- Chimera-users - RBVI Mailing Lists

Support chimera
by Jose Alirio Mendoza Mesa 03 Sep '19

03 Sep '19

Hi there, my name is Jose Alirio Mendoza. Currently, I am carrying out my PHD thesis in which I am using the chimera program to show the tomography results. Nevertheless, I am being presented some problems when trying to measure my particle in Chimera. The file of my product is “mrc” and I have been investigating about chimera usage where I have realized that the file must be “pdb” for the program to recognize it. I do not really know how to convert my molecule to the required file, and I guess that is the problem by which I cannot measure the distance of my particle. When I click “tools – structure analysis – distance” it does not appear the code of my molecule as in picture below [image: imagen.png] This is my particle and what I get when using the tool for measuring. I have other three tomography for one publication. [image: imagen.png] There is not any code in the tool square and that is why I guess to no be able to measure the particle. Other tool I tried to use is the scale bar, however the value of it is not according to my calibration. [image: imagen.png] How may I change that calibration? In our research group we want the publish the articles citing chimera as visualization tool so we would really appreciate your help. Here is attached the file we have worked in chimera. pollo 13.mrc <https://drive.google.com/a/unal.edu.co/file/d/1cAs2g1kP88o8im65xuTbOz11o9pk…> -- *Qco. JOSE ALIRIO MENDOZA MESA* Candidato a Doctor en ciencias Universidad Nacional de Colombia. 3165000 Ext. 14475 *LABORATORIO DE CATALISIS HETEREOGENEA*

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Re: [Chimera-users] code 256
by Greg Couch 30 Aug '19

30 Aug '19

Like I said before in http://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-August/016113.html, you need to use the daily build of Chimera. Go the Chimera download web page, http://www.cgl.ucsf.edu/chimera/download.html. Scroll down past the 1.13.1 downloads, and pick the 64-bit Linux daily build version to download. Then install it. When 1.14 comes out, it will not have this problem. -- Greg On 8/29/2019 11:22 PM, Aleksandra Jarmołowicz wrote: > > I am using Ubuntu 19.04. So what can I do to use Chimera with this > version? Before update of the system programme runs well. > > Aleksandra Jarmołowicz > Ph.D. Student > > Department of RNA Structural Genomics > Institute of Bioorganic Chemistry > Polish Academy of Sciences > Z. Noskowskiego str. 12/14 > 61-704 Poznań > Phone: +48 61 852 8503 ext 143 > ajarmolowicz(a)ibch.poznan.pl <mailto:ajarmolowicz@ibch.poznan.pl>

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Buried_area python function
by Kevin Wang 29 Aug '19

29 Aug '19

Hi, I am trying to use the buried_area function below. What are the arguments that I need to pass in? def buried_area(operation, atoms1, atoms2, probeRadius = 1.4, vertexDensity = 2.0): My current code is as follows: #calculate buried area import os import chimera import xlsxwriter from Measure import measure from chimera import * workbook = xlsxwriter.Workbook('contactArea.xlsx') worksheet = workbook.add_worksheet() Path = "/Users/kevinwang/desktop/VEGFR_NO_LIGAND/results/clustering/pdbfit/split" i = 0 filelist = os.listdir(Path) for x in filelist: if x.startswith("trp.pdb."): #if (x == "trp.pdb.00001"): opened = chimera.openModels.open(x, type ="PDB") chimera.update.checkForChanges() try: runCommand('surface :286-596') runCommand('surface :899-1230') y = measure.buried_area() worksheet.write(i,0,x) worksheet.write(i,1,y) except: worksheet.write(i,0,x) worksheet.write(i,1,"ERROR") i = i + 1 print("Processed: " + x) print("Total #: " + str(i)) runCommand('close all') chimera.update.checkForChanges() workbook.close() Best, Kevin

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copy transformation between volumes
by Oleksiy Kovtun 29 Aug '19

29 Aug '19

Dear community, I need your advice on the following problem. I align map #1 to the reference volume using fit command, and then need to confer this transformation to map #2. This could be done by using matrixcopy command. However in this particular case #1 has twice larger voxel size than #2. It is understod, that since transformation matrix describes shifts in non-scaled pixels, I can not use matrixcopy command. Is it correct to scale translations (column 4) in the fit matrix for #1 and apply it to #2 with matrixset command? Thank you and best regards, Oleksiy Dr Oleksiy Kovtun Research Fellow Briggs group MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH UK Tel: + 44 1223 267551 Email: okovtun(a)mrc-lmb.cam.ac.uk

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Python Script to Find Contact Area Between 2 Proteins
by Kevin Wang 29 Aug '19

29 Aug '19

Hi, I am writing a python script to find the area between 2 proteins using the contact_area python command below. def contact_area(p1, p2, d, color = None, offset = None, slab = None, smooth = False, optimize = True): Is there a specific object for p1 and p2 and if so how do I get it? My current code is as follows: import os import chimera from Measure import contactarea from chimera import * Path = "/Users/kevinwang/desktop/VEGFR_NO_LIGAND/results/clustering/pdbfit/split" filelist = os.listdir(Path) for x in filelist: #if x.startswith("trp.pdb."): if (x == "trp.pdb.00001"): print x opened = chimera.openModels.open(x, type ="PDB") runCommand('surface') y = contactarea.contact_area('0.1', '0.2', 2.5) text_file = open("buriedArea.txt", "w") text_file.write(y) text_file.close() The error message I am getting is as follows: AttributeError: 'str' object has no attribute 'geometry' File "/Applications/Chimera.app/Contents/Resources/share/Measure/contactarea.py", line 8, in contact_area v1, t1 = p1.geometry How should I be passing in my arguments? Best, Kevin

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code 256
by Aleksandra Jarmołowicz 29 Aug '19

29 Aug '19

Dear Sir or Madame, During chimera-1.13.1-linux_x86_64 installation process I have found some difficulties. I have not found any solutions on your website. After running instalation an error appears : ERROR in chimera_final_install: unable to install deskop icon: result code from installer: 256 I would be very greatful for any help. Kind regards, Aleksandra Jarmołowicz -- Aleksandra Jarmołowicz Ph.D. Student Department of RNA Structural Genomics Institute of Bioorganic Chemistry Polish Academy of Sciences Z. Noskowskiego str. 12/14 61-704 Poznań Phone: +48 61 852 8503 ext 143 ajarmolowicz(a)ibch.poznan.pl

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Can multiple marker sets be batch-saved into individual .cmm files?
by Jun Ha Song 28 Aug '19

28 Aug '19

Dear RBVI, I need to save around 340 market sets into individual .cmm files, 1 .cmm for each marker set I have in my Chimera session. I have been looking at UCSF Chimera documentation for some time ( https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/…) and I wanted to ask if multiple marker sets (each with its own unique model ID) can be saved in single batch command line. Is there a possibility of specifying commands like *save* or *write* or *export* with atom specification of all the model that I want to save to make Chimera save all my 340 marker sets as their individual .cmm files? I was hoping that I could simply use something like *save #1-340 individual UseModelIDasFilename format .cmm directory E:\LBNL\Individual_Models* to make it happen, but all the commands that I thought of as potential candidate for batch-save command doesn't mention whether it can work with volume tracer's "Save current marker set as...". or, if I can use Volume Tracer's "Save current marker set as..." using a script, I could handle this by making myself very simple macro, but I don't know whether volume tracer's codes would allow some quick script to substitute its "Save current marker set as..." function. So, in summary, I wanted to know if... Q1 : Is there a command in UCSF Chimera that allows batch saving multiple market sets as individual .cmm files? Q2 : Can Volume Tracer's "Save current marker set as..." function be used by using some kind of script? Sincerely, Junha Song.

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Get map contour level with python script or command
by Kyle Morris 28 Aug '19

28 Aug '19

Dear chimera users and dev, Is there a chimera or python command that can report the current contour level of a volume that is in model number #n back to the reply log or equivalent? I want to do this after executing 'volume #n sdLevel 3’ such that I can programmatically retrieve the contour level associated with a particular sigma level of a currently loaded volume. Apologies if in my searching I have missed this on the boards, I think this is a novel question though. Thanks as always for your help. Best wishes, Kyle

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How to read a volume in python script
by Huiya Zhou 28 Aug '19

28 Aug '19

Hello, I am trying to use UCSF Chimera to analysis cry-EM density maps. I would like to read a density map (for example: a .mrc file) in python script and get the array (or a three dimensional matrix) of all voxels of this density map. How could I realize this? By the way, I tried to learn some basic chimera functions which can be used in python on this website: https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/index.html <https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/index.html> However, it seems this website can’t be opened and it shows me a blank page. Best, Huiya

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Chimera Error
by Ryan Harlich 27 Aug '19

27 Aug '19

Hi Chimera, I am having trouble opening a pdb file. I get the following error: ValueError: can’t normalize zero length array File \Chimera1.13.1\share\chimera\tkgui.py, line 3030, In showLabelBalloon Objs = self.viewer.pick(event.x, event.y) All other PDBs are opening so I am not sure why this one won’t open. Best, Ryan Harlich Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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Subtracting the difference in EM volumes
by Y. Mutum 27 Aug '19

27 Aug '19

Hi Is there a way to subtract the non-overlapping bits and retain only the overlapping volumes between 2 EM density maps in Chimera? I have tried the vop subtract command, but it only seems to subtract the overlapping bits and not the inverse of it (non-overlapping bits)? Sorry, if I have missed it. Thanks Yilog

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Divided the Volume Data into two parts
by Huiya Zhou 23 Aug '19

23 Aug '19

Hello, I would like to divided a density map (volume data) into two parts. For example, the size of the whole density map is 320*320*320. I want to get one part which covers the region from (i,j,k) to (x,y,z), e.g. from (0,0,0) to (100,100,100). The rest is the other part. The transparency for the first part is 0 and for the second part is 0.5. And I still want to get the histogram of the first part. How could I achieve this in a python script? Actually, I want to get the histogram of different regions. I plan to run a loop for different regions (Change the (i,i,k) and (x,y,z) for the first part). Could I save all of the histograms in one file which is not a window of the Chimera but a picture. Best, Huiya

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Selecting bonds/pseudobonds with a cutt-off distance
by Yasser Almeida Hernández 23 Aug '19

23 Aug '19

Hi all, how can I select bonds/pseudobonds with a cutt-off distance, say bonds/pseudobonds with more than/less than X? Thanks in advance, Yasser

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回复： scipy problem
by William 22 Aug '19

22 Aug '19

Dear Eric, I have tried the instructions following the FAQ, but there is another problem. The scipy installed successfully. However, it installed a higher version of the numpy when installing scipy. And the older version of numpy is still in. The chimera can not work. Anyway, thanks a lot. ------------------ 原始邮件 ------------------ 发件人: "Eric Pettersen"<pett(a)cgl.ucsf.edu>; 发送时间: 2019年8月20日(星期二) 凌晨1:46 收件人: "William"<3121437640(a)qq.com>; 抄送: "chimera-users"<chimera-users(a)cgl.ucsf.edu>; 主题: Re: [Chimera-users] scipy problem Hi William, I don’t know why Jaime’s instructions don’t work. Maybe he can follow up. Regardless, we have our own instructions for installing pip (and pip-able packages like scipy). It’s in the Chimera Programming FAQ. Question 3b. If those instructions don’t work, please let us know. —Eric Eric Pettersen UCSF Computer Graphics Lab

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How to read a volume in python script
by Huiya Zhou 22 Aug '19

22 Aug '19

Hello, I am trying to use UCSF Chimera to analysis cry-EM density maps. I would like to read a density map (for example: a .mrc file) in python script and get the array (or a three dimensional matrix) of all voxels of this density map. How could I realize this? By the way, I tried to learn some basic chimera functions which can be used in python on this website: https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/index.html <https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/index.html> However, it seems this website can’t be opened and it shows me a blank page. Best, Huiya

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copy/combine molecular models
by Rui Chen 22 Aug '19

22 Aug '19

Hello, I am working on a homodimer. I modelled loops of each chain one by one. I chose the best loops for each chain. Now I want to save them as a pub file. Please see the following screenshot. How to decide the new model's ID? I know the coordinate system is the reference coordinate, how do I decide which chain to use as the reference chain? Should I choose rename them uniquely? Looking forward to hearing from you. Thank you. [image: Screen Shot 2019-08-22 at 12.01.28 AM.png] Best regards, Rui

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how to guess ligand's net charge?
by Thomas Evangelidis 21 Aug '19

21 Aug '19

Greetings, How does Chimera guess the net charge of a ligand when prompted to select the charge type (AM1-bcc or Gasteiger)? I am doing high throughput protein-ligand MD simulations and would like to know which open source library Chimera uses for this task. Thanks in advance. 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/

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color by zone in chimeraX
by Pranav Shah 20 Aug '19

20 Aug '19

Hi Elaine and Co., I am trying to color a virus map with the relevant pdb file, the series of commands I am running are as follows, open virus.mrc open virus.pdb color /A plum target c color /B lightgreen target c color /C dodger blue target c color zone #1 near #2 dist 3 However, the resultant surface is rendered in splotches of red and blue, which leads me to think the it is coloring the surface using atom type. Could you tell me how I can get Chimera X to color the surface using the colors of the chains only? FYI, color by zone works flawlessly in chimera. 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)

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scipy problem
by William 19 Aug '19

19 Aug '19

Hello, I tried to install scipy in chimera python following the steps below: When I tried the third step, it raised midaserror. The error is as follows： Is there anything wrong with my path? Thanks.

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Match showmatrix true motion in original coordinates
by Ahmad Khalifa 13 Aug '19

13 Aug '19

Hi, Running match showmatrix true, gives two matrices. What's the difference between the two? I already saved the file after fitting it so it should have only one set of coordinates, its original coordinates?! Regards Motion of #76 in #2 coordinate system Matrix rotation and translation 0.99998889 -0.00169318 0.00440013 -1.57825672 0.00165962 0.99996960 0.00761849 -4.96792547 -0.00441290 -0.00761111 0.99996130 169.74075587 Axis -0.85023004 0.49200930 0.18717833 Axis point 0.00000000 21533.64775327 2718.66675667 Rotation angle (degrees) 0.51315730 Shift along axis 30.66940614 Motion of #76 original coordinates in #2 coordinate system Matrix rotation and translation 0.78916125 0.61416829 0.00467203 -143.02960322 -0.61417583 0.78916918 0.00023085 242.10381668 -0.00354524 -0.00305162 0.99998906 98.04867640 Axis -0.00267220 0.00668954 -0.99997405 Axis point 281.92931592 330.08522286 0.00000000 Rotation angle (degrees) 37.89294229 Shift along axis -96.04436567

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Chimera bug report submission
by Tanara Arenhart 12 Aug '19

12 Aug '19

The following bug report has been submitted: Platform: Windows64 (WGL) Microsoft Windows Unknown 10.0 (Build 17134) x64 Chimera Version: 1.13.1_b41965 Description Hi! I'm trying to dock my protein with a ligand, but everytime appears this message: "receptor and ligand cannot be the same model". I don't know why, because i'm doing the same things I always do. What could be happening? Thank you! Open models #0 3dbs.pdb #1 smiles:CC1CCC2C3(CCC(... #2 AutoDock Vina Search Volume Reply log: Failed to translate SMILES to 3D structure via NCI web service (SMILES: receptor and ligand cannot be the same model) Failed to translate SMILES to 3D structure via Indiana University web service (SMILES: receptor and ligand cannot be the same model) Web services failed to translate SMILES string to 3D structure. Translated SMILES to 3D structure via NCI web service (SMILES: CC1CCC2C3(CCC(C(C3CCC2(C14CC5=C(O4)C(=CC(=O)C5=O)C)C)(C)C)O)C) No incomplete side chains Chain-initial residues that are actual N terminii: Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: Chain-final residues that are not actual C terminii: 0 hydrogen bonds Hydrogens added Charge model: AMBER ff14SB Assigning partial charges to residue STP (net charge +0) with gasteiger method Running ANTECHAMBER command: C:/Program Files/Chimera 1.13.1/bin/amber16/bin\antechamber -i c:\users\nara_\appdata\local\temp\tmpi9opye\ante.in.mol2 -fi mol2 -o c:\users\nara_\appdata\local\temp\tmpi9opye\ante.out.mol2 -fo mol2 -c gas -nc 0 -j 5 -s 2 -dr n (STP) (STP) Welcome to antechamber 17.3: molecular input file processor. (STP) (STP) Info: Finished reading file (c:\users\nara_\appdata\local\temp\tmpi9opye\ante.in.mol2). (STP) 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 (STP) (STP) (STP) Running: "C:/Program Files/Chimera 1.13.1/bin/amber16/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff (STP) Running: "C:/Program Files/Chimera 1.13.1/bin/amber16/bin/atomtype" -i ANTECHAMBER_GAS.AC -o ANTECHAMBER_GAS_AT.AC -d "C:/Program Files/Chimera 1.13.1/bin/amber16/dat/antechamber/ATOMTYPE_GAS.DEF" (STP) Charges for residue STP determined Total charge for #0: 0.000 #0, chain A: phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit γ isoform Traceback (most recent call last): File "C:\Program Files\Chimera 1.13.1\share\chimera\preferences\base.py", line 447, in save WindowsError: [Error 32] O arquivo j� est� sendo usado por outro processo Cannot replace previous preferences file: C:\Users\nara_\AppData\Roaming\.chimera\preferences: WindowsError: [Error 32] O arquivo j� est� sendo usado por outro processo File "C:\Program Files\Chimera 1.13.1\share\chimera\preferences\base.py", line 447, in save See reply log for Python traceback. Residues with incomplete side chains: MET 143.A GLU 322.A Replacing each by 'swapaa same (residue atom spec) lib Dunbrack preserve True' MET 143.A: phi none, psi -122.2 trans Chi angles for MET 143.A: GLU 322.A: phi -130.9, psi 172.4 trans Chi angles for GLU 322.A: Applying GLU rotamer (chi angles: -62.4 -179.4 -3.8) to GLU 322.A Applying MET rotamer (chi angles: -65.8 -61.8 -69.4) to MET 143.A Terminii for 3dbs.pdb (#0) chain A determined from SEQRES records Chain-initial residues that are actual N terminii: MET 143.A Chain-initial residues that are not actual N terminii: GLU 267.A, CYS 357.A, LEU 460.A, PHE 497.A, HIS 525.A, ARG 544.A, GLU 981.A Chain-final residues that are actual C terminii: Chain-final residues that are not actual C terminii: ALA 253.A, GLU 322.A, CYS 435.A, GLY 489.A, ASN 522.A, ALA 528.A, HIS 967.A, VAL 1091.A 718 hydrogen bonds Adding 'H' to GLU 267.A Adding 'H' to CYS 357.A Adding 'H' to LEU 460.A Adding 'H' to PHE 497.A Adding 'H' to HIS 525.A Adding 'H' to ARG 544.A Adding 'H' to GLU 981.A Removing spurious proton from 'C' of VAL 1091.A Hydrogens added Charge model: AMBER ff14SB Total charge for #0: -8.000 receptor and ligand cannot be the same model receptor and ligand cannot be the same model OpenGL Vendor: Intel OpenGL Renderer: Intel(R) HD Graphics OpenGL Version: 4.4.0 - Build 20.19.15.4835 Manufacturer: Dell Inc. Model: Inspiron 5452 TotalPhysicalMemory: 4203823104 ―――――――――――――――――――― Multisampling: False Shadows: False Shadow texture size: 2048 Silhouettes: False Depth cue: True Subdivision quality: 1.50 Single-layer transparency: True Transparent background: False Shaders supported: True Using shader: True Window size: 1366 663 Camera mode: mono Orthographic projection: False Center of rotation: front center Near/far clipping: False Key light: True Fill light: True Back light: False Ambient light: 0.20 Specular sharpness: 30.00 Specular reflectivity: 1.00 ―――――――――――――――――――― AntialiasLines: native AntialiasPoints: native BlendEquation: native BlendFuncSeparate: native BrokenAttribLocation: native, disabled ChoosePixelFormat: extension ColorTable: not supported CompileAndExecute: native CompiledVertexArray: extension CubeMap: native CullVertex: not supported DrawElementsInstanced: native, disabled DrawRangeElements: native FBConfig: not supported FBOShadows: native FastMultisampling: native, disabled FramebufferMultisample: native FramebufferObject: native LimitVertexAttribDivisor: native, disabled Multisample: native Multitexture: native PackedDepthStencil: native PalettedTexture: not supported PointParameters: native SeamlessCubeMap: native SeparateSpecularColor: native Shading: native Shadows: native StereoMultisample: native StereoRubberBanding: native Texture3D: native TextureColorTable: not supported TextureEdgeClamp: native TrustColorLogicBlend: native TrustNormals: native VertexArray: native VertexAttrib: native VertexAttribDivisor: native VertexBufferObject: native, disabled WindowPos: not supported

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A question about the Volume Viewer
by Grosman, Claudio F 09 Aug '19

09 Aug '19

Hello everyone, I have (what I think is) a very simple question: what is the particular value of "level" (that is, the threshold) that appears automatically when one opens a 3D density map? After playing around with the threshold, I always feel like the initial value is the best one, but I wonder what exactly this value is. In the online documentation of Chimera, this issue is addressed. The text reads that the initial value of this threshold is such that 1% of the voxels have density values above it. Is this really the case? Only voxels with intensities above the threshold are displayed. Am I seeing only 1% of the voxels, then? I am afraid, I am confused. Thank you very much, in advance. Claudio

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Selecting one ID 0 when two ID 0s are present
by Ryan Harlich 09 Aug '19

09 Aug '19

Hi Chimera, I have a problem where there are two ID 0. One is the normal density map the other is a solid (or what seems to be a movie of the protein). I want to select the density map. In the GUI interface I would open volume viewer and select radio button surface for category Style. Then a little below select All instead of One. I was wondering how to do this with command line? What I am trying to do is get a chain of the pdb structure and zone the density map. However the files are really big so I am trying to do it via ssh on another computer so I will be doing it with the –nogui flag. So if I can do everything via command line that would be great. Best, Ryan Harlich Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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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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