October 2017 - Chimera-users - RBVI Mailing Lists

How to write pdb file by script?
by 陈品 24 Oct '17

24 Oct '17

Dear developers, I use CHIMERA to add charge into protein file from PDB format to mol2 format, i found that the script: $ cat prep_protein.py import chimera from DockPrep import prep models = chimera.openModels.list(modelTypes=[chimera.Molecule]) prep(models) from WriteMol2 import writeMol2 writeMol2(models, "10gs_protein_charged.pdb") $ ~/.local/UCSF-Chimera64-1.12rc/bin/chimera --nogui 10gs_protein.pdb prep_protein.py This script works well, but how to write PDB format file. I can not find WriteDPB function. How Can i write the data to PDB format? Kind Regards. Pin. -------------------------------------------------------------------------------- 本邮件及其附件含有发送给特定个人和用于特定目的的保密信息。如果您不是预期的收件人，请立即删除本邮件并通知发件人。严禁任何非预期的收件人使用、传播、分发或复制本邮件或其附件。 This email and its attachments may contain confidential information intended for a specific individual and purpose. If you are not the intended recipient, you should delete this email and notify the sender immediately. Any use, dissemination, distribution, or copying of this email or its attachments by persons other than the intended recipient(s), is strictly prohibited.

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Parse error in reply log
by Dr. Samson Soon 24 Oct '17

24 Oct '17

Dear experienced chimera users, I’m constantly failing my auto docking experiments due to the problem attached. Solution to this problem is urgently required. Thank you for any kind assistance rendered. Best regards Samson

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Selecting residues in chains defined by segname
by Francesco Pietra 23 Oct '17

23 Oct '17

Hi Elaine: I am referring to Oct 28, 2005, at 9:50 AM, Eric Gillitzer wrote: and your answer: command: select :45.a-d > or > command: select :45.* > > Or, to select > residue 45 in just chains A and D: > > command: select :45.a,45.d > I have a more complex case, where chains are defined by segname, for example A1 A2 A3 A4 A5 etc while the standard PDB definition is "A" for all them. The same for standard "B", "C" etc. As I want to display a movie of ligand pathways, where the ligand moves from, say, "A1" to, say, "F3", I want in the first instance become able to select particular residues in particular chains, as defined by their segname. Could you imagine a simple way not requiring selection by atom numbers? Thanks francesco pietra .

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Chimera build instructions?
by Yuri 23 Oct '17

23 Oct '17

Are there build instructions anywhere? https://www.cgl.ucsf.edu/chimera/docs/sourcecode.html is rather discouraging, and doesn't contain a "Build" section. GNUmakefile prints "there is no default make target". Is there a script or a makefile that builds it? Thanks, Yuri

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Matrix Application
by Amanda Constantinides 23 Oct '17

23 Oct '17

I have a structure with two subunits. I am trying to show movement of the C-terminal subunit upon ligand binding by superposition with another structure from the same strain in the apo form. I want to superpose the N-terminal subunits (A), note the RMSD, then apply the resulting matrix to the superposition of both subunits of the molecule with both subunits of the other (B),then I want to superpose on the C-terminal subunits (C), and then measure the RMSD between (C) and the C-terminal subunits from (B). How can I do this in Chimera? I know how to superpose molecules and calculate the RMSD in Chimera, but I do not know how to apply the resulting matrix from (A) to (B). I tried to save the aligned structures from (A) as a PDB file to check and see if there was a matrix in the file, but an error message came up saying that I needed to save the file as $name or $number. I tried to save the file with $ in front of the name, but it didn't work. Thanks in advance, Amanda Constantinides Graduate Research Assistant Georgia State University

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Re: [Chimera-users] Chimera-users Digest, Vol 174, Issue 30
by Boaz Shaanan 22 Oct '17

22 Oct '17

Hi Elaine, That's perfect and works great. Thanks so much for your help. Regards, 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 Skype: boaz.shaanan 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: Saturday, October 21, 2017 6:47 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 174, Issue 30 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. Re: Distance tool: Line thickness of the number (of angstroms) in the picture (Elaine Meng) ---------------------------------------------------------------------- Message: 1 Date: Sat, 21 Oct 2017 08:47:21 -0700 From: Elaine Meng <meng(a)cgl.ucsf.edu> To: Boaz Shaanan <bshaanan(a)bgu.ac.il> Cc: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Distance tool: Line thickness of the number (of angstroms) in the picture Message-ID: <CDAC071B-A031-4704-8BD3-F016F10794CA(a)cgl.ucsf.edu> Content-Type: text/plain; charset="utf-8" Hi Boaz, The only user interface to the label font size and style is the Preferences (open from Favorites menu), category: Labels. You could change the size number and make the style bold. This is for all ?3D? atom and distance labels that move along with the structure; size/font of 2D labels that don?t move with the structure can be set individually. Looks like the Labels Preferences size menu only goes up to 36, but you can enter some bigger number? for example, I entered 50 (see screenshot attached). Smaller size changes were barely perceptible on my high-resolution screen; maybe that is what happened for you. If that doesn?t work, I?m at a loss? maybe some weird rendering problem? 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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Re: [Chimera-users] Distance tool: Line thickness of the number (of angstroms) in the picture
by Boaz Shaanan 21 Oct '17

21 Oct '17

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Distance tool: Line thickness of the number (of angstroms) in the picture
by Boaz Shaanan 21 Oct '17

21 Oct '17

Hi, The number that shows up after creating a distance is very thin and can hardly be seen. I couldn't find how to make it thicker (I did change the actual line thickness in the menu). I also tried in the preference menu that you pointed to a user a while ago but it didn't work for me. How can I change it? This is on the Windows 64b nightly build from 17 October. 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 Skype: boaz.shaanan 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: Saturday, October 21, 2017 1:17 AM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 174, Issue 28 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. Re: Trouble with Volume surface and active model not aligned (Elaine Meng) 2. Re: Selecting residues in chains defined by segname (Francesco Pietra) 3. Re: Selecting residues in chains defined by segname (Elaine Meng) 4. Re: Trouble with Volume surface and active model not aligned (Phan Trieu Truong) ---------------------------------------------------------------------- Message: 1 Date: Fri, 20 Oct 2017 13:41:34 -0700 From: Elaine Meng <meng(a)cgl.ucsf.edu> To: Phan Trieu Truong <truongp(a)uga.edu> Cc: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Trouble with Volume surface and active model not aligned Message-ID: <5596D972-35F9-4643-8CDB-6F7D4DE590FD(a)cgl.ucsf.edu> Content-Type: text/plain; charset=utf-8 Hi Phan, I?m not sure what happened either, since your images show the ?A? (active for motion) boxes in the Model Panel are checked for both the molecule and the orbitals, meaning that using the mouse should move both of them together. You could try command: reset ? to put them back together. If that doesn?t work, you may have to start over by quitting and reopening the files. However, if you didn?t uncheck the ?A? boxes or the ?Active models? boxes below the Command Line, mouse movements should always move them both together. Maybe you accidentally had one of the A(ctive) boxes unchecked and moved the other model. In that case, reset will work. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Oct 20, 2017, at 8:57 AM, Phan Trieu Truong <truongp(a)uga.edu> wrote: > > Hi, > > I have been using Chimera to visualize MO orbital on molecules from ORCA calculations. I have been able to visualize the MO orbitals as a surface volume from cube files. However, I just found out that when I try to reorient the molecule with the surface volume, they are no longer aligned. I don't know what I did to cause this. Any help is much appreciated. > > Attached is the picture of the molecules before and after I tried to reorient the molecule with the surface volume. > > Thank you, > Phan > <Before and after reorientation.jpg.png>_______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users ------------------------------ Message: 2 Date: Fri, 20 Oct 2017 23:37:32 +0200 From: Francesco Pietra <chiendarret(a)gmail.com> To: Eric Pettersen <pett(a)cgl.ucsf.edu> Cc: chimera <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Selecting residues in chains defined by segname Message-ID: <CAEv0nmsDA8dd+hQ8H_t9uK8-LntPucKQ7UiiqVybva3XWdBgjA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" A pity, in my view. As more and more complex proteins are being examined (thanks to faster clusters), working without segname would be practically impossible in the frame of today pdb files. For example, how visualizing the trajectory of a particular ligand in a 24-chain protein assembly? I can do that with vmd, but at the price of a less clear-cut trajectory and poorer graphics. But I understand that there may be different viewpoints. Cheers francesco On Fri, Oct 20, 2017 at 8:36 PM, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > Realistically no. Too many other priorities. The gap will eventually get > filled in in ChimeraX, but even that will be awhile. > > ?Eric > > On Oct 19, 2017, at 1:24 PM, Francesco Pietra <chiendarret(a)gmail.com> > wrote: > > Hi Eric: > > Any plan to fill this gap? > > thanks > > francesco > > On Thu, Oct 19, 2017 at 7:59 PM, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > >> Hi Francseco, >> Unfortunately, segment IDs are not preserved by the trajectory reader. >> >> ?Eric >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> >> >> On Oct 19, 2017, at 9:53 AM, Francesco Pietra <chiendarret(a)gmail.com> >> wrote: >> >> Hi Elaine: >> While, as I wrote, the commands for segname did work fine with .psf/.pdb >> namd files, >> in contrast, with .psf/.dcd files (movie) >> >> select @/pdbSegment=C1 >> >> selects all chains of the protein assembly, including ligands. The same >> occurs with >> >> select @/pdbSegment=O2C1 >> >> where O2C1 is the segname of the molecule dioxygen associated with chain. >> >> This occurs both on my desktop and on a large-memory nextscale cluster on >> remote visualization (the latter is the actual interest) >> >> Do you know of any remedy? >> >> thanks a lot >> >> francesco >> ---------- Forwarded message ---------- >> From: Francesco Pietra <chiendarret(a)gmail.com> >> Date: Mon, Oct 16, 2017 at 7:12 PM >> Subject: Re: [Chimera-users] Selecting residues in chains defined by >> segname >> To: UCSF Chimera Mailing List <chimera-users(a)cgl.ucsf.edu> >> >> >> Hi Elaine: >> >> Great! >> >> thank you >> francesco >> >> On Mon, Oct 16, 2017 at 5:58 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >> >>> Hi Francesco, >>> The symbol for intersection is ?&? ... in other words, you could use >>> >>> select :17 & @/pdbSegment=A1 >>> >>> Intersection and union symbols are explained here: >>> <http://www.rbvi.ucsf.edu/home/meng/docs/UsersGuide/midas/at >>> om_spec.html#combinations> >>> >>> I hope this helps, >>> Elaine >>> >>> > On Oct 16, 2017, at 12:29 AM, Francesco Pietra <chiendarret(a)gmail.com> >>> wrote: >>> > >>> > Hi Elaine: >>> > That works fine. However, I was unable to extend your suggestions to >>> pick up a specific residue within a specific chain. Neither "select :17 >>> @/pdbSegment=A1" nor "select @/pdbSegment=A1 :17" are valid commands >>> (obviously expected). >>> > >>> > On the other hand, with such complex situations, it is Xplor, with its >>> segname features, that helps. >>> > >>> > Should you need a pdb fine with segname, I could attach a simple one, >>> with a single chain. >>> > >>> > On Sun, Oct 15, 2017 at 8:04 PM, Elaine Meng <meng(a)cgl.ucsf.edu> >>> wrote: >>> > Hi Francesco, >>> > Although I don?t have an example file with segnames to try myself, I?m >>> told you can specify by the atom attribute pdbSegment, e.g. >>> > >>> > select @/pdbSegment=A1 >>> > color red @/pdbSegment=F3 >>> > >>> > I hope this helps, >>> > Elaine >>> > >>> > > On Oct 15, 2017, at 10:40 AM, Francesco Pietra < >>> chiendarret(a)gmail.com> wrote: >>> > > >>> > > Hi Elaine: >>> > > >>> > > I am referring to Oct 28, 2005, at 9:50 AM, Eric Gillitzer wrote: >>> > > and your answer: >>> > > >>> > > command: select :45.a-d > or > command: select :45.* > > Or, to >>> select residue 45 in just chains A and D: > > command: select :45.a,45.d >>> > > >>> > > I have a more complex case, where chains are defined by segname, >>> > > for example >>> > > >>> > > A1 A2 A3 A4 A5 etc >>> > > >>> > > while the standard PDB definition is "A" for all them. >>> > > >>> > > The same for standard "B", "C" etc. >>> > > >>> > > As I want to display a movie of ligand pathways, where the ligand >>> > > moves from, say, "A1" to, say, "F3", I want in the first instance >>> > > become able to select particular residues in particular chains, >>> > > as defined by their segname. >>> > > >>> > > Could you imagine a simple way not requiring selection by atom >>> numbers? >>> > > Thanks >>> > > francesco pietra >>> > >>> > >>> > _______________________________________________ >>> > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >>> > Manage subscription: http://plato.cgl.ucsf.edu/mail >>> man/listinfo/chimera-users >>> >>> >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >> Manage subscription: http://plato.cgl.ucsf.edu/mail >> man/listinfo/chimera-users >> >> >> > >

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Trouble with Volume surface and active model not aligned
by Phan Trieu Truong 20 Oct '17

20 Oct '17

Hi, I have been using Chimera to visualize MO orbital on molecules from ORCA calculations. I have been able to visualize the MO orbitals as a surface volume from cube files. However, I just found out that when I try to reorient the molecule with the surface volume, they are no longer aligned. I don't know what I did to cause this. Any help is much appreciated. Attached is the picture of the molecules before and after I tried to reorient the molecule with the surface volume. Thank you, Phan

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Map to CCP4 Style Mask
by Martin Lawrence 20 Oct '17

20 Oct '17

Hi All, Is there a quick and easy way in Chimera to impose a density level cutoff and write out a ccp4 style mask file? Thanks, Martin Martin Lawrence Department of Chemistry and Biochemistry Montana State University Bozeman, MT 59717 USA

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