Re: [PyMOL] APBS plugin for Sugars
Thank you so much for your quick answer! Now I can access the file and I was wondering how to get amber data for specific molecules. I know that the GLYCAM parameters exist, but as far as I understand I can see only bond information. If, for alanine, the amber.dat file has the following: ALA N -0.415700 1.8240 N ALA H 0.2719000.6000 H ALA CA 0.0337001.9080 CT ALA HA 0.0823001.3870 H1 ALA CB -0.182500 1.9080 CT ALA HB1 0.0603001.4870 HC ALA HB2 0.0603001.4870 HC ALA HB3 0.0603001.4870 HC ALA C 0.5973001.9080 C ALA O -0.567900 1.6612 O I was wondering how I could get this info for SIA (Sialic Acid). Is there any library where I could get it in this format? Or maybe some tool to get them from pdb information (if feasible, I am brainstorming!) Thanks again for your help and for your help in advance, Mario -Original Message- From: Thomas Holder Sent: Monday, June 15, 2020 9:37 AM To: Mario Garcia Urena Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] APBS plugin for Sugars Hi Mario, Incentive PyMOL 2.x includes regular APBS and PDB2QPR. You should be able to manually edit the files there as well. For example with PyMOL 2.4.0 on Linux, the AMBER force field data files can be found like this: $ find . -name "AMBER.*" ./lib/python3.7/site-packages/src/dat/AMBER.names ./lib/python3.7/site-packages/src/dat/AMBER.DAT Hope that helps. Cheers, Thomas > On Jun 14, 2020, at 6:35 PM, Mario Garcia Urena wrote: > > Hi all, > > I was trying to generate dipole moments with pymol using the APBS plugin. For > proteins I adapted a code and the dipole moments are correct and work just > fine, but for sugars it does not. I am well aware that the problem is that > many of the residues are not present in the AMBER force field data (or the > force field I want to use.) In APBS it is relatively easy to adapt and > introduce the sugars’ information manually, however in the APBS plugin for > pymol gets a little bit thorny. I cannot seem to find the files where I > should store the sugar information. Has anybody done this before? Any > alternatives with other programs or approaches are also welcome. > > Thank you in advance, > > Mario > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] Effect of different align method
Hello Julien Cappèle, Thank you for your response. I didn't mean to keep the input file in secrete. I have changed the access right to them, so you can download them freely. Best, Yeping Sun -- From:Julien CAPPELE Sent At:2020 Jun. 17 (Wed.) 17:05 To:孙业平 Subject:Re: [PyMOL] Effect of different align method Hello Sunyeping, I would suggest you to try TM-align, and a very good way to use it for multi-protein alignment is to use their server mTM-align. TM-align is a very robust alignment tool that will in most of the case, give you a better structural based alignment with low to zero input from the sequence. https://yanglab.nankai.edu.cn/mTM-align/ Also, if you are not working on secret stuff, you can give me access so I can rework the output files from mTM-align server to give you a RMSD-colored alignment in PyMOL. On PyMOL only, I didn't try to implement TM-align because I use Windows, but the developers said that a linux implementation could be possible if you are a bit familiar with compiling softwares. - Julien Cappèle Doctorant - 2ème année - ED C2MP Université de Lorraine CRM² - UMR CNRS 7036 julien.capp...@univ-lorraine.fr Tel: (+33)6 99 18 59 03 - Le mer. 17 juin 2020 à 05:06, sunyeping via PyMOL-users a écrit : Dear pymol users, I am trying to align two very similar trimeric molecules. I tried different alignment commands including "align", "cealign" and "super", but none of them gives satisfying effect. Athough the backbone conformations and orientations of two two molecules look very similar, there are obvious displacements between them after alignment with these three commands. The rmsd of the two molecules for these three methods are 2.250, 4.682, 2.206 and 2.206, respectively. I wonder whether there is any better alignment command or there are any parameters that can be passed to these three alignment commands to improve the effects. Could you help me check this? The pdb files of these two molecules, the image for the two molecules after using "super" command, and the alignment effect in the publication I mentioned can be found at the following link. https://drive.google.com/file/d/1ff3XgTexgdul-SezUz75dVoCx2cL5YPL/view?usp=sharing With many thanks. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] Install license file from CLI
Hi: I'm working with PyMol installed on a remote server, so I don't have access to the GUI. I already have an educational license. According to your FAQ at https://pymol.org/2/support.html?, the license file should be placed in $HOME/anaconda3/share/pymol/license.lic on a Linux computer. I already did it but PyMol isn't still activated. Any idea on how to completely install the license file using only the Command Line Interface? Many thx. BR, Antonio Serrano -- "Este mensaje es privado y confidencial y se dirige exclusivamente a su destinatario. Si usted recibe este mensaje por error, no debe revelar, distribuir o copiar este e-mail. Por favor, comuníquelo al remitente y borre el mensaje y los archivos adjuntos de su sistema. No hay renuncia a la confidencialidad ni a ningún privilegio a causa de una transmisión errónea o por mal funcionamiento". "This message is private and confidential and it is intended exclusively for the addressee. If your receive this message by mistake, you should not disseminate, distribute or copy this e-mail. Please inform the sender and delete the message and attachments from your system. No confidentiality or any privilege regarding the information is waived or lost by any mistransmission or malfunction". No me imprimas si no es necesario.Don't print me unless it's necessary. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] Write the number of molecules for each state in a file
Hello PyMOLers
I have PDB file that contains different frames ( or state or models) extracted
from a MD simulation and I would like to select the number the water near (say
3.5 Angstroms) a protein for each state and write the results in the file.
For instance like this where resid is a list of the water that satisfy the cut
off below
Frame 0 : residX, residY, ,
Frame 1: residZ, residY, ,
In the pml script I have selected the water molecules near the protein within
the pymol commands below
###
select GrA_Channel, (id 1-267+277-542) and name CA+C+O+N
select water_channel, resname SOL within 3.5 of GrA_Channel
f=open("toto.txt","w")
iterate_state 0, water_channel, state + ':' + water_channel ") ## How to use
this command
f.close()
but I do not know to use the iterate_state for each frame with above selected
command
Can you help me ?
Thank you in advance
Stéphane
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Re: [PyMOL] Effect of different align method
Hello Sunyeping, I would first point out that if you align on chain A of each molecule, then chain B of ASFV aligns with chain C of MTUB and vice versa. In other words you don't have the same assignment of chain ids in your trimer. The alignment of just alpha carbons of chain A with "align" gives an RMSD of 1.78 Å for 81 atoms and for "super" gives an RMSD of 1.746 Å for 81 atoms. That may be the best that you can do, but if you want to align the whole trimer than you need to rename chain B to chain C and chain C to chain B for one of your molecules. You can do that renaming within PyMOL with these commands: PyMOL>alter MTUB_trimer & c. B, chain="D" PyMOL>alter MTUB_trimer & c. C, chain="B" PyMOL>alter MTUB_trimer & c. D, chain="C" (I'm just using "D" as an intermediate name here) If you do that, then aligning all alpha carbons gives an RMSD of 2.189 Å for "align" and 1.845 Å for "super". Cheers, Rob On Wed, 2020-06-17 21:04 +0800, sunyeping via PyMOL-users wrote: > Hello Julien Cappèle, >Thank you for your response. I didn't mean to keep the input file > in secrete. I have changed the access right to them, so you can > download them freely. Best, Yeping Sun > -- > From:Julien CAPPELE > Sent At:2020 Jun. 17 (Wed.) 17:05 > To:孙业平 > Subject:Re: [PyMOL] Effect of different align method > > Hello Sunyeping, > > I would suggest you to try TM-align, and a very good way to use it > for multi-protein alignment is to use their server mTM-align. > TM-align is a very robust alignment tool that will in most of the > case, give you a better structural based alignment with low to zero > input from the sequence. > https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fyanglab.nankai.edu.cn%2FmTM-align%2Fdata=02%7C01%7Crobert.campbell%40queensu.ca%7C4e290e0f1c4044d3b1fc08d812bf8cca%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637279961201881850sdata=EOgyXD4A%2FemFaZHj6eRrx1h3nc%2BoCOHr94cFzpmIE3o%3Dreserved=0 > > > Also, if you are not working on secret stuff, you can give me access > so I can rework the output files from mTM-align server to give you a > RMSD-colored alignment in PyMOL. > > On PyMOL only, I didn't try to implement TM-align because I use > Windows, but the developers said that a linux implementation could be > possible if you are a bit familiar with compiling softwares. > > - > Julien Cappèle > Doctorant - 2ème année - ED C2MP > Université de Lorraine > CRM² - UMR CNRS 7036 > julien.capp...@univ-lorraine.fr > Tel: (+33)6 99 18 59 03 > - > > Le mer. 17 juin 2020 à 05:06, sunyeping via PyMOL-users > a écrit : Dear pymol users, > > I am trying to align two very similar trimeric molecules. I tried > different alignment commands including "align", "cealign" and > "super", but none of them gives satisfying effect. Athough the > backbone conformations and orientations of two two molecules look > very similar, there are obvious displacements between them after > alignment with these three commands. The rmsd of the two molecules > for these three methods are 2.250, 4.682, 2.206 and 2.206, > respectively. I wonder whether there is any better alignment command > or there are any parameters that can be passed to these three > alignment commands to improve the effects. Could you help me check > this? The pdb files of these two molecules, the image for the two > molecules after using "super" command, and the alignment effect in > the publication I mentioned can be found at the following link. > > https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F1ff3XgTexgdul-SezUz75dVoCx2cL5YPL%2Fview%3Fusp%3Dsharingdata=02%7C01%7Crobert.campbell%40queensu.ca%7C4e290e0f1c4044d3b1fc08d812bf8cca%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637279961201881850sdata=72dx0AyAPoHLvV4iXbEhmoGY18cXymzJRRWUqC7gdjE%3Dreserved=0 > > With many thanks. > > ___ > PyMOL-users mailing list > Archives: > https://can01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fpymol-users%40lists.sourceforge.netdata=02%7C01%7Crobert.campbell%40queensu.ca%7C4e290e0f1c4044d3b1fc08d812bf8cca%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637279961201881850sdata=PS%2BRq2rFtONyOjTtIS59OZnLnYEAG2spdQJXLzlpGzA%3Dreserved=0 > Unsubscribe: > https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fpymol%2Flists%2Fpymol-users%2Funsubscribedata=02%7C01%7Crobert.campbell%40queensu.ca%7C4e290e0f1c4044d3b1fc08d812bf8cca%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637279961201881850sdata=FMqipuYNGRnLNirUNl5hMdQtsm%2F%2F9GRkhNxzMKjP0LE%3Dreserved=0 > -- Robert L. Campbell, Ph.D. Academic Advisor, BHSc Program Assistant Professor, Dept. of Biomedical & Molecular Sciences, Queen's University, Kingston, ON K7L 3N6 Canada
Re: [PyMOL] hydrogen bond list for a series of files
Hi,
I would make one minor change to your script -- the command "run list_hb.py"
needs to be run only once at the beginning of the script so:
# multiple_hb.py
from pymol import cmd
from glob import glob
cmd.do("run list_hb.py")
for file in glob("model.000.*.pdb"):
print(file)
#file_list = [f'{m:02d}' for m in list(range(0,30,1))]
cmd.load(file)
obj=cmd.get_object_list('all')
print(obj)
#chains=[('A','F'),('B', 'F'),('C','F'),('D','F'),('E','F')]
cmd.do("list_hb chain F, chain A:E,
write_distances_file=hb_"+str(obj[0])+".txt") cmd.delete("all”)
Cheers,
Rob
On Tue, 2020-06-16 20:23 +, "Chen, Qiang" wrote:
> This script will have a memory issue. My pymol will stuck if I have
> more than 3 files be processed. file_list = [f'{m:02d}' for m in
> list(range(1,30,1))] [cmd.do("load
> model.000."+str(k)+"_minimized.pdb") for k in file_list]
> object_list=cmd.get_object_list('(model.000.*_minimized)')
> chains=[('A','F'),('B', 'F'),('C','F'),('D','F'),('E','F')] run
> C:\Users\user\AppData\Local\Programs\Python\Python38\lib\site-packages\pymol\pymol_path\Pymol-script-repo\list_hb.py
> [cmd.do("list_hb chain F, chain A:E,
> write_distances_file=hb_"+str(file)+".txt") for file in object_list ]
>
> I modified from the sample script here
>
> https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.pymolwiki.org%2Findex.php%2FProcess_All_Files_In_Directorydata=02%7C01%7Crobert.campbell%40queensu.ca%7C5a300643d81e4d7ea3f608d812359b34%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637279368764004254sdata=p5tXmvSD1QCS%2BdIXyJv58rEBk9GCIRtl8BFSnamwoNs%3Dreserved=0
>
> Save the following lines in a file named as, eg. multiple_hb.py and
> make sure list_hb.py in the working directory of searching directory.
>
> Then run multiple_hb.py in the pymol command line.
>
> from pymol import cmd
> from glob import glob
>
> for file in glob("model.000.*.pdb"):
> print(file)
> #file_list = [f'{m:02d}' for m in list(range(0,30,1))]
> cmd.load(file)
> obj=cmd.get_object_list('all')
> print(obj)
> #chains=[('A','F'),('B', 'F'),('C','F'),('D','F'),('E','F')]
> cmd.do("run list_hb.py")
> cmd.do("list_hb chain F, chain A:E,
> write_distances_file=hb_"+str(obj[0])+".txt") cmd.delete("all”)
>
>
> On Jun 16, 2020, at 11:15 AM,
> pymol-users-requ...@lists.sourceforge.net
> wrote:
>
> Send PyMOL-users mailing list submissions to
> pymol-users@lists.sourceforge.net
>
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> Today's Topics:
>
> 1. Re: hydrogen bond list for a series of files
> (Mooers, Blaine H.M. (HSC))
> 2. Re: hydrogen bond list for a series of files (Chen, Qiang)
>
>
> --
>
> Message: 1
> Date: Tue, 16 Jun 2020 14:51:38 +
> From: "Mooers, Blaine H.M. (HSC)"
> To: "Chen, Qiang" , "pymol-users@lists.sourceforge.net"
>
> Subject: Re: [PyMOL] hydrogen bond list for a series of files
> Message-ID:
> <87dcc6c40b22804192b6892e6429ec5fdbefd...@countach.hsc.net.ou.edu>
> Content-Type: text/plain; charset="Windows-1252"
>
> Hi Charlie,
>
> This will give the desired list.
>
> file_list = [f'{m:02d}' for m in list(range(1,30,1))]
> print(file_list)
>
> Best regards,
>
> Blaine
>
> Blaine Mooers, Ph.D.
> Associate Professor
> Department of Biochemistry and Molecular Biology
> College of Medicine
> University of Oklahoma Health Sciences Center
> S.L. Young Biomedical Research Center (BRC) Rm. 466
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
>
>
> From: Chen, Qiang [q...@pitt.edu]
> Sent: Tuesday, June 16, 2020 9:26 AM
> To: Mooers, Blaine H.M. (HSC); pymol-users@lists.sourceforge.net
> Subject: [EXTERNAL] Re: hydrogen bond list for a series of files
>
> Hi, Blaine,
>
> Then the question becomes how to generate a list with 30 or 300
> numbers.
>
> Will this work?
> file_list=list(range(00, 30))
>
> Thanks!
>
> Charles
>
>
>
> From: Mooers, Blaine H.M. (HSC)
> Sent: Tuesday, June 16, 2020 9:57 AM
> To: Chen, Qiang ; pymol-users@lists.sourceforge.net
> Subject: RE: hydrogen bond list
> for a series of files
>
> Hi Charles,
>
> You are right and I am wrong about the files
[PyMOL] Color by index
hello everyone! I am trying to color an explicit distribution by color (say blue to red) pls help me with the command color by index thanks! Vertika Gautam Research Assistant Drug Design and Development Research Group (DDDRG) Department of Chemistry, Faculty of Science University of Malaya *e-mail address: vartikapis...@gmail.com vartikapis...@hotmail.com 01112294191* ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] help
hello everyone! I am trying to color an explicit distribution by color (say blue to red) pls help me with the command color by index thanks! -- Vertika Gautam Research Assistant Drug Design and Development Research Group (DDDRG) Department of Chemistry, Faculty of Science University of Malaya *e-mail address: vartikapis...@gmail.com vartikapis...@hotmail.com 01112294191* ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
