- Chimera-users - RBVI Mailing Lists

MD chimera bug
by Fabian Glaser 31 Jan '20

31 Jan '20

Dear Chimera developers, I think I have found abug in the MD movies tool in Chimera, when trying to use the Per-Frame command Script: When selecting residues > :1000 (which have a residue number > 1000) it does not select the the residue, since it adds to the residue number the frame number, for example see the figure attached, with this logic, and trying to apply the script, if the I try to select residue :1000 the script gives a mistake and this is because it tries to select residue frame + residue number (in this case 96000) which of course does not exist. The same sequence works perfectly if the selection is done outside the script Best, Fabian Best, Fabian Fabian Glaser PhD Bioinformatics Knowledge Unit - BKU The Lorry I. Lokey Center for Life Sciences and Engineering Technion - Israel Institute of Technology, Haifa, Israel Web https://lokey.technion.ac.il/bioinformatic-knowledge-unit/ <https://lokey.technion.ac.il/bioinformatic-knowledge-unit/> Tel +972 (0) 4 8293701

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conjugate moiety to protein PDB
by Michael Scott Bowers 30 Jan '20

30 Jan '20

Hi power users, I have 2 tasks that I hope you can help with. Both of these require conjugation of a moiety to multiple places on a large, multi chain protein. Command line solutions are fine. Task 1. Conjugate some group like a tosyl to selected cystine residues. There could be about 200 residues needing conjugation across 4 chains of a protein PDB file. Task 2. Conjugate a peptide chain to the N or C terminus of a multi chain protein PDB file. I am already familiar with build structure protein and smiles, but connecting models without severe steric hindrance is problematic. Also, given the number of needed conjugations, it would be great it I could do this via command line (or some other function that I am currently not aware of) so that the tosyl or peptide chains needing connecting do not have to be positioned prior to making the covalent bond. Much thanks to everyone in advance. Best, Scott

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Auto-associate define attribute/render by attribute
by Healey, Joseph 24 Jan '20

24 Jan '20

Hi Chimera team, I’m working on a script to automatically render proteins in a complex by attributes (in this case, a number of scores obtained from different immunogenicity prediction algorithms). I currently have the script outputting attribute files as intended, but ideally I’d like to define the same attributes across all the chains of the model, which are made up of a number of different proteins. Is there any way for me to define the attribute file, or utilise some functionality to auto-associate an attribute file with all of the chains which have the correct sequence (similarly to how the sequence alignment input works at the moment?). Currently the attribute file is only using ‘numbered’ coordinates (:1, :2, :3…etc) , rather than the actual sequence. Since there’s no chain information in the attribute files, I’m not sure how I can go about connecting it to the right structure, other than manually at the moment? Many thanks, Joe Dr. Joseph Healey Ph.D. M.Sc. B.Sc. (Hons) MRSB Research Fellow Warwick Medical School University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Twitter: @JRJHealey<https://twitter.com/JRJHealey> | Website<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> Email: J.Healey.1(a)warwick.ac.uk<mailto:J.Healey.1@warwick.ac.uk> | ORCID: orcid.org/0000-0002-9569-6738

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Fourier transform
by Angus McDonald 23 Jan '20

23 Jan '20

I am having trouble using the fourier transform tool in Chimera. I have tried looking for it in the Tools/Volume Data menu and I don't see it. I have also tried the start fourier which returned an error message. I suspect I am doing something wrong . Can you please help with this issue. I am using 1.13.1 build 41965 Platform Windows 64. Thanks for your help -- Angus McDonald amcdonald(a)boisestate.edu

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Can't connect to your website
by Ilona Nudelman 22 Jan '20

22 Jan '20

Hi, I am trying to connect to the UCSF Chimera website at https://www.cgl.ucsf.edu/chimera/ and it is not available with the error message "The server at www.cgl.ucsf.edu is taking too long to respond" I spoke with the IT department of my university to see if it was perhaps due to our firewall, but they say the problem is on your end. Are you guys aware of this issue? Thanks, Ilona

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save selected region to .mrc file: box size changed?
by jingchuansun 20 Jan '20

20 Jan '20

Hello, after segmentation, I can save a selected region to a .mrc file, but the box size is changed. Can I keep the original box size (and the relative position in original map)? Thanks! Jim ---------------------------------- http://www.rbvi.ucsf.edu/chimera/current/docs/UsersGuide/framecore.html Segment Map Save selected regions to .mrc file... save density map masked by the selected segmentation regions to an MRC file (map dimensions set to the minimal box containing the regions)

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Problem with autodock vina in chimera
by De campos, Luana J 17 Jan '20

17 Jan '20

Hi, I am using the option autodocking vina in chimera and I have a problem related to the docking results. I set up the docking parameters all correct and initiate the docking run. Apparently, everything goes well, I even receive a message in chimera saying that I can see the results in the directory chosen. However, when I use the option "ViewDock" I can not see the results and I get I message saying that the file .pdbt does not appear to be dock out. Also, the docking calculation goes really fast, not like before that I used to take some time. In my inspection of the .pdbqt file created in the directory from the docking calculation (using note pad) it just has the compounds and the flexible bonds, it does not have the energies of the complexes ligand-protein. Is there any way to correct this bug? Thank you very much. Luana de Campos Pharmaceutical sciences PhD. student University of Nebraska Medical Center The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.

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Placing a model at 0,0,0?
by Divjak Maja 14 Jan '20

14 Jan '20

Hi there, I'm not sure this is possible, but what I would like to do is edit molecules in Chimera, position them at 0,0,0, save the PDB and then import the molecules into Maya, so that they are positioned at 0,0,0 in the viewport, instead of in some random position away from the work grid. I can actually edit molecules, then position them by eye in the Chimera viewport and save as PDB, which will position them near the grid in roughly the right orientation when imported into Maya. So what I'm looking for is a way of setting the molecules exactly to 0,0,0 in Chimera, so that they appear at 0,0,0 when imported into Maya. I'm not sure this is actually a valid concept in Chimera? Thanks so much for your help and best wishes, Maja Disclaimer: This email (including any attachments or links) may contain confidential and/or legally privileged information and is intended only to be read or used by the addressee. If you are not the intended addressee, any use, distribution, disclosure or copying of this email is strictly prohibited. Confidentiality and legal privilege attached to this email (including any attachments) are not waived or lost by reason of its mistaken delivery to you. If you have received this email in error, please delete it and notify us immediately by telephone or email. Peter MacCallum Cancer Centre provides no guarantee that this transmission is free of virus or that it has not been intercepted or altered and will not be liable for any delay in its receipt.

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Issues with writesel
by Kevin Wang 14 Jan '20

14 Jan '20

Hi, I am trying to use the writesel command: writesel test. However, Chimera is not saving a list anywhere and I do not get an error message. Am I missing something in the command? Best, Kevin

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Chimera X commands
by Andrew Waight 14 Jan '20

14 Jan '20

Hello all, I've been an exclusive Chimera user for over 15 years. I have been scripting a lot in python lately and am super excited to learn that ChimeraX is written in python3. I totally want to import some chimera functions into my programs. Problem is, the ChimeraX command syntax seems all new (i can't even really figure out how to select properly, is there a ChimeraX command index that I am missing and is ChimeraX for me? ChimeraX looks beautiful by the way. Thanks you guys are amazing! Drew

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Fwd: Downloading HIV PDB 3j3q?
by Elaine Meng 13 Jan '20

13 Jan '20

> > From: Divjak Maja <Maja.Divjak(a)petermac.org> > Subject: Downloading HIV PDB 3j3q? > Date: April 1, 2019 at 5:23:39 AM PDT > To: Elaine Meng <meng(a)cgl.ucsf.edu> > > Hi Elaine, > > It's me again! Hope you had a nice weekend... > > I'm having some trouble downloading the HIV capsid file, PDB 3j3q. When I try to import it to Chimera it begins downloading, but the molecule never quite appears, even though it ends up in the entry list. The screen stays blue like it has yet to be uploaded. If I try to upload it from the list, again, nothing appears. I realise the molecule is very large, but I think I'm missing something important here? > > Thanks so much for your help, as always, > > Maja > > Dr Maja Divjak > BAppSc(Hons), PhD, Grad Cert 3D Animation (AFTRS) > Biomedical Animator > Office of Cancer Research > Hi Maja, (forwarding to the address that should be used for for Chimera questions) It is probably just too big for the memory on your computer to open this structure in Chimera. Depending on what you’re trying to do with this capsid, maybe you could try using ChimeraX instead of Chimera. It handles large structures much more efficiently, but it does not have the same set of features as Chimera. <http://www.rbvi.ucsf.edu/chimerax/index.html <http://www.rbvi.ucsf.edu/chimerax/index.html>> If you are just trying to get the atomic coordinates of the entire capsid, they are already in the file(s) you could download directly from the RCSB PDB without using any visualization program. <https://www.rcsb.org/structure/3j3q <https://www.rcsb.org/structure/3j3q>> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Placing a model at 0,0,0?
by Divjak Maja 13 Jan '20

13 Jan '20

Hi there, I'm not sure this is possible, but what I would like to do is edit molecules in Chimera, position them at 0,0,0, save the PDB and then import the molecules into Maya, so that they are positioned at 0,0,0 in the viewport, instead of in some random position away from the work grid. I can actually edit molecules, then position them by eye in the Chimera viewport and save as PDB, which will position them near the grid in roughly the right orientation when imported into Maya. So what I'm looking for is a way of setting the molecules exactly to 0,0,0 in Chimera, so that they appear at 0,0,0 when imported into Maya. I'm not sure this is actually a valid concept in Chimera? Thanks so much for your help and best wishes, Maja Disclaimer: This email (including any attachments or links) may contain confidential and/or legally privileged information and is intended only to be read or used by the addressee. If you are not the intended addressee, any use, distribution, disclosure or copying of this email is strictly prohibited. Confidentiality and legal privilege attached to this email (including any attachments) are not waived or lost by reason of its mistaken delivery to you. If you have received this email in error, please delete it and notify us immediately by telephone or email. Peter MacCallum Cancer Centre provides no guarantee that this transmission is free of virus or that it has not been intercepted or altered and will not be liable for any delay in its receipt.

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Selecting multiple residues in one chain
by Yehuda Halfon 12 Jan '20

12 Jan '20

HI all, I want to select and color multiple residues in one chain. When I use select #1: 15, 18, 20 .B It select 15, 18 and 20 in all the chains. But when I use select #1: 15.B, 18.B, 20.B It select 15, 18 and 20 in chain B. Is there another way to select residues in one chain without adding .B after each one? It makes the script much bigger and less clean. Yehuda

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Re: [Chimera-users] Chimera on macOS Catalina (10.15)
by Chiara Rapisarda 10 Jan '20

10 Jan '20

Hello, I arrive a bit late to the discussion. After the Catalina upgrade, the open button in chimera is greyed out and I cannot open more than one file at any one time. Would anybody have any idea what is wrong? I have downloaded the latest build of chimera. Thank you for your help. Best, Chiara

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Electrostatic Potential
by Fernando Villa 10 Jan '20

10 Jan '20

Dear all Chimera users In UCSF ChimeraX version 0.91 (2019-08-30) I opened a .pqr file (generated with pdb2pqr in Chimera 1.14) and then I opened a .dx file (generated with APBS in Chimera 1.14) Then I input the commands: >surface >color electrostatic #1 map #2 palette -10,red:0,white:10,blue [image: image.png] Is it possible to calculate the red and blue area in Å2 of the molecule? Best regards, Fernando ATTE Fernando Villa Díaz

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Fit model and density map
by Guo, Wangbiao 02 Jan '20

02 Jan '20

Is there any one knows how to fit the density map to this red model? [cid:71FF4B2F-87EA-443B-B280-CE3ABEA9B11B@its.yale.internal] On Dec 24, 2019, at 12:26 PM, chimera-users-request(a)cgl.ucsf.edu<mailto:chimera-users-request@cgl.ucsf.edu> wrote: Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> To subscribe or unsubscribe via the World Wide Web, visit https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fplato.cgl.… 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: Problem with DelPhi in chimera (labe boye) (Boaz Shaanan) - correction (Boaz Shaanan) ---------------------------------------------------------------------- Message: 1 Date: Tue, 24 Dec 2019 17:26:14 +0000 From: Boaz Shaanan <bshaanan(a)bgu.ac.il> To: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Problem with DelPhi in chimera (labe boye) (Boaz Shaanan) - correction Message-ID: <81ea8ecae3d04575b9c13ac2142612bf(a)bgu.ac.il> Content-Type: text/plain; charset="windows-1255" In my previous message I meant of course linux Delphi v.6. Sorry. 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: Tuesday, December 24, 2019 7:10 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 200, Issue 20 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fplato.cgl.… 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: Problem with DelPhi in chimera (labe boye) (Boaz Shaanan) ---------------------------------------------------------------------- Message: 1 Date: Tue, 24 Dec 2019 17:09:46 +0000 From: Boaz Shaanan <bshaanan(a)bgu.ac.il> To: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Problem with DelPhi in chimera (labe boye) Message-ID: <a2abfa7a83394a56b27584878c181426(a)bgu.ac.il> Content-Type: text/plain; charset="windows-1255" Hi, The Chimera v.6 that I used was the linux version NOT windows. The answer you got from the Delphi people sounds familiar to me which is why I switched to APBS interface on Chimera (works on both Windows and linux). The .dx file produced by APBS is read and contoured nicely by Chimera. If you need to ionize the structure, there is a Windows PDB2PQR executable as mentioned by Elaine (I understand that you're using Windows). 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: Tuesday, December 24, 2019 6:34 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 200, Issue 19 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fplato.cgl.… 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: Problem with DelPhi in chimera (Elaine Meng) 2. Re: Chimera-users Digest, Vol 200, Issue 18 (Boaz Shaanan) 3. Re: Problem with DelPhi in chimera (Elaine Meng) ---------------------------------------------------------------------- Message: 1 Date: Mon, 23 Dec 2019 12:55:29 -0800 From: Elaine Meng <meng(a)cgl.ucsf.edu> To: "sintaspirulina(a)gmail.com" <sintaspirulina(a)gmail.com> Cc: Chimera BB <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Problem with DelPhi in chimera Message-ID: <B59A5D0E-CA80-4151-9CD6-11B33435CA4A(a)cgl.ucsf.edu> Content-Type: text/plain; charset=utf-8 We saw your Chimera bug report. However, the file you attached was not the ?.phi? file (electrostatic potential map) output from DelPhi. It was just the text output from the DelPhi program. If DelPhi runs successfully on your structure, it will create a separate file, with name ending in .phi, that is the electrostatic potential map. If by ?cube? you mean Gaussian cube grid, Chimera does read that format. <https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.u…> However, this format is handled simply as a map that is not necessarily electrostatic potential, so it would require more steps in Chimera to get the coloring you want. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco On Dec 23, 2019, at 10:01 AM, sintaspirulina(a)gmail.com wrote: OK, I tried all the three academic versions of DelPhi for windows; and none is working for me. I contacted the DelPhi supporters and SUGGESTED to use CUBE output format which isn't possible in Chimera. In the mean time, the two Chimera versions I installed read 3eeb.phi file from the tutorial. I will report the problem. regards, Sintayehu M. Shenkutie, Dr. rer. nat. Assistant Professor of Biochemistry. Department of Chemistry Hawassa University Ethiopia Mobile: +251902432925 Email: dr.sintayehu(a)hu.edu.et Sintayehu.M.Shenkutie(a)bot3.bio.uni-giessen.de On Monday, December 23, 2019, 08:30:26 PM GMT+3, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: It should be any DelPhi version that you get from the academic website, which was a link in this page I sent earlier: The DelPhi files that Chimera can read are from the academic version of DelPhi, as mentioned here: <https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.u…> ?specifically this is their academic website <https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fcompbio.cl…> I don?t remember what version I used several years ago to make 3eebB.phi, but as far as I know the format didn?t change. It is possible it changed and we didn?t know about it, but we would need example(s) of the files. If you believe you used the academic version of DelPhi but you get the error opening the phi file, you could try using Chimera menu Help? Report a Bug and attach your phi file so we could take a look at it. However, that does not guarantee it will be possible to fix. I hope this helps, Elaine On Dec 22, 2019, at 4:23 AM, labe boye <sintaspirulina(a)gmail.com> wrote: Hi Thank you for your reply. Could you please let me know which version of DelPhi academic version is compatible with Chimera? Which DelPhi version was used to generate the 3eeb.phi file in the tutorial? kindest regards, On Fri, Dec 20, 2019 at 11:16 PM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: Hi, Chimera is saying that your phi file output from Delphi contains inconsistent information, like maybe it got truncated. I do not know if it is possible to fix the phi file, sorry. The DelPhi files that Chimera can read are from the academic version of DelPhi, as mentioned here: <https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.u…> If you have some other version of DelPhi associated with a commercial package, maybe the format is different and Chimera does not know how to read it. Linked to the last section of this tutorial, there is an example DelPhi phi file (3eebB.phi) that Chimera can read: <https://nam05.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 Dec 20, 2019, at 10:33 AM, labe boye <sintaspirulina(a)gmail.com> wrote: Hi, I use windows, UCSF Chimera 1.14 and tried all versions of DelPhi for windows but I get the following error Error reading file default.phi, format delphi Record size > file size What is the solution? regards, -- Sintayehu M. Shenkutie, Dr. rer. nat. Assistant Professor of Biochemistry. Department of Chemistry Hawassa University Ethiopia Mobile: +251902432925 Email: dr.sintayehu(a)hu.edu.et Sintayehu.M.Shenkutie(a)bot3.bio.uni-giessen.de The bamboo that bends is stronger than the oak that resists _______________________________________________ Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu Manage subscription: https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fplato.cgl.… _______________________________________________ Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu Manage subscription: https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fplato.cgl.… ------------------------------ Message: 2 Date: Mon, 23 Dec 2019 21:21:35 +0000 From: Boaz Shaanan <bshaanan(a)bgu.ac.il> To: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Chimera-users Digest, Vol 200, Issue 18 Message-ID: <d539fbf953d74b6783b5dc0a632313d3(a)bgu.ac.il> Content-Type: text/plain; charset="windows-1255" Hi, I ran into this Chimera/Delphi problem a few months ago (and discussed it with the Chimera/Delphi people). The latest Delphi version that I tried (8.4) produced a cube format file which formally can be read and contoured in the Chimera volume viewer. I hated the way the electrostatic surface produced that way looked and abandoned it. Delphi v. 6 which I have (and which I think Elaine used 3 years ago) produced the good old .phi which is file properly displayed in Chimera . I think one can still get hold of V.6 from the Delphi distribution site. To avoid this mess I used the APBS interface of Chimera which worked fine and produced a nice, familiar style, looking electrostatic surface (see for example Fig. S10 in the supplementary of doi: 10.1093/nar/gkz604). 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 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: Monday, December 23, 2019 10:48 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 200, Issue 18 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fplato.cgl.… 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: Problem with DelPhi in chimera (Elaine Meng) 2. need your assistance (Asmi Mahmood) 3. Re: Problem with DelPhi in chimera (labe boye) 4. Re: Problem with DelPhi in chimera (Elaine Meng) 5. dock prep for many ligands (Elaine Meng) 6. Re: Problem with DelPhi in chimera (sintaspirulina(a)gmail.com) ---------------------------------------------------------------------- Message: 1 Date: Fri, 20 Dec 2019 12:16:20 -0800 From: Elaine Meng <meng(a)cgl.ucsf.edu> To: labe boye <sintaspirulina(a)gmail.com> Cc: chimera-users(a)cgl.ucsf.edu Subject: Re: [Chimera-users] Problem with DelPhi in chimera Message-ID: <1158BCF0-F94F-4B55-98DA-27166E19CEDC(a)cgl.ucsf.edu> Content-Type: text/plain; charset=us-ascii Hi, Chimera is saying that your phi file output from Delphi contains inconsistent information, like maybe it got truncated. I do not know if it is possible to fix the phi file, sorry. The DelPhi files that Chimera can read are from the academic version of DelPhi, as mentioned here: <https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.u…> If you have some other version of DelPhi associated with a commercial package, maybe the format is different and Chimera does not know how to read it. Linked to the last section of this tutorial, there is an example DelPhi phi file (3eebB.phi) that Chimera can read: <https://nam05.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 Dec 20, 2019, at 10:33 AM, labe boye <sintaspirulina(a)gmail.com> wrote: Hi, I use windows, UCSF Chimera 1.14 and tried all versions of DelPhi for windows but I get the following error Error reading file default.phi, format delphi Record size > file size What is the solution? regards, ------------------------------ Message: 2 Date: Sat, 21 Dec 2019 15:10:00 +0000 (UTC) From: Asmi Mahmood <asmi_mahmood(a)yahoo.com> To: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu>, "chimera-bugs(a)cgl.ucsf.edu" <chimera-bugs(a)cgl.ucsf.edu> Subject: [Chimera-users] need your assistance Message-ID: <844676351.2239559.1576941000519(a)mail.yahoo.com> Content-Type: text/plain; charset="utf-8" Hi Hope you are doing good. I need your assistance regarding chimera. I'm working on virtual docking and need to prepare more than 10k ligands (in a single file as SDF) for docking process. I need to know that if chimera desktop latest version can fulfill my need. If yes please give me a tutorial pdf or video. Regards Waiting for a quick response Asma Tariq

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need your assistance
by Asmi Mahmood 30 Dec '19

30 Dec '19

Hi Hope you are doing good. I need your assistance regarding chimera. I'm working on virtual docking and need to prepare more than 10k ligands (in a single file as SDF) for docking process. I need to know that if chimera desktop latest version can fulfill my need. If yes please give me a tutorial pdf or video. Regards Waiting for a quick response Asma Tariq

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Re: [Chimera-users] Problem with DelPhi in chimera
by Elaine Meng 24 Dec '19

24 Dec '19

Hello, That sounds like a problem with your DelPhi setup, or you didn’t wait long enough for the calculation to finish. Sometimes it takes several minutes. Instead of DelPhi, you could try using PDB2PQR and then (on the resulting pqr file) using APBS. Chimera has interfaces to both of these: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/apbs/pdb2pqr.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/apbs/apbs.html> …or you can use their web server directly, outside of Chimera: <http://nbcr-222.ucsd.edu/pdb2pqr_2.1.1/> <https://apbs-pdb2pqr.readthedocs.io/en/latest/downloads.html#web-servers> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 23, 2019, at 9:45 PM, sintaspirulina(a)gmail.com wrote: > > FYI > I tried DelPhi for windows F95 v6 as suggested by Boaz S. but in my case the out put .phi is empty file not even truncated. > regards, > Sintayehu M. Shenkutie, Dr. rer. nat. > Assistant Professor of Biochemistry. > Department of Chemistry > Hawassa University > Ethiopia > Mobile: +251902432925 > Email: dr.sintayehu(a)hu.edu.et > Sintayehu.M.Shenkutie(a)bot3.bio.uni-giessen.de > > On Tuesday, December 24, 2019, 08:13:52 AM GMT+3, sintaspirulina(a)gmail.com <sintaspirulina(a)gmail.com> wrote: > > Hello again, > Thank you very much for your reply. > For the bug report, my bad I might have attached the wrong file. I repeated the same thing with the .phi file. The email from another user, that is probably helpful. I will see if I can get the old DelPhi version. > kindest regards, > > > On Tuesday, December 24, 2019, 12:27:54 AM GMT+3, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > > In case you didn’t see it, another user says this: > >> Begin forwarded message: >> >> From: Boaz Shaanan <bshaanan(a)bgu.ac.il> >> Subject: Re: [Chimera-users] Chimera-users Digest, Vol 200, Issue 18 >> Date: December 23, 2019 at 1:21:35 PM PST >> To: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> >> >> Hi, >> >> I ran into this Chimera/Delphi problem a few months ago (and discussed it with the Chimera/Delphi people). The latest Delphi version that I tried (8.4) produced a cube format file which formally can be read and contoured in the Chimera volume viewer. I hated the way the electrostatic surface produced that way looked and abandoned it. Delphi v. 6 which I have (and which I think Elaine used 3 years ago) produced the good old .phi which is file properly displayed in Chimera . I think one can still get hold of V.6 from the Delphi distribution site. >> >> To avoid this mess I used the APBS interface of Chimera which worked fine and produced a nice, familiar style, looking electrostatic surface (see for example Fig. S10 in the supplementary of doi: 10.1093/nar/gkz604). >> >> Regards, >> Boaz >>

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Re: [Chimera-users] Problem with DelPhi in chimera (labe boye) (Boaz Shaanan) - correction
by Boaz Shaanan 24 Dec '19

24 Dec '19

In my previous message I meant of course linux Delphi v.6. Sorry. 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: Tuesday, December 24, 2019 7:10 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 200, Issue 20 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: Problem with DelPhi in chimera (labe boye) (Boaz Shaanan) ---------------------------------------------------------------------- Message: 1 Date: Tue, 24 Dec 2019 17:09:46 +0000 From: Boaz Shaanan <bshaanan(a)bgu.ac.il> To: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Problem with DelPhi in chimera (labe boye) Message-ID: <a2abfa7a83394a56b27584878c181426(a)bgu.ac.il> Content-Type: text/plain; charset="windows-1255" Hi, The Chimera v.6 that I used was the linux version NOT windows. The answer you got from the Delphi people sounds familiar to me which is why I switched to APBS interface on Chimera (works on both Windows and linux). The .dx file produced by APBS is read and contoured nicely by Chimera. If you need to ionize the structure, there is a Windows PDB2PQR executable as mentioned by Elaine (I understand that you're using Windows). 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: Tuesday, December 24, 2019 6:34 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 200, Issue 19 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: Problem with DelPhi in chimera (Elaine Meng) 2. Re: Chimera-users Digest, Vol 200, Issue 18 (Boaz Shaanan) 3. Re: Problem with DelPhi in chimera (Elaine Meng) ---------------------------------------------------------------------- Message: 1 Date: Mon, 23 Dec 2019 12:55:29 -0800 From: Elaine Meng <meng(a)cgl.ucsf.edu> To: "sintaspirulina(a)gmail.com" <sintaspirulina(a)gmail.com> Cc: Chimera BB <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Problem with DelPhi in chimera Message-ID: <B59A5D0E-CA80-4151-9CD6-11B33435CA4A(a)cgl.ucsf.edu> Content-Type: text/plain; charset=utf-8 We saw your Chimera bug report. However, the file you attached was not the ?.phi? file (electrostatic potential map) output from DelPhi. It was just the text output from the DelPhi program. If DelPhi runs successfully on your structure, it will create a separate file, with name ending in .phi, that is the electrostatic potential map. If by ?cube? you mean Gaussian cube grid, Chimera does read that format. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#volume> However, this format is handled simply as a map that is not necessarily electrostatic potential, so it would require more steps in Chimera to get the coloring you want. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 23, 2019, at 10:01 AM, sintaspirulina(a)gmail.com wrote: > > OK, > I tried all the three academic versions of DelPhi for windows; and none is working for me. I contacted the DelPhi supporters and SUGGESTED to use CUBE output format which isn't possible in Chimera. In the mean time, the two Chimera versions I installed read 3eeb.phi file from the tutorial. > I will report the problem. > regards, > > Sintayehu M. Shenkutie, Dr. rer. nat. > Assistant Professor of Biochemistry. > Department of Chemistry > Hawassa University > Ethiopia > Mobile: +251902432925 > Email: dr.sintayehu(a)hu.edu.et > Sintayehu.M.Shenkutie(a)bot3.bio.uni-giessen.de > > > > > On Monday, December 23, 2019, 08:30:26 PM GMT+3, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > > It should be any DelPhi version that you get from the academic website, which was a link in this page I sent earlier: > > > The DelPhi files that Chimera can read are from the academic version of DelPhi, as mentioned here: > > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#esp> > > ?specifically this is their academic website <http://compbio.clemson.edu/delphi> > > I don?t remember what version I used several years ago to make 3eebB.phi, but as far as I know the format didn?t change. It is possible it changed and we didn?t know about it, but we would need example(s) of the files. > > If you believe you used the academic version of DelPhi but you get the error opening the phi file, you could try using Chimera menu Help? Report a Bug and attach your phi file so we could take a look at it. However, that does not guarantee it will be possible to fix. > > I hope this helps, > Elaine > > > On Dec 22, 2019, at 4:23 AM, labe boye <sintaspirulina(a)gmail.com> wrote: > > > > Hi > > Thank you for your reply. > > Could you please let me know which version of DelPhi academic version is compatible with Chimera? Which DelPhi version was used to generate the 3eeb.phi file in the tutorial? > > kindest regards, > > > > On Fri, Dec 20, 2019 at 11:16 PM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > Hi, > > Chimera is saying that your phi file output from Delphi contains inconsistent information, like maybe it got truncated. I do not know if it is possible to fix the phi file, sorry. > > > > The DelPhi files that Chimera can read are from the academic version of DelPhi, as mentioned here: > > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#esp> > > > > If you have some other version of DelPhi associated with a commercial package, maybe the format is different and Chimera does not know how to read it. > > > > Linked to the last section of this tutorial, there is an example DelPhi phi file (3eebB.phi) that Chimera can read: > > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html> > > > > I hope this helps, > > Elaine > > ----- > > Elaine C. Meng, Ph.D. > > UCSF Chimera(X) team > > Department of Pharmaceutical Chemistry > > University of California, San Francisco > > > > > On Dec 20, 2019, at 10:33 AM, labe boye <sintaspirulina(a)gmail.com> wrote: > > > > > > Hi, > > > I use windows, UCSF Chimera 1.14 and tried all versions of DelPhi for windows but I get the following error > > > Error reading file default.phi, format delphi > > > Record size > file size > > > What is the solution? > > > regards, > > > > > > > > > > > -- > > Sintayehu M. Shenkutie, Dr. rer. nat. > > Assistant Professor of Biochemistry. > > Department of Chemistry > > Hawassa University > > Ethiopia > > Mobile: +251902432925 > > Email: dr.sintayehu(a)hu.edu.et > > Sintayehu.M.Shenkutie(a)bot3.bio.uni-giessen.de > > > > The bamboo that bends is stronger than the oak that resists > > > _______________________________________________ > > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users ------------------------------ Message: 2 Date: Mon, 23 Dec 2019 21:21:35 +0000 From: Boaz Shaanan <bshaanan(a)bgu.ac.il> To: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Chimera-users Digest, Vol 200, Issue 18 Message-ID: <d539fbf953d74b6783b5dc0a632313d3(a)bgu.ac.il> Content-Type: text/plain; charset="windows-1255" Hi, I ran into this Chimera/Delphi problem a few months ago (and discussed it with the Chimera/Delphi people). The latest Delphi version that I tried (8.4) produced a cube format file which formally can be read and contoured in the Chimera volume viewer. I hated the way the electrostatic surface produced that way looked and abandoned it. Delphi v. 6 which I have (and which I think Elaine used 3 years ago) produced the good old .phi which is file properly displayed in Chimera . I think one can still get hold of V.6 from the Delphi distribution site. To avoid this mess I used the APBS interface of Chimera which worked fine and produced a nice, familiar style, looking electrostatic surface (see for example Fig. S10 in the supplementary of doi: 10.1093/nar/gkz604). 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 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: Monday, December 23, 2019 10:48 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 200, Issue 18 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: Problem with DelPhi in chimera (Elaine Meng) 2. need your assistance (Asmi Mahmood) 3. Re: Problem with DelPhi in chimera (labe boye) 4. Re: Problem with DelPhi in chimera (Elaine Meng) 5. dock prep for many ligands (Elaine Meng) 6. Re: Problem with DelPhi in chimera (sintaspirulina(a)gmail.com) ---------------------------------------------------------------------- Message: 1 Date: Fri, 20 Dec 2019 12:16:20 -0800 From: Elaine Meng <meng(a)cgl.ucsf.edu> To: labe boye <sintaspirulina(a)gmail.com> Cc: chimera-users(a)cgl.ucsf.edu Subject: Re: [Chimera-users] Problem with DelPhi in chimera Message-ID: <1158BCF0-F94F-4B55-98DA-27166E19CEDC(a)cgl.ucsf.edu> Content-Type: text/plain; charset=us-ascii Hi, Chimera is saying that your phi file output from Delphi contains inconsistent information, like maybe it got truncated. I do not know if it is possible to fix the phi file, sorry. The DelPhi files that Chimera can read are from the academic version of DelPhi, as mentioned here: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#esp> If you have some other version of DelPhi associated with a commercial package, maybe the format is different and Chimera does not know how to read it. Linked to the last section of this tutorial, there is an example DelPhi phi file (3eebB.phi) that Chimera can read: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 20, 2019, at 10:33 AM, labe boye <sintaspirulina(a)gmail.com> wrote: > > Hi, > I use windows, UCSF Chimera 1.14 and tried all versions of DelPhi for windows but I get the following error > Error reading file default.phi, format delphi > Record size > file size > What is the solution? > regards, > ------------------------------ Message: 2 Date: Sat, 21 Dec 2019 15:10:00 +0000 (UTC) From: Asmi Mahmood <asmi_mahmood(a)yahoo.com> To: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu>, "chimera-bugs(a)cgl.ucsf.edu" <chimera-bugs(a)cgl.ucsf.edu> Subject: [Chimera-users] need your assistance Message-ID: <844676351.2239559.1576941000519(a)mail.yahoo.com> Content-Type: text/plain; charset="utf-8" Hi Hope you are doing good. I need your assistance regarding chimera. I'm working on virtual docking and need to prepare more than 10k ligands (in a single file as SDF) for docking process. I need to know that if chimera desktop latest version can fulfill my need. If yes please give me a tutorial pdf or video. Regards Waiting for a quick response Asma Tariq

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Re: [Chimera-users] Problem with DelPhi in chimera (labe boye)
by Boaz Shaanan 24 Dec '19

24 Dec '19

Hi, The Chimera v.6 that I used was the linux version NOT windows. The answer you got from the Delphi people sounds familiar to me which is why I switched to APBS interface on Chimera (works on both Windows and linux). The .dx file produced by APBS is read and contoured nicely by Chimera. If you need to ionize the structure, there is a Windows PDB2PQR executable as mentioned by Elaine (I understand that you're using Windows). 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: Tuesday, December 24, 2019 6:34 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 200, Issue 19 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: Problem with DelPhi in chimera (Elaine Meng) 2. Re: Chimera-users Digest, Vol 200, Issue 18 (Boaz Shaanan) 3. Re: Problem with DelPhi in chimera (Elaine Meng) ---------------------------------------------------------------------- Message: 1 Date: Mon, 23 Dec 2019 12:55:29 -0800 From: Elaine Meng <meng(a)cgl.ucsf.edu> To: "sintaspirulina(a)gmail.com" <sintaspirulina(a)gmail.com> Cc: Chimera BB <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Problem with DelPhi in chimera Message-ID: <B59A5D0E-CA80-4151-9CD6-11B33435CA4A(a)cgl.ucsf.edu> Content-Type: text/plain; charset=utf-8 We saw your Chimera bug report. However, the file you attached was not the ?.phi? file (electrostatic potential map) output from DelPhi. It was just the text output from the DelPhi program. If DelPhi runs successfully on your structure, it will create a separate file, with name ending in .phi, that is the electrostatic potential map. If by ?cube? you mean Gaussian cube grid, Chimera does read that format. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#volume> However, this format is handled simply as a map that is not necessarily electrostatic potential, so it would require more steps in Chimera to get the coloring you want. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 23, 2019, at 10:01 AM, sintaspirulina(a)gmail.com wrote: > > OK, > I tried all the three academic versions of DelPhi for windows; and none is working for me. I contacted the DelPhi supporters and SUGGESTED to use CUBE output format which isn't possible in Chimera. In the mean time, the two Chimera versions I installed read 3eeb.phi file from the tutorial. > I will report the problem. > regards, > > Sintayehu M. Shenkutie, Dr. rer. nat. > Assistant Professor of Biochemistry. > Department of Chemistry > Hawassa University > Ethiopia > Mobile: +251902432925 > Email: dr.sintayehu(a)hu.edu.et > Sintayehu.M.Shenkutie(a)bot3.bio.uni-giessen.de > > > > > On Monday, December 23, 2019, 08:30:26 PM GMT+3, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > > It should be any DelPhi version that you get from the academic website, which was a link in this page I sent earlier: > > > The DelPhi files that Chimera can read are from the academic version of DelPhi, as mentioned here: > > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#esp> > > ?specifically this is their academic website <http://compbio.clemson.edu/delphi> > > I don?t remember what version I used several years ago to make 3eebB.phi, but as far as I know the format didn?t change. It is possible it changed and we didn?t know about it, but we would need example(s) of the files. > > If you believe you used the academic version of DelPhi but you get the error opening the phi file, you could try using Chimera menu Help? Report a Bug and attach your phi file so we could take a look at it. However, that does not guarantee it will be possible to fix. > > I hope this helps, > Elaine > > > On Dec 22, 2019, at 4:23 AM, labe boye <sintaspirulina(a)gmail.com> wrote: > > > > Hi > > Thank you for your reply. > > Could you please let me know which version of DelPhi academic version is compatible with Chimera? Which DelPhi version was used to generate the 3eeb.phi file in the tutorial? > > kindest regards, > > > > On Fri, Dec 20, 2019 at 11:16 PM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > Hi, > > Chimera is saying that your phi file output from Delphi contains inconsistent information, like maybe it got truncated. I do not know if it is possible to fix the phi file, sorry. > > > > The DelPhi files that Chimera can read are from the academic version of DelPhi, as mentioned here: > > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#esp> > > > > If you have some other version of DelPhi associated with a commercial package, maybe the format is different and Chimera does not know how to read it. > > > > Linked to the last section of this tutorial, there is an example DelPhi phi file (3eebB.phi) that Chimera can read: > > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html> > > > > I hope this helps, > > Elaine > > ----- > > Elaine C. Meng, Ph.D. > > UCSF Chimera(X) team > > Department of Pharmaceutical Chemistry > > University of California, San Francisco > > > > > On Dec 20, 2019, at 10:33 AM, labe boye <sintaspirulina(a)gmail.com> wrote: > > > > > > Hi, > > > I use windows, UCSF Chimera 1.14 and tried all versions of DelPhi for windows but I get the following error > > > Error reading file default.phi, format delphi > > > Record size > file size > > > What is the solution? > > > regards, > > > > > > > > > > > -- > > Sintayehu M. Shenkutie, Dr. rer. nat. > > Assistant Professor of Biochemistry. > > Department of Chemistry > > Hawassa University > > Ethiopia > > Mobile: +251902432925 > > Email: dr.sintayehu(a)hu.edu.et > > Sintayehu.M.Shenkutie(a)bot3.bio.uni-giessen.de > > > > The bamboo that bends is stronger than the oak that resists > > > _______________________________________________ > > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users ------------------------------ Message: 2 Date: Mon, 23 Dec 2019 21:21:35 +0000 From: Boaz Shaanan <bshaanan(a)bgu.ac.il> To: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Chimera-users Digest, Vol 200, Issue 18 Message-ID: <d539fbf953d74b6783b5dc0a632313d3(a)bgu.ac.il> Content-Type: text/plain; charset="windows-1255" Hi, I ran into this Chimera/Delphi problem a few months ago (and discussed it with the Chimera/Delphi people). The latest Delphi version that I tried (8.4) produced a cube format file which formally can be read and contoured in the Chimera volume viewer. I hated the way the electrostatic surface produced that way looked and abandoned it. Delphi v. 6 which I have (and which I think Elaine used 3 years ago) produced the good old .phi which is file properly displayed in Chimera . I think one can still get hold of V.6 from the Delphi distribution site. To avoid this mess I used the APBS interface of Chimera which worked fine and produced a nice, familiar style, looking electrostatic surface (see for example Fig. S10 in the supplementary of doi: 10.1093/nar/gkz604). 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 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: Monday, December 23, 2019 10:48 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 200, Issue 18 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: Problem with DelPhi in chimera (Elaine Meng) 2. need your assistance (Asmi Mahmood) 3. Re: Problem with DelPhi in chimera (labe boye) 4. Re: Problem with DelPhi in chimera (Elaine Meng) 5. dock prep for many ligands (Elaine Meng) 6. Re: Problem with DelPhi in chimera (sintaspirulina(a)gmail.com) ---------------------------------------------------------------------- Message: 1 Date: Fri, 20 Dec 2019 12:16:20 -0800 From: Elaine Meng <meng(a)cgl.ucsf.edu> To: labe boye <sintaspirulina(a)gmail.com> Cc: chimera-users(a)cgl.ucsf.edu Subject: Re: [Chimera-users] Problem with DelPhi in chimera Message-ID: <1158BCF0-F94F-4B55-98DA-27166E19CEDC(a)cgl.ucsf.edu> Content-Type: text/plain; charset=us-ascii Hi, Chimera is saying that your phi file output from Delphi contains inconsistent information, like maybe it got truncated. I do not know if it is possible to fix the phi file, sorry. The DelPhi files that Chimera can read are from the academic version of DelPhi, as mentioned here: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#esp> If you have some other version of DelPhi associated with a commercial package, maybe the format is different and Chimera does not know how to read it. Linked to the last section of this tutorial, there is an example DelPhi phi file (3eebB.phi) that Chimera can read: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 20, 2019, at 10:33 AM, labe boye <sintaspirulina(a)gmail.com> wrote: > > Hi, > I use windows, UCSF Chimera 1.14 and tried all versions of DelPhi for windows but I get the following error > Error reading file default.phi, format delphi > Record size > file size > What is the solution? > regards, > ------------------------------ Message: 2 Date: Sat, 21 Dec 2019 15:10:00 +0000 (UTC) From: Asmi Mahmood <asmi_mahmood(a)yahoo.com> To: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu>, "chimera-bugs(a)cgl.ucsf.edu" <chimera-bugs(a)cgl.ucsf.edu> Subject: [Chimera-users] need your assistance Message-ID: <844676351.2239559.1576941000519(a)mail.yahoo.com> Content-Type: text/plain; charset="utf-8" Hi Hope you are doing good. I need your assistance regarding chimera. I'm working on virtual docking and need to prepare more than 10k ligands (in a single file as SDF) for docking process. I need to know that if chimera desktop latest version can fulfill my need. If yes please give me a tutorial pdf or video. Regards Waiting for a quick response Asma Tariq

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Re: [Chimera-users] Chimera-users Digest, Vol 200, Issue 18
by Boaz Shaanan 23 Dec '19

23 Dec '19

Hi, I ran into this Chimera/Delphi problem a few months ago (and discussed it with the Chimera/Delphi people). The latest Delphi version that I tried (8.4) produced a cube format file which formally can be read and contoured in the Chimera volume viewer. I hated the way the electrostatic surface produced that way looked and abandoned it. Delphi v. 6 which I have (and which I think Elaine used 3 years ago) produced the good old .phi which is file properly displayed in Chimera . I think one can still get hold of V.6 from the Delphi distribution site. To avoid this mess I used the APBS interface of Chimera which worked fine and produced a nice, familiar style, looking electrostatic surface (see for example Fig. S10 in the supplementary of doi: 10.1093/nar/gkz604). 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 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: Monday, December 23, 2019 10:48 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 200, Issue 18 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: Problem with DelPhi in chimera (Elaine Meng) 2. need your assistance (Asmi Mahmood) 3. Re: Problem with DelPhi in chimera (labe boye) 4. Re: Problem with DelPhi in chimera (Elaine Meng) 5. dock prep for many ligands (Elaine Meng) 6. Re: Problem with DelPhi in chimera (sintaspirulina(a)gmail.com) ---------------------------------------------------------------------- Message: 1 Date: Fri, 20 Dec 2019 12:16:20 -0800 From: Elaine Meng <meng(a)cgl.ucsf.edu> To: labe boye <sintaspirulina(a)gmail.com> Cc: chimera-users(a)cgl.ucsf.edu Subject: Re: [Chimera-users] Problem with DelPhi in chimera Message-ID: <1158BCF0-F94F-4B55-98DA-27166E19CEDC(a)cgl.ucsf.edu> Content-Type: text/plain; charset=us-ascii Hi, Chimera is saying that your phi file output from Delphi contains inconsistent information, like maybe it got truncated. I do not know if it is possible to fix the phi file, sorry. The DelPhi files that Chimera can read are from the academic version of DelPhi, as mentioned here: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#esp> If you have some other version of DelPhi associated with a commercial package, maybe the format is different and Chimera does not know how to read it. Linked to the last section of this tutorial, there is an example DelPhi phi file (3eebB.phi) that Chimera can read: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 20, 2019, at 10:33 AM, labe boye <sintaspirulina(a)gmail.com> wrote: > > Hi, > I use windows, UCSF Chimera 1.14 and tried all versions of DelPhi for windows but I get the following error > Error reading file default.phi, format delphi > Record size > file size > What is the solution? > regards, > ------------------------------ Message: 2 Date: Sat, 21 Dec 2019 15:10:00 +0000 (UTC) From: Asmi Mahmood <asmi_mahmood(a)yahoo.com> To: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu>, "chimera-bugs(a)cgl.ucsf.edu" <chimera-bugs(a)cgl.ucsf.edu> Subject: [Chimera-users] need your assistance Message-ID: <844676351.2239559.1576941000519(a)mail.yahoo.com> Content-Type: text/plain; charset="utf-8" Hi Hope you are doing good. I need your assistance regarding chimera. I'm working on virtual docking and need to prepare more than 10k ligands (in a single file as SDF) for docking process. I need to know that if chimera desktop latest version can fulfill my need. If yes please give me a tutorial pdf or video. Regards Waiting for a quick response Asma Tariq

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Problem with DelPhi in chimera
by labe boye 23 Dec '19

23 Dec '19

Hi, I use windows, UCSF Chimera 1.14 and tried all versions of DelPhi for windows but I get the following error Error reading file default.phi, format delphi Record size > file size What is the solution? regards, -- Sintayehu M. Shenkutie, Dr. rer. nat. Assistant Professor of Biochemistry. Department of Chemistry Hawassa University Ethiopia Mobile: +251902432925 Email: dr.sintayehu(a)hu.edu.et Sintayehu.M.Shenkutie(a)bot3.bio.uni-giessen.de *The bamboo that bends is stronger than the oak that resists *

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problems with multifit in chimera
by Nimit Jain 16 Dec '19

16 Dec '19

Hello I have recently been encountering problems with MultiFit within Chimera on both Ubuntu and Windows 10 (trace from reply log below--I get the same error on both operating systems). Even fitting with datasets that was working earlier in the year (~August-September) is not working anymore. My guess is that some changes have happened on the server that hosts Multifit. Could someone please try and reproduce the bug and let me know how I should troubleshoot this? I am trying to fit a single protein structure to an EM map and as I said, this was working earlier this year. I also tried downloading IMP on my Windows machine and using MultiFit from in there. This was running into some separate issues which I will not go into here since they are not directly related to Chimera. Thanks and best Nimit Trace from reply log: Application stderr ----- Traceback (most recent call last): File "/home/socr/a/yz/local/imp-repository/modules/multifit2/bin/generate_assembly_input.py", line 2, in <module> import IMP.multifit File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 25, in <module> _IMP_multifit = swig_import_helper() File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 17, in swig_import_helper import _IMP_multifit ImportError: libfftw3.so.3: cannot open shared object file: No such file or directory Traceback (most recent call last): File "/home/socr/a/yz/local/imp-repository/modules/multifit2/bin/create_all_surfaces.py", line 2, in <module> import IMP.multifit File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 25, in <module> _IMP_multifit = swig_import_helper() File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 17, in swig_import_helper import _IMP_multifit ImportError: libfftw3.so.3: cannot open shared object file: No such file or directory Traceback (most recent call last): File "/home/socr/a/yz/local/imp-repository/modules/multifit2/bin/generate_assembly_anchor_graph.py", line 3, in <module> import IMP.multifit File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 25, in <module> _IMP_multifit = swig_import_helper() File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 17, in swig_import_helper import _IMP_multifit ImportError: libfftw3.so.3: cannot open shared object file: No such file or directory Traceback (most recent call last): File "/home/socr/a/yz/local/imp-repository/modules/multifit2/bin/run_fitting_fft.py", line 2, in <module> import IMP.multifit File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 25, in <module> _IMP_multifit = swig_import_helper() File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 17, in swig_import_helper import _IMP_multifit ImportError: libfftw3.so.3: cannot open shared object file: No such file or directory Traceback (most recent call last): File "/home/socr/a/yz/local/imp-repository/modules/multifit2/bin/generate_indexes_from_fitting_solutions.py", line 2, in <module> import IMP.multifit File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 25, in <module> _IMP_multifit = swig_import_helper() File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 17, in swig_import_helper import _IMP_multifit ImportError: libfftw3.so.3: cannot open shared object file: No such file or directory Traceback (most recent call last): File "/home/socr/a/yz/local/imp-repository/modules/multifit2/bin/create_auto_proteomics_file.py", line 6, in <module> import IMP.multifit File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 25, in <module> _IMP_multifit = swig_import_helper() File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 17, in swig_import_helper import _IMP_multifit ImportError: libfftw3.so.3: cannot open shared object file: No such file or directory Traceback (most recent call last): File "/home/socr/a/yz/local/imp-repository/modules/multifit2/bin/align_proteomics_em_atomic_plan.py", line 3, in <module> import IMP.multifit File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 25, in <module> _IMP_multifit = swig_import_helper() File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 17, in swig_import_helper import _IMP_multifit ImportError: libfftw3.so.3: cannot open shared object file: No such file or directory Traceback (most recent call last): File "/usr/local/opal-local/bin/multifitWS.py", line 438, in <module> main() File "/usr/local/opal-local/bin/multifitWS.py", line 46, in main VersionMap[cf["version"]](cf) File "/usr/local/opal-local/bin/multifitWS.py", line 98, in v1_run asymWriteSolution(cf) File "/usr/local/opal-local/bin/multifitWS.py", line 411, in asymWriteSolution raise RuntimeError("Unable to find file combinations.output") RuntimeError: Unable to find file combinations.output -----

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view MD ChimeraX
by Fabian Glaser 16 Dec '19

16 Dec '19

Hi, I installed Molecular Dynamics Viewer in ChimeraX but I am not able to use it, . I use it successfully in Chimera (no X). But in ChimeraX. Can you please help me? Best, Fabian Fabian Glaser PhD Bioinformatics Knowledge Unit - BKU The Lorry I. Lokey Center for Life Sciences and Engineering Technion - Israel Institute of Technology, Haifa, Israel Web http://bku.technion.ac.il/ Tel +972 (0) 4 8293701

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Regarding the UNDO issue raised by Luca
by Boaz Shaanan 13 Dec '19

13 Dec '19

Hi, Is not possible to install an automatic 'save session' at intervals determined by the user just as done in an MS word session? This at least may rescue the last operations. Following my own Chimera 'disasters' of this kind, I actually save session quite frequently when it becomes heavily loaded, particularly prior to a major new operation. My 2p. Happy and warm Thanksgiving. 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: Wednesday, November 27, 2019 11:07 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 199, Issue 25 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. secondary structure restraints and crosslink restraints (Fr?nze M?ller) 2. Undo option? (Luca Pellegrini) 3. Re: Undo option? (Elaine Meng) 4. Re: secondary structure restraints and crosslink restraints (Elaine Meng) 5. Re: Auto-associate define attribute/render by attribute (Elaine Meng) ---------------------------------------------------------------------- Message: 1 Date: Wed, 27 Nov 2019 13:50:32 +0100 From: Fr?nze M?ller <fraenze.mueller(a)biologie.uni-freiburg.de> To: chimera-users(a)cgl.ucsf.edu Subject: [Chimera-users] secondary structure restraints and crosslink restraints Message-ID: <cde7ad0e-503b-b0cc-5466-006d64019f5a(a)biologie.uni-freiburg.de> Content-Type: text/plain; charset="utf-8"; Format="flowed" Dear Chimera developers, I would like to perform homology modelling using Modeller in Chimera. At the moment I am using just distance restraints formatted like in the Chimera documentation (res1 res2 dist stdev). This file only contains crosslinking data. Is there a way to also include secondary structure restraints, that can serve as additional information during homology modelling? Or can I provide some were another file including this information separate from the crosslink information? Best wishes and Thanks for your help, -- *Fr?nze M?ller* Postdoctoral Researcher *Biochemistry and Functional Proteomics, Warscheid Lab* University of Freiburg|Sch?nzlestr. 1|79104 Freiburg|Germany Phone +49 761 203 2681

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