achieve gridSpacing 1. An alternative if possible would be to have the .ent/.pdb saved to the new location where the .mrc density map is and reopened to this same location because then I can do the rest from there. Best, Ryan Harlich Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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Looking for an image...
by David Cohen 27 Jun '19

27 Jun '19

Hello, Let me preface this by saying that I am not a user of Chimera, I just find the images it creates interesting. My name is Dave and I have a metal band we have named Entropathy. Don't go looking for us on the internet, we aren't anywhere yet, just a bunch of guys in my studio making loud crazy music. The band name is a mashup of Entropy and the suffix "pathy" a condition we have defined as "A degenerative fixation on the ultimate disintegration of all matter". I was surfing the internet looking for some kind of images that would fit as an album cover and came across a few of Chimera's images. I was wondering if you might have some older images sitting around nobody has licensed that might be considered an artistic rendering of molecular entropy. We don't really have any money to spend, but I thought I would reach out and see if you had something that would be of interest to us and would not be an issue to share. Thank you for your time, David Cohen Progammer, Writer, Musician, Dad (not necessarily in that order) djcohen66(a)gmail.com

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Re: [Chimera-users] Sudden Chimera issues with OSX Mojave?
by Geoffrey Sametz 27 Jun '19

27 Jun '19

You may already know this, but: the latest Tk (8.6.9) doesn't play well with tkinter. Python's solution seems to have been to bundle 8.6.8 with new installs. In my own projects I installed 8.6.8 to regain functionality. I posted an answer to a related question on stackoverflow and included links: https://stackoverflow.com/questions/54957374/tkinter-window-opens-as-black-… --Geoff Sametz On Wed, Jun 26, 2019 at 2:41 PM <chimera-users-request(a)cgl.ucsf.edu> wrote: > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 26 Jun 2019 10:58:21 -0700 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > To: Neil Rzechorzek <njr48(a)cam.ac.uk> > Cc: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Sudden Chimera issues with OSX Mojave? > Message-ID: <E66B6410-56F4-46D9-8596-C5AD33EE4C8D(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="utf-8" > > Hi Neil, > I don?t know why your systems would have started having problems > in the last 48 hours. Nonetheless, I suggest you try using the daily build > instead of the production release. The daily build uses a newer version of > the Tk windowing toolkit that Chimera relies on to draw windows, handle > scrolling, etc. and that newer version in particular has some fixes for bad > scrolling behavior. If the daily build fails to remedy the problem, try > using Chimera?s Help?Report a Bug to make a bug report. The bug report > will include many details of your hardware and software setup that will > help us investigate the problem. > > ?Eric > > > Eric Pettersen > UCSF Computer Graphics Lab > > > > -- Dr. Geoffrey Sametz QDH 104 Department of Chemistry and Biochemistry University of Delaware sametz(a)udel.edu (302) 831-3621

3 2

coloring mmCIF files
by Josef Sprinzak 27 Jun '19

27 Jun '19

Dear Chimera Support I am a developer of consurf (http://consurf.tau.ac.il/) for displaying evolutionary conservation of amino/nucleic acid positions in a protein/DNA. Till now we have been working with PDB files and inserting the coloring values in the b-factor (temperature) field in the ATOM part. In the chimera script we use the color commands: color CONS1 @/bfactor=1 color CONS2 @/bfactor=2 color CONS3 @/bfactor=3 ... Now we wish to start using mmCIF files. Where should we insert the coloring values in the mmCIF file, and how do we reference then with the chimera commands ? Best Josef

2 2

Sudden Chimera issues with OSX Mojave?
by Neil Rzechorzek 27 Jun '19

27 Jun '19

Dear Chimera users, Has anyone else started seeing issues with the latest stable version of Chimera on OSX Mojave? We have two new identical systems that were running perfectly as recently as 48 hours ago, but now Chimera is constantly crashing whenever we do something as trivial as File>Open or if we attempt to save a map. To our knowledge there has been no update to Mojave, and we haven't changed our Chimera installation. An example of the error log generated by Chimera when trying to, for example, save a map is: while executing "4642906592_scrollBothNow" ("after" script) File>Open windows do not scroll properly, and will instantly crash the entire program unless we change preferences to 'Open dialog starts in directory from last session = false' Does anyone know of any recent (last ~36 hours...) changes to any supporting software? We're wondering whether there has been some silent security update at Apple that has interefered with, for example, the windowing toolkit? Many thanks, Neil -- Dr. Neil Rzechorzek Senior Research Associate Department of Biochemistry University of Cambridge Sanger Building 80 Tennis Court Road Cambridge, UK CB2 1GA www.bioc.cam.ac.uk Biochemistry Enterprise Champion www.enterprise.cam.ac.uk Advisory Chairman - Entrepreneurial Postdocs Of Cambridge www.epoc.group.cam.ac.uk Email: njr48(a)cam.ac.uk Tel: +44 (0)1223 333652

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time counter
by CLARA BLANES MIRA 26 Jun '19

26 Jun '19

Thank you all!!!. I am going to try all your suggestions, with chimera commands script and with chimera python script (this is still too much for me!!, but I will try with your directions). Thank you all again for your fantastic work and your attention! All the best, clara

1 0

time counter
by CLARA BLANES MIRA 26 Jun '19

26 Jun '19

Dear chimera users, I have two doubts regarding per-frame actions: 1) I am trying to add a counter in my script (commands script, no python script). It works when I do it as a per-frame action in the MD Movie window (just as Elaine does in the’Trajectory and ensemble Analysis Tutorial’) but I am not able to do insert it in my command script: Something like this: movie record 2dlabels create timer text “frame 0" size 40 color white alias ^actions 2dlabels change timer text "frame <FRAME>" perframe actions; coordset #0 1,216000,1000 load false; wait 216; ~perframe movie encode movie.mp4 2) What I really want is to show nanoseconds, not frames. In my case 1000 frames = 1 ns. When I write frame <FRAME>/1000 in MD Movie window, obviously, it does not work. Any suggestion to make it work and insert it in the commands script? Thank you very much!, Clara

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Unsubscribe
by Ina Oestroem 26 Jun '19

26 Jun '19

Hi, I'd like to unsubscribed. Thank you Ina

2 1

installing vintage chimera
by Francesco Pietra 25 Jun '19

25 Jun '19

Hello Although, as a chimera user, i use the latest linux release, I was also interested to install chimera-1.1442-linux.exe francesco@vaio64:~/tmp$ chmod 755 chimera-1.1442-linux.exe francesco@vaio64:~/tmp$ ./chimera-1.1442-linux.exe bash: ./chimera-1.1442-linux.exe: No such file or directory francesco@vaio64:~/tmp$ ls -ls 20420 -rwxr-xr-x 1 francesco francesco 20909040 Jun 25 10:59 chimera-1.1442-linux.exe I also tried chimera-1.1602-linux.exe and chimera-1.5-linux.bin with the same problem. I must confess that I am quite confused about that. In contrast, no problem with the current stable version for linux. Thanks for advice francesco

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full pdb path
by petra wendler 24 Jun '19

24 Jun '19

Dear All, I have a silly question. Having opened a three year old chimera session, I unfortunately have no clue which pdbs on my computer the pdb names in my session refer to (pdbs in session are renamed). Is there a way to somehow open the session in a verbose manner or get the full path of the session pdbs? Cheers, Petra ------------------------------------------------------------ Petra Wendler, Prof. Dr. Dipl. Ing. Universität Potsdam Institut für Biochemie und Biologie Biochemie Karl-Liebknecht-Str. 24-25 D-14476 Potsdam- Golm email: petra.wendler(a)uni-potsdam.de phone: 0049 331 9775130 fax: 0049 331 9775128 ------------------------------------------------------------

2 1

segment and group density together
by Yangqi Gu 21 Jun '19

21 Jun '19

Hi Chinera users, I have a density map of a filament. After I segmented the map, I want to group all the outer globular domain (which is part of a monomer) together. Instead of group them one by one, is there a quicker way to do this? I have the helical symmetry of the filaments. Best, Yangqi -- Yangqi Gu Graduate Student Malvankar Lab Yale University, West Campus

2 1

chimera help in spacing out two structures within the same session
by #LAI KEI ONN# 21 Jun '19

21 Jun '19

Dear Chimera team would appreciate if you have any advice in spacing out two/or more structures within the same chimera session (e.g. the green structure away from the beige ones) so as to clearly visualise the intercrosslinks (red and blue sticks) between two different structures. Currently everything is superimposed with one another and i tried separating all the structures into different sessions and recombining it again but it didnt work. I am using xlinkanalyzer plugin with chimera. Would appreciate your kind advice, [cid:a79ad9c6-047a-493c-abc9-3ac3d537f4df] thank you! Best Regards Kei Onn LAI|黎啟諳 Phd Student Lee Kong Chian School of Medicine

2 1

Chimera - mask after vop
by Ryan Harlich 18 Jun '19

18 Jun '19

Hi Chimera team, Is it possible to mask after vop. I got it to work in Chimera’s command line in the gui but when I run it from my python script it does not work. I am trying to change this working solution to this solution without ground truth: WORKING SOLUTION #chimera_script.write('open ' + paths['input'] + '\n' # 'open ' + paths['ground_truth'] + '\n' # 'molmap #1 6 gridSpacing 1\n' # 'volume #1.1 level 0.1\n' # 'mask #0 #1.1\n' # 'vop resample #2 onGrid #1.1\n' # 'volume #3 save ' + paths['cleaned_map']) NEW SOLUTION chimera_script.write('open ' + paths['input'] + '\n' 'vop gaussian #0 sDev 2\n' 'vop median #1 iterations 5 modelId #2.1\n' 'volume #2.1 level 0.1\n' 'mask #0 #2.1\n' 'vop resample #3 onGrid #2.1\n' 'volume #4 save ' + paths['cleaned_map']) While mask after vop works with GUI command line it gets a NoneType error when doing this: subprocess.run(['/usr/local/bin/chimera', '--nogui', chimera_script.name]). It seems like this might be a bug of chimera? Since it tries to return None to a tuple and crashes. For some reason no triangles in the new surface with vop. Here is a snippet from the depthmask.py where it crashes. [cid:image001.png@01D525AB.830ADC20] Thank you, Ryan Harlich Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

2 1

Chimera local resolution color
by Dmitry Semchonok 14 Jun '19

14 Jun '19

Dear colleagues, I have a cryo-em map after resmap local resolution. I would like to see not just the 2D colored slices but the hole model (not in the movie mode). How to color the model model in chimera based o remap? I would like the final result be similar to https://discuss.cryosparc.com/t/view-coloured-3d-map-in-chimera-using-outpu… <https://discuss.cryosparc.com/t/view-coloured-3d-map-in-chimera-using-outpu…> Thank you. Sincerely, Dmitry

2 1

Stereo glasses
by Jonathan Sheehan 13 Jun '19

13 Jun '19

Hi all, What stereo setup are people recommending these days? It seems that NVIDIA has discontinued the 3D Vision 2 goggles+emitter. Is there something else that is available and works well? Thanks for any advice! -Jonathan

2 2

Script to generate and fit structures
by Ahmad Khalifa 12 Jun '19

12 Jun '19

I want to write a script that can copy combine my structure, translate it up, down, left or right a certain distance, fit it into its new place. Is it feasible, how can I do it? Regards.

2 3

counter ions
by patrizio.arrigo＠ge.ismac.cnr.it 12 Jun '19

12 Jun '19

Dear All I would like to use counter ions of nucleic acids not included in the default list of Chimera. I do not know how to perform this action. The option add ions offers only a limited set of ionic species I guess that is necessary to use amber18. Can you give me some suggestions Dr. Patrizio Arrigo CNR SMAC

2 1

Chimera silent installer options for RHEL 7.6
by Darin Lory 11 Jun '19

11 Jun '19

Chimera Gurus, Are there linux silent install options for the Chimera so I can specify the installation directory, etc. I have chimera working via the regular installation method. My team and I are trying to automate the installation via Ansible playbook. Kindly advise, -Darin "The most exciting phrase to hear in science, the one that heralds new discoveries, is not 'Eureka!' (I found it!) but 'That's funny ...'" -Issac Asimov [image: --] Darin S. Lory [image: https://]about.me/darin.lory <https://about.me/darin.lory?promo=email_sig&utm_source=email_sig&utm_medium…>

2 2

Chimera - can I tweak the red color on the Red-cyan stereo view
by Tweten, Rodney K. (HSC) 11 Jun '19

11 Jun '19

We are displaying our protein structures on a large TV in the Red-Cyan stereo view, which works pretty good for 3D viewing (except the required loss of specific colors). We tend to see a bit of ghosting of the red structure, which I suspect is that the red color lens of the Red-Cyan glasses we have (we’ve tried a few with the same results) is not quite matched to that being used by Chimera in its Red-Cyan stereo view. I was wondering if there is any way the user could tweak the red color being used by chimera in this stereo view to more closely match that of the glasses (assuming that this is responsible for the ghosting of the red structure). Thanks! Rodney Tweten George Lynn Cross Professor "Anti-intellectualism has been a constant thread winding its way through our political and cultural life, nurtured by the false notion that democracy means that my ignorance is just as good as your knowledge.” Isaac Asimov BMSB-1053 940 Stanton L. Young Blvd. The University of Oklahoma Health Sciences Center Oklahoma City OK 73104 USA Work phone: 405 271-1205 FAX: 405 271-3117 Skype: toxlab1

2 1

APBS
by Karl R Voigtritter 11 Jun '19

11 Jun '19

Hello, I am trying to display an APBS surface. I loaded a .pqr file that was generated using the http://nbcr-222.ucsd.edu/pdb2pqr_2.1.1 server. I then ran the APBS tool in the surface/binding analysis tab in Chimera. I left everything to default and clicked OK. It launched the executable and then executed it. The newly generated files came into the Surface Color window correctly. Upon trying to color the surface with the "color" nothing happens. -Karl Voigtritter, Ph.D. California State University, Chico

2 3

Regarding MD simulation
by Divakar S 10 Jun '19

10 Jun '19

Hi, I have been trying to do MD simulation in chimera. However, i could not understand the exact procedure from the user help menu. Plz give us a detailed procedure for simulation and analysis if possible. I also tried to learn the procedures from previously published papers but i couldn't find any articles using MD simulation from chimera. Thank you -- *Dr. Divakar S, M. Pharm (Pharmacology), PhD.,* *Lecturer, **Department of Pharmacology,* *JSS College of Pharmacy,* *(A Constitute College of JSS Academy of Higher Education and Research, Mysuru)* *Ooty, The Nilgris, Tamilnadu.* *Mobile: +91-9944036345* *Email: divakar.s(a)jssuni.edu.in <divakar.s(a)jssuni.edu.in>, diva.niru(a)gmail.com <diva.niru(a)gmail.com>*

3 2

viewing same size atoms within multiple molecules
by Andrew Garven 10 Jun '19

10 Jun '19

Hi, I am trying to implement a script so that each individual atom in each molecule I view on chimera is the same size (ie each carbon atom i view, regardless of the size of the molecule views a the same size). I realize this must be a function of the scale factor which changes the size of the molecules to appropriate viewing size. Is there a way to properly scale each molecule so that they have a standard atom viewing size. I would appreciate any help in this regard. Andrew

2 3

voxel coordinates
by Andrew Garven 07 Jun '19

07 Jun '19

Hi I am trying to get a voxel encodings (coordinates) of molecules that are run through Chimera, as a deep learning model will have an easier time with such data. I am unsure how to retrieve such data from chimera. Any help would be greatly appreciated Andrew

2 1

Re: [Chimera-users] THANKS! Chimera question
by Mike de la Flor 06 Jun '19

06 Jun '19

Hello, Thank you to all of you for getting back to me so fast. Thanks for the help. I am looking forward to ChimeraX Best, Mike de la Flor, CMI Board Certified Medical Illustrator PhD Candidate Biology and Biochemistry Natural Sciences and Mathematics University of Houston From: Greg Couch [mailto:gregc@cgl.ucsf.edu] Sent: Thursday, June 06, 2019 1:28 AM To: Mike de la Flor; UCSF Chimera users mailing list Subject: Re: [Chimera-users] Chimera question 1f16 is a NMR structure and as such has 20 different variations of the structure. Using the command line, you can hide all except for the first structure with the command: ~modeldisplay #0.2-20. To do that graphically, bring up the Model Panel, then click on the group/ungroup button to show controls for the individual structures. Then select the structures you don't want (click, drag, control-click, and shift-click as appropriate), and click on the hide button to leave the one you want. HTH, Greg On 6/5/2019 8:44 PM, Mike de la Flor wrote: Hello Mr. Pettersen, I apologize for bothering you but I had a Chimera question that is best explained by the screenshot attached. For some reason Chimera is importing multiple copies of 1f16.pdb. PyMol does not do this, but I prefer to use Chimera. Do you have any suggestions as to how to fix this? Thank you in advance. Mike de la Flor, CMI Board Certified Medical Illustrator PhD Candidate Biology and Biochemistry Natural Sciences and Mathematics University of Houston _______________________________________________ Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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Chimera question
by Mike de la Flor 05 Jun '19

05 Jun '19

Hello Mr. Pettersen, I apologize for bothering you but I had a Chimera question that is best explained by the screenshot attached. For some reason Chimera is importing multiple copies of 1f16.pdb. PyMol does not do this, but I prefer to use Chimera. Do you have any suggestions as to how to fix this? Thank you in advance. Mike de la Flor, CMI Board Certified Medical Illustrator PhD Candidate Biology and Biochemistry Natural Sciences and Mathematics University of Houston

3 2

split map based on resolution or surface color
by Shu-Hao Liou 03 Jun '19

03 Jun '19

Hi Chimera User, Is that possible to split a density map base on its resolution? That means I have a surface color file contained all local resolution distribution through a density map. Best, Shu-hao

2 1

animation commands in a morph movie
by Natesh Singh 31 May '19

31 May '19

Dear Chimera development team, I am trying to add a simple animation into the morphed trajectory that was developed using two unique conformations (protein and proten-ligand complex). I want the ligand to fly into the binding site (of course ligand is not considered in the morph since it was not a part of a chain), but I guess this could be done. contents of my model panel. ID 0 ligand surface ID 0 conformation A (protein-ligand complex) ID 1 conformation B (protein) ID 2 Morph (400 frames) I am adding the following commands into the perframe box of md movie: # Save bound view. savepos p1 # Move ligand away and save unbound view. move y -10 model #0 ; turn z -30 model #0 center #0 scale 0.2 savepos p2 #fly ligand into the binding site reset p1 100 wait But it's not working the way I want. I just want the ligand to fly slowly into its original position may be within 25-50 frames. Could we execute the commands at a specific frame number? Kindly let me know what would be the correct commands to achieve this effect. Many thanks for your help. Sincerely, Natesh University of Lille

2 1

I forgot where I saved my Chimera session
by Ahmad Khalifa 31 May '19

31 May '19

Is there anyway I can know from logs, history etc where I had saved my session? Regards.

2 1

Select by attribute value in a .psf file
by MARIA CLARA BLANES MIRA 29 May '19

29 May '19

Hello Chimera users, I am trying to see the movement of some phospholipids in a lipid bilayer when a peptide is anchoring to this membrane. I have a .pdb, .psf and several .dcd files. When I select one of these phospholipids I obtain four molecules selected (with the same name due to the segments). I have been trying with ’Select by attribute value’/atoms/pdbSegment and it works perfect because this way I can specify the segment where it is. But I can’t find the way to do the same with the .psf file. Could you tell me how should I do it?. Thank you very much, clara

3 4

How to get the best references
by temban billyhp 28 May '19

28 May '19

HiI used UCSF chimera for MOLECULAR DOCKING. Are these citations below enough for me to cite. Could you please help me with more citations. 1.Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.C., and Ferrin, T.E., UCSF Chimera--a visualization system for exploratory research and analysis, J. Comput. Chem., 2004, vol. 25, p. 1605. 2. Maier, J.A., Martinez, C., Kasavajhala, K., Wickstrom, L., Hauser, K.E., and C. Simmerling, ff14SB: Improving the accuracy of protein side chain and backbone parameters from ff99SB, J. Chem. Theory Comput., 2015, vol. 11, p. 3696. 3. Shapovalov, M.V. and Dunbrack, R.L., A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions, Structure, 2011, vol. 19, p. 844. 4. Trott, O. and Olson, A.J., AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading, Journal of Computational Chemistry, 2010, vol. 31, p. 455. Best regards. Sent from Yahoo Mail on Android

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How to get the best references
by temban billyhp 28 May '19

28 May '19

HiI used UCSF chimera for MOLECULAR DOCKING. Are these citations below enough for me to cite. Could you please help me with more citations. 1.Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.C., and Ferrin, T.E., UCSF Chimera--a visualization system for exploratory research and analysis, J. Comput. Chem., 2004, vol. 25, p. 1605. 2. Maier, J.A., Martinez, C., Kasavajhala, K., Wickstrom, L., Hauser, K.E., and C. Simmerling, ff14SB: Improving the accuracy of protein side chain and backbone parameters from ff99SB, J. Chem. Theory Comput., 2015, vol. 11, p. 3696. 3. Shapovalov, M.V. and Dunbrack, R.L., A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions, Structure, 2011, vol. 19, p. 844. 4. Trott, O. and Olson, A.J., AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading, Journal of Computational Chemistry, 2010, vol. 31, p. 455. Best regards. Sent from Yahoo Mail on Android

1 0

(no subject)
by MARIA CLARA BLANES MIRA 23 May '19

23 May '19

Dear Chimera users, I have a .psf and multiple .dcd files for a peptide movement and I need to make a movie combining certain frames for each dcd file. First, I have tried to load more than one dcd file in the MD movie interface but my computer hungs. I think I should use a metafile in this situation. Something like this: namd(psf/dcd) pam.psf pam1.dcd But I have all the other pam2.dcd, pam3.dcd, etc until 40, each having 3000 frames. How could I include them in the same metafile to be able to open one, record 20-30 frames, open the second, record some other frames and so on? And how could I include the frames number? Thank you in advance, Clara Blanes

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Re: [Chimera-users] Question on chimera app
by Elaine Meng 22 May '19

22 May '19

On May 21, 2019, at 4:38 PM, temban billyhp <btemban(a)yahoo.com> wrote: > > Hi > During the auto dock vina operation, when building the grid box. What is the unit of the dimensions. I will equally like to know how to find the grid spacing value. > Best regards. Chimera questions should be sent to chimera-users(a)cgl.ucsf.edu (CC’d here). The Autodock Vina tool in Chimera does not have a grid spacing setting. It only has the box center and size, which are in X,Y,Z coordinates of your atomic structure. Atomic structures are generally in Angstrom units. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html> Maybe there is a setting to control grid spacing if you downloaded and used the Autodock Vina program directly (not using the tool in Chimera) but I do not know. You would have to look at the Autodock Vina website for that information. <http://vina.scripps.edu/> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Fwd: Re: ImportError: /lib/x86_64-linux-gnu/libfontconfig.so.1: undefined symbol: FT_Done_MM_Var
by Greg Couch 20 May '19

20 May '19

Yes, this bug was fixed after the 1.13.1 release. -- Greg On 5/17/2019 6:52 AM, Thomas Evangelidis wrote: > Strangely, the alpha version (May 09, 2019) works fine! > > On Fri, 17 May 2019 at 12:19, Thomas Evangelidis <tevang3(a)gmail.com > <mailto:tevang3@gmail.com>> wrote: > > Greetings, > > I did a fresh installation of Chimera on Ubuntu 19.04 but although > the installation finished successfully, I get this error message > whenever I launch the executable: > > > Traceback (most recent call last): > File > "/home2/thomas/Programs/Chimera-1.13.1/share/__main__.py", > line 73, in <module> > value = chimeraInit.init(sys.argv) > File > "/home2/thomas/Programs/Chimera-1.13.1/share/chimeraInit.py", > line 666, in init > import chimera > File > "/home2/thomas/Programs/Chimera-1.13.1/share/chimera/__init__.py", > line 2777, in <module> > from SimpleSession import BEGIN_RESTORE_SESSION, > END_RESTORE_SESSION > File > "/home2/thomas/Programs/Chimera-1.13.1/share/SimpleSession/__init__.py", > line 14, in <module> > from save import saveSession, sessionID, noAutoRestore, > autoRestorable, \ > File > "/home2/thomas/Programs/Chimera-1.13.1/share/SimpleSession/save.py", > line 13, in <module> > from chimera import replyobj, selection, SessionPDBio, version > File > "/home2/thomas/Programs/Chimera-1.13.1/share/chimera/replyobj.py", > line 24, in <module> > import Tkinter > File > "/home2/thomas/Programs/Chimera-1.13.1/lib/python2.7/lib-tk/Tkinter.py", > line 39, in <module> > import _tkinter # If this fails your Python may not be > configured for Tk > ImportError: /lib/x86_64-linux-gnu/libfontconfig.so.1: > undefined symbol: FT_Done_MM_Var > > > What is strange is that the following works without error: > > /home2/thomas/Programs/Chimera-1.13.1/bin/python2.7 -c 'import > _tkinter' > > > Any idea what might be wrong? > > Best, > Thomas > > > -- > > ====================================================================== > > Dr. Thomas Evangelidis > > Research Scientist > > IOCB - Institute of Organic Chemistry and Biochemistry of the > Czech Academy of Sciences > <https://www.uochb.cz/web/structure/31.html?lang=en>, Prague, > Czech Republic > > & > CEITEC - Central European Institute of Technology > <https://www.ceitec.eu/>, Brno, Czech Republic > > email: tevang3(a)gmail.com <mailto:tevang3@gmail.com>, Twitter: > tevangelidis <https://twitter.com/tevangelidis>, LinkedIn: Thomas > Evangelidis > <https://www.linkedin.com/in/thomas-evangelidis-495b45125/> > > website: https://sites.google.com/site/thomasevangelidishomepage/ > > > > > > > -- > > ====================================================================== > > Dr. Thomas Evangelidis > > Research Scientist > > IOCB - Institute of Organic Chemistry and Biochemistry of the Czech > Academy of Sciences > <https://www.uochb.cz/web/structure/31.html?lang=en>, Prague, Czech > Republic > > & > CEITEC - Central European Institute of Technology > <https://www.ceitec.eu/>, Brno, Czech Republic > > email: tevang3(a)gmail.com <mailto:tevang3@gmail.com>, Twitter: > tevangelidis <https://twitter.com/tevangelidis>, LinkedIn: Thomas > Evangelidis <https://www.linkedin.com/in/thomas-evangelidis-495b45125/> > > website: https://sites.google.com/site/thomasevangelidishomepage/ > > > > > > _______________________________________________ > Chimera-users mailing list:Chimera-users@cgl.ucsf.edu > Manage subscription:http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

1 0

Help in validation of Mutant Structure
by carlo cast 20 May '19

20 May '19

Good Morning to everyone, it’s my first time here writing at you, I hope I’m doing right. The point is that I’m working with a wild type enzyme from which I got mutant versions by using swap aa command. My goal is to look at the effects that mutations have on the structure by superimposing the mutant form with the wild type one. When I perform matchmaker command, RMSD is equal to 0 and the structures overlap perfectly; thus I thought to minimize structure before superimposing and in this way I see a little difference in RMSD but it could be due to the different steps of the minimize process (e.g. adding protons) than the actual effect of mutations. Moreover when I perform multiple sequence alignment, the amminoacids I swapped actually are not different from the Wild type ones. If I point the cursor on the swapped aa I see the difference in name and side chain but by doing multiple sequence alignment they do not appear. Any suggestions? Inviato da Posta<https://go.microsoft.com/fwlink/?LinkId=550986> per Windows 10

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Re: [Chimera-users] Contact area between 2 Proteins
by Elaine Meng 17 May '19

17 May '19

Dear Fer Villa, (better to send questions to chimera-users(a)cgl.ucsf.edu, CC’d here) It is not really a matter of right and wrong. Instead it depends on what you want… If you want to measure buried solvent-accessible and solvent-excluded surface areas of atomic structures, use “measure buriedArea”. The “measure contactArea” command is similar but if the goal is measurement (rather than coloring for a figure), it is generally used for other kinds of surfaces that are not necessarily associated with any atoms, like density map isosurfaces. In that case, the appropriate cutoff value really depends on the judgment of the user based on what kinds of surfaces these are and what the user is trying to do. The tutorial you mention is for making a figure where the interaction surfaces of two proteins are colored, which is a different purpose than getting a measurement value. It explains that different cutoffs could be used with “measure contactArea", but the example has 2.5 because it gave similar appearance to using the other (buriedArea) method. The tutorial shows both methods because if you are making a figure, you could use either one as you like. It actually discusses three methods. For the other people on the list, here is that tutorial: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/openbook.html> … 3 methods of coloring the interface: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/openbook.html#in…> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On May 10, 2019, at 12:17 AM, Fernando Villa <fer.vdl1928(a)gmail.com> wrote: > > Dear Chimera users, > I would like to know which is the correct method to know what is the surface area of contact between two proteins: > measure contactArea or measure buriedArea? > When I apply the command: measure contactArea # 0.1 # 0.2 2.5 color yellow offset 0 that comes in the tutorial, it says that the cutting distance is equal to 2.5 A2 > But, is it correct? > How can I know that? > this example states that if this cut-off distance (2.5 A) is applied compared with a cut distance for measure buriedArea: > Command: measure buriedArea # 0.1 # 0.2 > Command: color yellow #0.1@/buriedSESArea> 1 > Command: color hot pink #0.2@/buriedSESArea> 1 > measure buried Area # 0.1 & protein # 0.2 & protein > atoms with> 1.0 Å2 > How can I know which is the correct contact area (protein protein interaction) of two models or crystals? > What is the correct cutting area that I should apply? > Could it be the default cut area of 1A? > Which method of calculation is better, measure contactArea or measure buriedArea? > I would thank you in advance for a possible solution to my problem. > > Best regards. > > Fer Villa. > Enviar comentarios > Historial > Guardadas > Comunidad > > <image.png> > > Command:open 1avx > Command: ~longbond > Command: split > Command: preset apply int 2 > Command: repr stick > Command: delete solvent > Command: color sea green #0.1 > Command: color medium purple #0.2 > Command: surface > Command: measure contactArea #0.1 #0.2 2.5 color yellow offset 0 > Command: measure contactArea #0.2 #0.1 2.5 color hotpink offset 0 > > > or > > Command: measure buriedArea #0.1 #0.2 > Command: color yellow #0.1@/buriedSESArea>1 > Command: color hot pink #0.2@/buriedSESArea>1 > > Command: measure buriedArea #0.1&protein #0.2&protein > > ATTE > Fernando Villa Díaz >

2 6

display bond lengths and angles
by Thomas Evangelidis 17 May '19

17 May '19

Hello, Is it possible to load a small molecule in Chimera and display all bond lengths and angle values, pretty much as you can do using labelopt option for the atom names? If not directly, could you please give me some hints about how to write a Python script to do it? I thank you in advance for your help. Thomas -- ====================================================================== Dr. Thomas Evangelidis Research Scientist IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en>, Prague, Czech Republic & CEITEC - Central European Institute of Technology <https://www.ceitec.eu/>, Brno, Czech Republic email: tevang3(a)gmail.com, Twitter: tevangelidis <https://twitter.com/tevangelidis>, LinkedIn: Thomas Evangelidis <https://www.linkedin.com/in/thomas-evangelidis-495b45125/> website: https://sites.google.com/site/thomasevangelidishomepage/

2 1

ImportError: /lib/x86_64-linux-gnu/libfontconfig.so.1: undefined symbol: FT_Done_MM_Var
by Thomas Evangelidis 17 May '19

17 May '19

Greetings, I did a fresh installation of Chimera on Ubuntu 19.04 but although the installation finished successfully, I get this error message whenever I launch the executable: > > Traceback (most recent call last): > File "/home2/thomas/Programs/Chimera-1.13.1/share/__main__.py", line 73, > in <module> > value = chimeraInit.init(sys.argv) > File "/home2/thomas/Programs/Chimera-1.13.1/share/chimeraInit.py", line > 666, in init > import chimera > File "/home2/thomas/Programs/Chimera-1.13.1/share/chimera/__init__.py", > line 2777, in <module> > from SimpleSession import BEGIN_RESTORE_SESSION, END_RESTORE_SESSION > File > "/home2/thomas/Programs/Chimera-1.13.1/share/SimpleSession/__init__.py", > line 14, in <module> > from save import saveSession, sessionID, noAutoRestore, > autoRestorable, \ > File > "/home2/thomas/Programs/Chimera-1.13.1/share/SimpleSession/save.py", line > 13, in <module> > from chimera import replyobj, selection, SessionPDBio, version > File "/home2/thomas/Programs/Chimera-1.13.1/share/chimera/replyobj.py", > line 24, in <module> > import Tkinter > File > "/home2/thomas/Programs/Chimera-1.13.1/lib/python2.7/lib-tk/Tkinter.py", > line 39, in <module> > import _tkinter # If this fails your Python may not be configured for > Tk > ImportError: /lib/x86_64-linux-gnu/libfontconfig.so.1: undefined symbol: > FT_Done_MM_Var > What is strange is that the following works without error: /home2/thomas/Programs/Chimera-1.13.1/bin/python2.7 -c 'import _tkinter' > Any idea what might be wrong? Best, Thomas -- ====================================================================== Dr. Thomas Evangelidis Research Scientist IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en>, Prague, Czech Republic & CEITEC - Central European Institute of Technology <https://www.ceitec.eu/>, Brno, Czech Republic email: tevang3(a)gmail.com, Twitter: tevangelidis <https://twitter.com/tevangelidis>, LinkedIn: Thomas Evangelidis <https://www.linkedin.com/in/thomas-evangelidis-495b45125/> website: https://sites.google.com/site/thomasevangelidishomepage/

1 1

Still won't work after libfreetype.so* and libz.so* removal
by Яцкевич Максим 14 May '19

14 May '19

Hi! I am running Fedora 29. Now I'm trying to install chimera-1.13.1-linux_x86_64.bin. After successful installation it failed to create a window in a desktop applecation menu. So I followed the instructions on the web-site (http://www.cgl.ucsf.edu/chimera/data/downloads/1.13.1/linux_x86_64.html) After running the command <dir_name>/bin/xdg-setup install it stumbled upon the same error that was discussed in this thread (https://www.cgl.ucsf.edu/pipermail/chimera-users/2018-November/015237.html) Traceback (most recent call last): File "/home/sec/.local/chimera/share/__main__.py", line 73, in <module> value = chimeraInit.init(sys.argv) File "/home/sec/.local/chimera/share/chimeraInit.py", line 666, in init import chimera File "/home/sec/.local/chimera/share/chimera/__init__.py", line 2777, in <module> from SimpleSession import BEGIN_RESTORE_SESSION, END_RESTORE_SESSION File "/home/sec/.local/chimera/share/SimpleSession/__init__.py", line 14, in <module> from save import saveSession, sessionID, noAutoRestore, autoRestorable, \ File "/home/sec/.local/chimera/share/SimpleSession/save.py", line 13, in <module> from chimera import replyobj, selection, SessionPDBio, version File "/home/sec/.local/chimera/share/chimera/replyobj.py", line 24, in <module> import Tkinter File "/home/sec/.local/chimera/lib/python2.7/lib-tk/Tkinter.py", line 39, in <module> import _tkinter # If this fails your Python may not be configured for Tk ImportError: /usr/lib64/libfontconfig.so.1: undefined symbol: FT_Done_MM_Var So I followed your advise and removed the corresponding files: > rm ~/.local/chimera/lib/libz.so* > rm ~/.local/chimera/lib/libfreetype.so* Unfortunately it didn't solve the problem. So after typing: > ~/.local/chimera/bin/xdg-setup install It complained that it cannot find the libz.so file! Traceback (most recent call last): File "/home/sec/.local/chimera/share/__main__.py", line 73, in <module> value = chimeraInit.init(sys.argv) File "/home/sec/.local/chimera/share/chimeraInit.py", line 659, in init initialize_ssl_cert_dir() File "/home/sec/.local/chimera/share/chimeraInit.py", line 309, in initialize_ssl_cert_dir import ssl File "/home/sec/.local/chimera/lib/python2.7/ssl.py", line 146, in <module> import base64 # for DER-to-PEM translation File "/home/sec/.local/chimera/lib/python2.7/base64.py", line 11, in <module> import binascii ImportError: libz.so: cannot open shared object file: No such file or directory I will be grateful for any help. Best regards, Maxim. PhD Student, Physical Faculty, Lomonosov Moscow State University

2 1

Upload color scheme
by Cornelius Hunter 10 May '19

10 May '19

I am looking for a 3D protein viewer that allows me to visualize the protein tertiary structure using my own color assignments, for each residue (or alpha carbon). In other words I would upload a file, with a value for each residue, which would drive the color assignments. Thx

2 2

Volume Step default
by Rebecca Swett 10 May '19

10 May '19

HI all, I was wondering if it was possible to set the Volume Viewer step to 1 as default instead of 4. Is this something I could add to my .chimera/preferences file? Cheers, Rebecca This email message and any attachments are confidential and intended for use by the addressee(s) only. If you are not the intended recipient, please notify me immediately by replying to this message, and destroy all copies of this message and any attachments. Thank you.

2 1

to hide atoms using command lines
by C.J. 08 May '19

08 May '19

Dear specialist, I know how to use hide selected atoms (Menu: Actions => Atoms/Bonds => Hide), but I would like to use command lines instead. Anyone could help me with that? Thank you! Best regards! C.J.

2 2

FW: Association info
by Hernando J Sosa 08 May '19

08 May '19

Thanks Eric, it works. To summarize: #---------------------------------------------------------------------- def findMAV(): from chimera.extension import manager from MultAlignViewer.MAViewer import MAViewer mavs = [inst for inst in manager.instances if isinstance(inst, MAViewer)] if not mavs: raise AssertionError("No MAV instances") return mavs[-1] #---------------------------------------------------------------------- mav = findMAV() mav.saveAssocInfo('myfile.asc') #---------------------------------------------------------------------- Best Hernando

2 1

Re: [Chimera-users] Non-standard atom names
by Sid Majaha 08 May '19

08 May '19

Hi Eric So I have been only using dock6 for docking and now want to venture in using dock3. I tried checking online for tutorials that I could look at but there are just a couple of them. On the UCSF website, there is a tutorial but requires the use of dock blaster. I just have a few questions; Is there another way of using dock3.6 without using dock blaster? Is there another simpler tutorial for dock3.6 that you could recommend me to use? Are the dock 3.6 steps similar to the steps of dock6? Sid Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10 From: Eric Pettersen <pett(a)cgl.ucsf.edu> Sent: Tuesday, April 16, 2019 6:46:31 AM To: Sid Majaha Cc: Elaine Meng Subject: Re: [Chimera-users] Non-standard atom names You’re welcome. AM1-BCC does take considerably longer than Gasteiger, but in this case the great majority of the time is spent adding the missing side chains. —Eric > On Apr 15, 2019, at 1:18 AM, Sid Majaha <sidumomajaha(a)live.com <mailto:sidumomajaha@live.com>> wrote: > > Hi Eric > > Thank you so much for your help. I was able to see as well that my protein might have been too large for the calculations of the charges to take place efficiently because after following the procedure you gave me, it took a much longer time than using Gasteiger. Thank you so much for your help. > > Sid > > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10 > > From: Eric Pettersen <pett(a)cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> > Sent: Saturday, April 13, 2019 2:18:39 AM > To: Sid Majaha > Cc: chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> > Subject: Re: [Chimera-users] Non-standard atom names > > Hi Sid, > The 2BXF structure has many, many missing heavy side-chain atoms. I recommend using the Dock Prep tool (Tools→Structure Editing→Dock Prep), which will use a rotamer library to fill out missing/incomplete side chains before adding hydrogens and assigning charges. Use the dialog check boxes to turn off any Dock Prep steps you don’t want (e.g. Write Mol2 file). Applying a lot of rotamers takes a few minutes, so you might want to bring up the Reply Log first (Favorites→Reply Log) so you can keep an eye on the Dock Prep progress while you possibly do something else. > > ―Eric > > Eric Pettersen > UCSF Computer Graphics Lab > >> On Apr 11, 2019, at 8:26 PM, Sid Majaha <sidumomajaha(a)live.com <mailto:sidumomajaha@live.com>> wrote: >> >> >> Hi Eric >> >> Problems with atom names in adding charge to a receptor using Chimera v1.13.1 >> (ToolsàSurface Binding/AnalysisàAdd charge) >> I first added my H to prepare my receptor. And I am using the protein PDB ID 2BXF. >> Net Charge is +0 for the residue HIS using charge method AM1_BCC >> >> Chimera warning received >> Correct charges are unknown for 9 non-standard atom names in otherwise standard residues. >> Charges of 0.0 were assigned to the unknown atoms. >> 1 model(s) had non-intergral total charge. >> >> Reply log is as follows, >> >> Charge model: AMBER ff14SB >> Assigning partial charges to residue HIS (net charge +0) with am1-bcc method >> Running ANTECHAMBER command: C:/Program Files/Chimera 1.13.1/bin/amber16/bin\antechamber -ek qm_theory='AM1', -i c:\users\hp\appdata\local\temp\tmplj8p6o\ante.in.mol2 -fi mol2 -o c:\users\hp\appdata\local\temp\tmplj8p6o\ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 -dr n >> (HIS) >> >> (HIS) Welcome to antechamber 17.3: molecular input file processor. >> >> (HIS) >> >> (HIS) Info: Finished reading file (c:\users\hp\appdata\local\temp\tmplj8p6o\ante.in.mol2). >> >> (HIS) Running: "C:/Program Files/Chimera 1.13.1/bin/amber16/bin/bondtype" -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac >> >> (HIS) >> >> (HIS) >> >> (HIS) Running: "C:/Program Files/Chimera 1.13.1/bin/amber16/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff >> >> (HIS) Info: Total number of electrons: 78; net charge: 0 >> >> (HIS) >> >> (HIS) Running: "C:/Program Files/Chimera 1.13.1/bin/amber16/bin/sqm" -O -i sqm.in -o sqm.out >> >> (HIS) >> >> (HIS) Running: "C:/Program Files/Chimera 1.13.1/bin/amber16/bin/am1bcc" -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program Files/Chimera 1.13.1/bin/amber16/dat/antechamber/BCCPARM.DAT" -s 2 -j 1 >> >> (HIS) >> >> (HIS) Running: "C:/Program Files/Chimera 1.13.1/bin/amber16/bin/atomtype" -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC >> >> (HIS) >> >> Charges for residue HIS determined >> Non-standard atom names: >> VAL HB1 (VAL 551.A HB1) >> VAL HB2 (VAL 551.A HB2) >> ILE HB3 (ILE 509.A HB3, ILE 1087.B HB3) >> VAL HB3 (VAL 551.A HB3) >> ILE HB2 (ILE 509.A HB2, ILE 1087.B HB2) >> THR HB1 (THR 79.A HB1, THR 621.B HB1, THR 657.B HB1) >> ILE HB1 (ILE 509.A HB1, ILE 1087.B HB1) >> THR HB3 (THR 79.A HB3, THR 621.B HB3, THR 657.B HB3) >> THR HB2 (THR 79.A HB2, THR 621.B HB2, THR 657.B HB2) >> Total charge for #0: -66.402 >> The following residues had non-integral charges: >> LYS 16.A 0.0867 >> LEU 27.A -0.0471 >> GLN 29.A 0.0392 >> LYS 37.A 0.0867 >> LYS 47.A 0.0733 >> ASP 52.A -0.2088 >> GLU 53.A -0.2103 >> GLU 56.A -0.1137 >> LYS 69.A 0.0867 >> ARG 77.A 0.0612 >> GLU 78.A -0.1137 >> THR 79.A 0.3128 >> TYR 80.A 0.0451 >> GLU 82.A -0.1137 >> GLN 90.A 0.0152 >> GLU 91.A -0.1137 >> GLU 93.A -0.1137 >> ARG 94.A 0.0612 >> PHE 98.A 0.0352 >> GLN 100.A 0.0392 >> ASN 107.A 0.0397 >> ARG 110.A 0.0612 >> LYS 132.A 0.0867 >> LYS 133.A 0.2148 >> LYS 155.A 0.0867 >> LYS 158.A 0.0733 >> GLN 166.A 0.0152 >> LYS 170.A 0.0733 >> LEU 174.A -0.0471 >> LYS 186.A 0.0867 >> GLN 200.A 0.0152 >> LYS 201.A 0.0733 >> ARG 205.A 0.153 >> LYS 221.A 0.0867 >> LYS 229.A 0.0733 >> LYS 236.A 0.0733 >> LEU 247.A -0.0471 >> LYS 272.A 0.0733 >> GLU 273.A -0.1137 >> GLU 276.A -0.1137 >> LYS 277.A 0.0733 >> GLU 281.A -0.1137 >> LYS 282.A 0.0733 >> GLU 293.A -0.1137 >> LEU 298.A -0.0471 >> LYS 309.A 0.0733 >> LYS 319.A 0.0867 >> ASP 320.A -0.2088 >> LYS 355.A 0.0867 >> ASP 361.A -0.2088 >> LYS 368.A 0.0867 >> LYS 374.A 0.0733 >> GLU 378.A -0.1137 >> GLU 392.A -0.1137 >> GLN 393.A 0.0152 >> LYS 398.A 0.0733 >> LEU 404.A -0.0471 >> LYS 428.A 0.0867 >> LYS 432.A 0.0867 >> LYS 462.A 0.0733 >> LYS 496.A 0.0867 >> GLU 497.A -0.2103 >> ASN 499.A 0.0397 >> ILE 509.A 0.0431 >> LYS 515.A 0.0733 >> GLU 516.A -0.1137 >> LYS 520.A 0.0733 >> LEU 528.A -0.0471 >> LYS 532.A 0.0733 >> LYS 534.A 0.0733 >> LYS 537.A 0.0733 >> LYS 541.A 0.0733 >> PHE 547.A 0.0352 >> VAL 551.A 0.1935 >> LYS 553.A 0.2148 >> LYS 556.A 0.0733 >> ASP 558.A -0.2088 >> LYS 560.A 0.0733 >> GLU 561.A -0.1137 >> GLU 566.A -0.2103 >> LYS 569.A 0.0733 >> LYS 570.A 0.0733 >> GLN 576.A 0.0152 >> LYS 586.B 0.0733 >> LEU 605.B -0.0471 >> GLN 606.B 0.0152 >> THR 621.B 0.3128 >> LYS 625.B 0.0733 >> ASP 630.B -0.2088 >> GLU 634.B -0.1137 >> ASN 635.B 0.0397 >> LYS 638.B 0.0867 >> GLU 656.B -0.1137 >> THR 657.B 0.3128 >> TYR 658.B 0.0451 >> GLU 660.B -0.1137 >> MET 661.B 0.0564 >> LYS 667.B 0.0733 >> GLN 668.B 0.0152 >> GLU 671.B -0.1137 >> ARG 672.B 0.0612 >> PHE 676.B 0.0352 >> GLN 678.B 0.0152 >> ARG 688.B 0.0612 >> LEU 689.B -0.0471 >> LYS 733.B 0.0733 >> GLN 744.B 0.0152 >> LYS 748.B 0.0733 >> LEU 752.B -0.0471 >> LYS 755.B 0.0733 >> ARG 760.B 0.0612 >> GLU 762.B -0.1137 >> LYS 764.B 0.2148 >> GLN 778.B 0.0152 >> LYS 779.B 0.0867 >> ARG 783.B 0.3792 >> LYS 799.B 0.0867 >> LYS 807.B 0.0733 >> LYS 814.B 0.0733 >> LEU 849.B -0.0471 >> LYS 850.B 0.0733 >> GLU 851.B -0.1137 >> GLU 854.B -0.1137 >> LYS 855.B 0.0867 >> LYS 860.B 0.0733 >> GLU 871.B -0.1137 >> ASP 875.B -0.2088 >> LYS 887.B 0.0733 >> LYS 891.B 0.0733 >> GLU 895.B -0.1137 >> LYS 897.B 0.0867 >> LYS 933.B 0.2148 >> GLU 942.B -0.1137 >> LYS 952.B 0.0867 >> GLU 956.B -0.1137 >> LYS 963.B 0.2148 >> LYS 976.B 0.0867 >> ARG 984.B 0.3792 >> LYS 1010.B 0.0867 >> LYS 1018.B 0.2148 >> LYS 1040.B 0.0733 >> GLU 1075.B -0.1137 >> ASP 1086.B -0.2088 >> ILE 1087.B 0.0431 >> LYS 1093.B 0.0733 >> GLU 1094.B -0.1137 >> GLN 1096.B 0.0152 >> LYS 1098.B 0.0867 >> LYS 1099.B 0.0867 >> LYS 1110.B 0.0733 >> LYS 1115.B 0.0733 >> LYS 1119.B 0.2148 >> ASP 1124.B -0.2088 >> PHE 1128.B 0.0352 >> LYS 1131.B 0.0733 >> ASP 1136.B -0.2088 >> LYS 1138.B 0.0733 >> GLU 1139.B -0.1137 >> GLU 1144.B -0.1137 >> LYS 1147.B 0.0733 >> LYS 1148.B 0.0733 >> LEU 1149.B -0.0471 >> GLN 1154.B 0.0152 >> Correct charges are unknown for 9 non-standard atom names in otherwise standard residues >> >> Charges of 0.0 were assigned to the unknown atoms >> >> 1 model(s) had non-integral total charge >> Details in reply log. >> >> How do I work around this? >> >> Sid >> >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>

2 3

RR distance map, scale normalization
by Arvind SHARMA 07 May '19

07 May '19

Hi, I am comparing four drug bound structures of homologous proteins to their unbound structures in chimera RR distance maps. These structures vary to different degree to unbound structures and I want to show that in four individual RR distance maps (each bound structure to unbound structure). The problem is that the scale varies each time and I was wondering if there is a way to normalize the scale? or set the color code so that, for e.g, for stdv of 10 its red in all cases and below 5 its always white. Thanks. Best wishes, Arvind.

4 10

Handling electrostatic potential in cube format
by Boaz Shaanan 06 May '19

06 May '19

Hi, It seems as if the new Delphi version (v8.4) only knows to produce potential phi files in cube format. Oh well. I'm beginning to play with this format via the volume viewer but so far the fit of the surface to the atomic model is bad, let alone that potential values on the surface (as reported by moving the mouse on the surface) make no sense. I'm wondering whether there is a chance to achieve as nice a fit of the cube surface to the protein model as is easily achieved with the good old .phi format and surface command. So far I'm lost. I'd appreciate any clues. Luckily, I still keep the older version but there might be some improvements in the potential calculations in the newer version. Thanks for your help. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710

3 4

Re: [Chimera-users] [chimera-dev] Loop refinement in chain A and Chain B
by Elaine Meng 06 May '19

06 May '19

Hi Aashish, The address for questions about using Chimera is chimera-users(a)cgl.ucsf.edu (CC’d here). Chimera-dev is for programming questions. It sounds like you did find the “model/refine loops” dialog for using the Modeller web service. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> In that dialog, you would need to choose either “non-terminal missing structure” (if the missing residues are in the middle) or “all missing structure” (if some of the missing residues are in the termini), and also enter a license key for running Modeller. However, I have no idea what you mean by “not running,” so I can’t give any more help than that. Also, be aware that in Chimera using this dialog, you can only model one chain at a time. I.e. when it is adding the residues to chain A it does not care if they are in a bad place relative to chain B, and vice versa. Our newer program ChimeraX has the advantage that you can sensibly model the dimer using the Modeller web service, with the two chains “seeing” each other. However, to use that you would have to download and learn a different program. <http://www.rbvi.ucsf.edu/chimerax/index.html> <http://www.rbvi.ucsf.edu/chimerax/download.html> <http://www.rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html#comparative> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On May 6, 2019, at 5:39 AM, Aashish Bhatt <aashish.ph16221(a)inst.ac.in> wrote: > > Dear Sir/ Ma'am > > I have dimer PDB structure in which 40 amino acid is missing in both chain A and B. > Is it possible to make a model with a chimera? I have tried the same with chain A and but it is not running. > > Can you please give me an idea of how to build the complete structure? > > Best regards > > Aashish > INST-Mohali > India

1 0

How do I find the active site?
by Abryn Jeuness Luna 06 May '19

06 May '19

Good day! I am currently using UCSF Chimera for my protein structure analysis. However, I cannot find the active site of my protein structure. How do I find the active site, including the amino acids in it using UCSF Chimera? Thank you. Regards, Abryn

2 1

regarding to minimization and preparation of sdf files for docking.
by prasad ssv 05 May '19

05 May '19

hi, i had a database which contains a set of molecules,all molecules in sdf format i would like to minimize all sdf files and dock preparation.can you please help me do that. i had performed dock prep for those sdf files but it showing some reply log and bugs.when i am adding hydrogens it is gvng reply log as attached in below files. can you please go through and suggest me a solution. thanking you,

3 4

Re: [Chimera-users] Chimera-users Digest, Vol 193, Issue 5
by Boaz Shaanan 05 May '19

05 May '19

Hi Again, Following my complaint on the cube format I started to play with .dx format of APBS which so far seems more promising in how it projects on the protein surface. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: Chimera-users <chimera-users-bounces(a)cgl.ucsf.edu> on behalf of chimera-users-request(a)cgl.ucsf.edu <chimera-users-request(a)cgl.ucsf.edu> Sent: Sunday, May 5, 2019 8:18 AM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 193, Issue 5 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. save sequence alignment (Hernando J Sosa) 2. Re: save sequence alignment (Eric Pettersen) 3. Re: RR distance map, scale normalization (Arvind SHARMA) 4. Handling electrostatic potential in cube format (Boaz Shaanan) 5. How to select residues/atoms only those within my cryo-EM map region (Kim, Doo Nam) ---------------------------------------------------------------------- Message: 1 Date: Fri, 3 May 2019 21:03:33 +0000 From: Hernando J Sosa <hernando.sosa(a)einstein.yu.edu> To: Chimera <chimera-users(a)cgl.ucsf.edu> Subject: [Chimera-users] save sequence alignment Message-ID: <F0E461AAE34D0448B6EE7D31E433B7080154B87577(a)AEWEXCPM21.yuad.uds.yu.edu> Content-Type: text/plain; charset="utf-8" Dear Chimera, Is there a command option to save a sequence alignment (after executing matchmaker) or a way to do it in a python script? Thanks H. ------------------------------ Message: 2 Date: Fri, 3 May 2019 15:19:36 -0700 From: Eric Pettersen <pett(a)cgl.ucsf.edu> To: Hernando J Sosa <hernando.sosa(a)einstein.yu.edu> Cc: Chimera <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] save sequence alignment Message-ID: <EFACEFC8-FD06-4C10-AE7B-704CD8925BCF(a)cgl.ucsf.edu> Content-Type: text/plain; charset="utf-8" Hi Hernando, This old chimera-users message shows how to find the alignment in Python and save it: [Chimera-users] easy way to make alignments in chimera <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-June/010017.html>. You can?t do it in nogui mode since the MAV window has the alignment data. You would be able to do it in nogui mode in ChimeraX, but the code would be significantly different of course. Anyway, if you are doing this in a loop you may want to call mav.Quit() after saving your alignment in order to quit MAV and conserve memory. ?Eric Eric Pettersen UCSF Computer Graphics Lab > On May 3, 2019, at 2:03 PM, Hernando J Sosa <hernando.sosa(a)einstein.yu.edu> wrote: > > Dear Chimera, > > Is there a command option to save a sequence alignment (after executing matchmaker) or a way to do it in a python script? > > Thanks > > H. > > > > > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

1 0

AutoDock Vina
by Hernando J Sosa 02 May '19

02 May '19

Is it possible to specify more than 10 'Number of Binding models' on the AtoDock Vina dialogue? Thanks Hernando

3 5

get_view, set_view
by Pranav Shah 02 May '19

02 May '19

Dear Devs, Apologies for asking a naive question, but i was wondering if there exists a function similar to pymols' get_view and set_view in chimera/chimeraX? If yes, is there a way to do this? Cheers, Pranav -- Pranav Shah Postdoctoral Research Fellow. Hogle Lab Department of Biological Chemistry and Molecular Pharmacology, Building C2 - First Floor 240 Longwood Avenue Boston, MA 02115 (617) 432-4360 (fax) (617) 432-3839 (lab)

2 3

Installing vina webserver?
by Antoine Daina 01 May '19

01 May '19

Dear, Is there any possibility to install a local AutoDock Vina webserver (not the executable, really the WS) through the scripts I can see in the Chimera install directories? Thanks a lot in advance fro your help. Best, Antoine. -- Antoine Daina, PhD SIB | Swiss Institute of Bioinformatics | Molecular Modeling Group Quartier Sorge | Bâtiment Amphipôle | CH-1015 Lausanne | Switzerland

2 1

Re: [Chimera-users] Reading electrostatic potential map in cube format into Chimera
by Boaz Shaanan 30 Apr '19

30 Apr '19

1 0

Reading electrostatic potential map in cube format into Chimera
by Boaz Shaanan 30 Apr '19

30 Apr '19

Hi, Does Chimera accept electrostatic potential in cube format (apparently that's what the new Delphi version 8.4 produces). I noticed a cube input under gaussian cube grid, is that the one I should use? Apparently the source of my recent problem with reading an electrostatic potential map had to do with this change of format. I'd appreciate your input. Thanks, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710

2 1

Deleting data contained in a session
by David Sáez 29 Apr '19

29 Apr '19

Dear Chimera experts: I have saved multiple sessions of molecular dynamics trajectories. Each session is about 5MB. Nevertheless, one of those files is huge, about 120MB. Checking the differences, I noticed that one of the files contained in the session, which normally is a one-frame .pdb, in the large case corresponds to a .nc file, a whole trajectory containing a large number of frames. I did not notice this before because when I opened the .py file, the MD movie box is not shown. As I am only interested in the currently displayed frame of this .nc file, is there a way to delete the additional frames? Some command line trick that would allow me to get rid of the uninteresting frames, and decrease the file size, without having to re-make the whole session again? My most immediate concern is that the file size is too large to be uploaded to a journal online platform. Any help is appreciated, Regards.

2 2

How to join two modelled chain of protein using chimera
by Bhanu Sharma 29 Apr '19

29 Apr '19

I have modelled two chains of protein(A,B) sepratrely. now i want to join these two chains as like of original protein and want to save it as a pdb file format . Can anyone please help me? Best regards, Bhanu sharma

2 2

A query
by Bhanu Sharma 26 Apr '19

26 Apr '19

Dear sir/mam I have done homology modelling for a protein having two chains (A,B). I have modelled them seprately one after another. Now i want to join these two chains to make complete protein. And i want to do it using chimera. Can you please help me how to do this. Best regards, Bhanu sharma

1 0

Changing the default temp folder for chimera
by Yehuda Halfon 25 Apr '19

25 Apr '19

Hi all, I try to make a movie in chimera and it fills my C drive. Can I change the temp folder, in which the pics are stored, to another empty drive? Thanks, Yehuda Halfon

2 1