From meng at cgl.ucsf.edu  Mon Jan  1 11:33:20 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 1 Jan 2018 11:33:20 -0800
Subject: [Chimera-users] substituting atoms
In-Reply-To: <CAJPu8_63fUvHZTybU-zzNz6dOa+kXY91LH32_-+_fYidGh+5cQ@mail.gmail.com>
References: <CAJPu8_4BERfN66uP9s4eNa0Drw4MvAzwyDEcJKpB8uQjSMyKDQ@mail.gmail.com>
 <D54630F4-AFE0-4AE7-8BC8-20DAE3F5F8CF@cgl.ucsf.edu>
 <CAJPu8_63fUvHZTybU-zzNz6dOa+kXY91LH32_-+_fYidGh+5cQ@mail.gmail.com>
Message-ID: <22F2B48B-4F2B-4AF1-9DC4-D345A604826B@cgl.ucsf.edu>

Hi Simon,
The calculation runs on your own computer and as far as I know, there isn?t a limit on the run time.  The  ?Run Parameters? section of the Molecular Dynamics SImulation dialog allows you to enter the numbers of steps for minimization, equilibration, and production.  If you click on ?minimization? you can see it is actually a little a menu that can switch to ?equilibration? and ?production? subsections.

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/md/md.html#run>

You can also specify a restart file for the production run, for subsequently doing another production run starting from the endpoint of the current one.  As far as I know, there isn?t an upper limit to the number of steps per run, but it might be wiser to do multiple production runs anyway (so that if something happens, you don?t lose so much prior computation). 

The tool was intended more to make MD simulations accessible to many people without too steep of a learning curve, rather than for very large-scale, long simulations which might be accomplished more efficiently with a dedicated MD package (AMBER, GROMACS, etc.), but you can certainly try.

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 30, 2017, at 4:10 AM, simon chapman <rowanlodge19 at gmail.com> wrote:
> 
> Hello Elaine. Yes,remiss of me to leave out so much info! I'm new-ish  to Chimera and wasn't really sure if there would be a reply (as has happened with some other MD products)
> 
> So thanks for your prompt response. 
> 
> I had no problems with Build Structure after being pointed in the right direction. I will try text editor eventually just for the experience.  I have successfully substituted S for O in a guanine complex, and will extend that to a Se substitution later.
> 
> The MD simulation runs much  faster if I exclude the Periodic Boundary Conditions option.  Is there a way to extend the run-time?  Currently  it covers 1000fs. Is getting to picosecond region a possibility? 
> 
> Best wishes and congrats to whoever put Chimera MD together!    Simon
> 
> On 28 December 2017 at 17:09, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Simon,
> It would have been helpful if you said how you substituted S for O and what the error messages were.  I have no idea what you did.
> 
> You can change atom type and element inside of Chimera or use a text editor (not in Chimera) to change the PDB file before opening it in Chimera.
> 
> The way to change the atom inside of Chimera is to select the atom and then use Build Structure (in menu under Tools? Structure Editing), the Modify Structure section. Use the option to change the name of the residue since if you keep the name the same, Chimera is expecting that residue, not something different with a sulphur in it.
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#modify>
> 
> If you try text-editing instead, remember spacing is important in PDB files, so don?t change the spacing. There's a summary of PDB format here:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.html>
> 
> In the text-editor of your choice, in the ATOM line for that atom, I would change the atom name, the element symbol (if present, would be near the end of the line), and in the ATOM lines for the whole residue, change the residue name.
> 
> Regardless of how you change the atom, however, another problem is that this nonstandard residue must be parametrized if you are going to run MD.  Chimera will try to do this automatically using AMBER?s Antechamber module, but especially with highly charged residues such as nucleotides it may fail.  In that case, I don?t really have any solution other than to try the simpler Gasteiger charges if it gives you a choice of Gasteiger or AM1-BCC.
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/addcharge.html#antechamber>
> 
> 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 27, 2017, at 1:49 PM, simon chapman <rowanlodge19 at gmail.com> wrote:
> >
> > Hello...for my Master's dissertation, I need to substitute a sulphur atom for an oxygen in a Molecular Dynamics simulation. The run works fine with my target molecule 1KF1.pdb uploaded into Chimera, but the substituted version sends quite a few error messages and won't run. It doesn't appear to recognise the novel S atom.
> >
> > Any help would be much appreciated...I've been stuck on this for nearly a week!
> >
> > Best wishes   Simon
> 
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users




From rowanlodge19 at gmail.com  Mon Jan  1 13:15:01 2018
From: rowanlodge19 at gmail.com (simon chapman)
Date: Mon, 1 Jan 2018 21:15:01 +0000
Subject: [Chimera-users] substituting atoms
In-Reply-To: <22F2B48B-4F2B-4AF1-9DC4-D345A604826B@cgl.ucsf.edu>
References: <CAJPu8_4BERfN66uP9s4eNa0Drw4MvAzwyDEcJKpB8uQjSMyKDQ@mail.gmail.com>
 <D54630F4-AFE0-4AE7-8BC8-20DAE3F5F8CF@cgl.ucsf.edu>
 <CAJPu8_63fUvHZTybU-zzNz6dOa+kXY91LH32_-+_fYidGh+5cQ@mail.gmail.com>
 <22F2B48B-4F2B-4AF1-9DC4-D345A604826B@cgl.ucsf.edu>
Message-ID: <CAJPu8_6FMut2yL7MLESGLaVDS8x4FOEh5E3_=eDCc8bSjtSbAA@mail.gmail.com>

Very kind Elaine.Many thanks.  I found a route to atomic substitution after
a bit of tinkering. Tools>structure edit>build structure>modify structure.
I'm getting some great data now! Very pleased.

I will try your suggestions re extending the run-time. I don't really need
anything more than a few ps at moment: my hypothesis is that a guanine
quadruplex will be destabilised by incremental substitution at O6. So far
the data are going my way!

AMBER gave me real headaches...I have it set up in UBUNTU but on a Win10
machine, and the commands get a bit 'sticky'. It rather feels like the
package has been poorly ported into UBUNTU in several stages over a long
period by different designers. Also an over-detailed guide doesn't help.
GROMACS is another LINUX-based system. NAMD works reasonably well, but
Chimera tops the list so far. It will be a subsection of my dissertation.

Best wishes   Simon

(Looks like you and I are the only folk working on New Year's Day!)



On 1 January 2018 at 19:33, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Simon,
> The calculation runs on your own computer and as far as I know, there
> isn?t a limit on the run time.  The  ?Run Parameters? section of the
> Molecular Dynamics SImulation dialog allows you to enter the numbers of
> steps for minimization, equilibration, and production.  If you click on
> ?minimization? you can see it is actually a little a menu that can switch
> to ?equilibration? and ?production? subsections.
>
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/md/md.html#run>
>
> You can also specify a restart file for the production run, for
> subsequently doing another production run starting from the endpoint of the
> current one.  As far as I know, there isn?t an upper limit to the number of
> steps per run, but it might be wiser to do multiple production runs anyway
> (so that if something happens, you don?t lose so much prior computation).
>
> The tool was intended more to make MD simulations accessible to many
> people without too steep of a learning curve, rather than for very
> large-scale, long simulations which might be accomplished more efficiently
> with a dedicated MD package (AMBER, GROMACS, etc.), but you can certainly
> try.
>
> 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 30, 2017, at 4:10 AM, simon chapman <rowanlodge19 at gmail.com>
> wrote:
> >
> > Hello Elaine. Yes,remiss of me to leave out so much info! I'm new-ish
> to Chimera and wasn't really sure if there would be a reply (as has
> happened with some other MD products)
> >
> > So thanks for your prompt response.
> >
> > I had no problems with Build Structure after being pointed in the right
> direction. I will try text editor eventually just for the experience.  I
> have successfully substituted S for O in a guanine complex, and will extend
> that to a Se substitution later.
> >
> > The MD simulation runs much  faster if I exclude the Periodic Boundary
> Conditions option.  Is there a way to extend the run-time?  Currently  it
> covers 1000fs. Is getting to picosecond region a possibility?
> >
> > Best wishes and congrats to whoever put Chimera MD together!    Simon
> >
> > On 28 December 2017 at 17:09, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> > Hi Simon,
> > It would have been helpful if you said how you substituted S for O and
> what the error messages were.  I have no idea what you did.
> >
> > You can change atom type and element inside of Chimera or use a text
> editor (not in Chimera) to change the PDB file before opening it in Chimera.
> >
> > The way to change the atom inside of Chimera is to select the atom and
> then use Build Structure (in menu under Tools? Structure Editing), the
> Modify Structure section. Use the option to change the name of the residue
> since if you keep the name the same, Chimera is expecting that residue, not
> something different with a sulphur in it.
> > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/
> editing.html#modify>
> >
> > If you try text-editing instead, remember spacing is important in PDB
> files, so don?t change the spacing. There's a summary of PDB format here:
> > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/
> tutorials/framepdbintro.html>
> >
> > In the text-editor of your choice, in the ATOM line for that atom, I
> would change the atom name, the element symbol (if present, would be near
> the end of the line), and in the ATOM lines for the whole residue, change
> the residue name.
> >
> > Regardless of how you change the atom, however, another problem is that
> this nonstandard residue must be parametrized if you are going to run MD.
> Chimera will try to do this automatically using AMBER?s Antechamber module,
> but especially with highly charged residues such as nucleotides it may
> fail.  In that case, I don?t really have any solution other than to try the
> simpler Gasteiger charges if it gives you a choice of Gasteiger or AM1-BCC.
> > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/
> addcharge.html#antechamber>
> >
> > 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 27, 2017, at 1:49 PM, simon chapman <rowanlodge19 at gmail.com>
> wrote:
> > >
> > > Hello...for my Master's dissertation, I need to substitute a sulphur
> atom for an oxygen in a Molecular Dynamics simulation. The run works fine
> with my target molecule 1KF1.pdb uploaded into Chimera, but the substituted
> version sends quite a few error messages and won't run. It doesn't appear
> to recognise the novel S atom.
> > >
> > > Any help would be much appreciated...I've been stuck on this for
> nearly a week!
> > >
> > > Best wishes   Simon
> >
> >
> > _______________________________________________
> > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> > Manage subscription: http://plato.cgl.ucsf.edu/
> mailman/listinfo/chimera-users
>
>
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From conrad at cgl.ucsf.edu  Tue Jan  2 12:34:29 2018
From: conrad at cgl.ucsf.edu (Conrad Huang)
Date: Tue, 2 Jan 2018 12:34:29 -0800
Subject: [Chimera-users] Chimera software error
In-Reply-To: <1514656121409.65693@tu.edu.sa>
References: <1514656121409.65693@tu.edu.sa>
Message-ID: <d7b98327-95cf-4e34-e150-93d144806b27@cgl.ucsf.edu>

Hi, Mohammed.

It looks like you are trying to use a locally installed copy of vina. 
Is that correct?  If so, please try putting quotes around the entire 
path to the vina executable and let me know whether that helps.  Thanks.

Conrad

On 12/30/2017 9:49 AM, ???? ??? ??? ???? wrote:
> Hello everyone.
> I am interested in using the builtin vina docking tool in Chimera.
> I get stuck several times at the following Error:
> ( Running AutoDock Vina for 5x5d failed; see Reply Log for more information:
> Application stderr
> -----
> 'C:\Program' is not recognized as an internal or external command, 
> operable program or batch file.
> -----
> Application stdout)
> I check for several tutorials but got the same error,
> the version I used is Chimera 1.12 and Ulpha version 1.13 in windows 10 
> platform (64bit)
> Thank you?
> Mohammed Khalid
> Department of Chemistry
> University of Taif
> Saudi Arabia
> 
> 
> '
> ------------------------------------------------------------------------
> 
> ??? ??????? ????????? (?? ????) ???? ????? ???? ?? ????? ??? ??????? 
> ????? ?????? ?????? ???????, ?? ?? ??? ????? ?????? ???? ??????? ??? 
> ???? ????? ?????? ???? ?????? ???? ???? ??????? ????????? (?? ????) ?? 
> ?????? ????? ????? ?? ??????? ?? ??? ??? ??????? ?? ???????? (?? ????) 
> ?? ?? ??? ???? ?? ????? ?????????? ??? ??? ?? ????????? ??? ??? ???? ??? 
> ???????? ??????? ???? ??????? ??? ??????? ???? ??? ?? ??? ?????? ???? 
> ???????? ??? ????? ?????? ??? ????? ????? ?????? ?? ??????? ?? ??????? 
> ??????? ?? ?? ???????? ?? ?????? ??? ?????? .
> The information in this email and in any files transmitted with it is 
> intended only for the addressee and may contain confidential and/or 
> privileged material. Access to this email by anyone else is 
> unauthorized. If you receive this in error, please contact the sender 
> immediately and delete the material from any computer. If you are not 
> the intended recipient, any disclosure, copying, distribution or any 
> action taken or omitted to be taken in reliance on it, is strictly 
> prohibited. Statement and opinions expressed in this e-mail are those of 
> the sender, and do not necessarily reflect those of the Taif University.
> '. If the disclaimer can't be applied, attach the message to a new 
> disclaimer message. '
> ------------------------------------------------------------------------
> 
> ??? ??????? ????????? (?? ????) ???? ????? ???? ?? ????? ??? ??????? 
> ????? ?????? ?????? ???????, ?? ?? ??? ????? ?????? ???? ??????? ??? 
> ???? ????? ?????? ???? ?????? ???? ???? ??????? ????????? (?? ????) ?? 
> ?????? ????? ????? ?? ??????? ?? ??? ??? ??????? ?? ???????? (?? ????) 
> ?? ?? ??? ???? ?? ????? ?????????? ??? ??? ?? ????????? ??? ??? ???? ??? 
> ???????? ??????? ???? ??????? ??? ??????? ???? ??? ?? ??? ?????? ???? 
> ???????? ??? ????? ?????? ??? ????? ????? ?????? ?? ??????? ?? ??????? 
> ??????? ?? ?? ???????? ?? ?????? ??? ?????? .
> The information in this email and in any files transmitted with it is 
> intended only for the addressee and may contain confidential and/or 
> privileged material. Access to this email by anyone else is 
> unauthorized. If you receive this in error, please contact the sender 
> immediately and delete the material from any computer. If you are not 
> the intended recipient, any disclosure, copying, distribution or any 
> action taken or omitted to be taken in reliance on it, is strictly 
> prohibited. Statement and opinions expressed in this e-mail are those of 
> the sender, and do not necessarily reflect those of the Taif University.
> '. If the disclaimer can't be applied, attach the message to a new 
> disclaimer message.
> 
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 



From liuz1970 at yahoo.com  Thu Jan  4 07:09:49 2018
From: liuz1970 at yahoo.com (Zheng Liu)
Date: Thu, 4 Jan 2018 15:09:49 +0000 (UTC)
Subject: [Chimera-users] How to set volume view step size in "vop morph"
	command
References: <1637594479.348368.1515078589230.ref@mail.yahoo.com>
Message-ID: <1637594479.348368.1515078589230@mail.yahoo.com>

I want create a morph volume between 2 maps (#0, and #1), as a command I wrote:vop morph #0,1 step 1 playStep 0.04 frames 200 step 1

However, the new model #4 morph was display in step "8", not step "1" in the volume view window. How to set the step size in the vop morph command? Thanks!
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From meng at cgl.ucsf.edu  Thu Jan  4 11:30:23 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 4 Jan 2018 11:30:23 -0800
Subject: [Chimera-users] How to set volume view step size in "vop morph"
 command
In-Reply-To: <1637594479.348368.1515078589230@mail.yahoo.com>
References: <1637594479.348368.1515078589230.ref@mail.yahoo.com>
 <1637594479.348368.1515078589230@mail.yahoo.com>
Message-ID: <A6D0676A-60C3-45EC-B71E-6EECD97BC557@cgl.ucsf.edu>

Hi Zheng Liu,
Your command has ?step 1? twice, but that should be OK? I believe it indicates using the full data in the calculation of the morph map.  
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#morph>

I'm not sure why the display uses step 8 of that map, or if it?s a bug, but here is one idea:
There is a volume option that by default, if a map is larger than a certain size, the display step size is automatically increased.  You could try turning off that behavior, for example with command:

volume #4 limitVoxelCount false

Details on that option
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#sampling>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jan 4, 2018, at 7:09 AM, Zheng Liu <liuz1970 at yahoo.com> wrote:
> 
> I want create a morph volume between 2 maps (#0, and #1), as a command I wrote:
> vop morph #0,1 step 1 playStep 0.04 frames 200 step 1
> 
> However, the new model #4 morph was display in step "8", not step "1" in the volume view window. How to set the step size in the vop morph command? Thanks!




From dongming618 at gmail.com  Fri Jan  5 13:01:52 2018
From: dongming618 at gmail.com (Ming)
Date: Fri, 5 Jan 2018 16:01:52 -0500
Subject: [Chimera-users] regarding opening mouth or poc file on chimera
Message-ID: <CADDqwcK9Vx9WtiXcc8B-LyMynxW4=AXEd8th9QK2pvfH6NW4Cg@mail.gmail.com>

Hi Chimera team,

I have a quick question regarding opening CASTp file on Chimera. I
downloaded the pdb file together with mouth and poc file and saved them in
the same folder. I also made sure the names are consistent among these
files. However, I am still getting error messages as following.


Error reading 3mbg.poc:
ValueError: Mouth info header missing or IDs not consecutive

  File "/home/ming/.local/UCSF-Chimera64-1.11.2/share/CASTp/__init__.py",
line 88, in processInfoFile
    " IDs not consecutive" % label.capitalize())

See reply log for Python traceback.


I looked up the Chimera manual online and it looks pretty straight forward
to open either the mouth or poc file but I am not sure why I keep getting
the error messages.

Any help will be appreciated.

Thanks,

Ming
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From pett at cgl.ucsf.edu  Fri Jan  5 13:16:40 2018
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Fri, 5 Jan 2018 13:16:40 -0800
Subject: [Chimera-users] regarding opening mouth or poc file on chimera
In-Reply-To: <CADDqwcK9Vx9WtiXcc8B-LyMynxW4=AXEd8th9QK2pvfH6NW4Cg@mail.gmail.com>
References: <CADDqwcK9Vx9WtiXcc8B-LyMynxW4=AXEd8th9QK2pvfH6NW4Cg@mail.gmail.com>
Message-ID: <FE5F3EEB-B518-4822-AE24-6D13F5EB9E80@cgl.ucsf.edu>

Hi Ming,
	Does the start of your .mouthInfo file look similar to this:



i.e. there is a header line, and then the IDs in the following lines start at 1 and increase by 1 each line?
	If they do, maybe you should send me the files (directly) and I could give you a better diagnosis of the problem?

?Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Jan 5, 2018, at 1:01 PM, Ming <dongming618 at gmail.com> wrote:
> 
> Hi Chimera team,
> 
> I have a quick question regarding opening CASTp file on Chimera. I downloaded the pdb file together with mouth and poc file and saved them in the same folder. I also made sure the names are consistent among these files. However, I am still getting error messages as following.
> 
> 
> Error reading 3mbg.poc:
> ValueError: Mouth info header missing or IDs not consecutive
> 
>   File "/home/ming/.local/UCSF-Chimera64-1.11.2/share/CASTp/__init__.py", line 88, in processInfoFile
>     " IDs not consecutive" % label.capitalize())
> 
> See reply log for Python traceback.
> 
> 
> I looked up the Chimera manual online and it looks pretty straight forward to open either the mouth or poc file but I am not sure why I keep getting the error messages. 
> 
> Any help will be appreciated.
> 
> Thanks,
> 
> Ming
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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From stu118506 at mail.uni-kiel.de  Mon Jan  8 05:51:13 2018
From: stu118506 at mail.uni-kiel.de (stu118506)
Date: Mon, 08 Jan 2018 14:51:13 +0100
Subject: [Chimera-users] write prmtop, source leaprc.ff14SB
Message-ID: <0de40ac8bca3498b056326fc4c702aec@mail.uni-kiel.de>

Dear Chimera users, 

I'd like to save a prmtop file of my protein after preparation for
molecular dynamics simulation. 

I tried to do it by using Tools - Amber - write Prmtop . 

I get this reply log entry: 

_command:
['/gpfs/fs5/home-sh/sumbi463/.local/UCSF-Chimera64-2017-12-05/bin/amber16/bin/sleap',
'-f', '/scratch/tmpOlw0GO/solvate.cmd']_
_Running sleap command:
/gpfs/fs5/home-sh/sumbi463/.local/UCSF-Chimera64-2017-12-05/bin/amber16/bin/sleap
-f /scratch/tmpOlw0GO/solvate.cmd_
_(writeprmtop) [gtkleap]$ source leaprc.ff14SB_ 

_(writeprmtop) Error: can not find file leaprc.ff14SB in all the search
path._ 

_Failure running sleap_ 

I guess that it should source oldff/leaprc.ff14SB because the file seems
to be in the directory oldff. But I don't know if that is right and were
I have to change the path. 

Additionally, addions works perfectly although leaprc.ff14SB is also
needed. So there the path seems to be set correctly. 

Is there anything I can do about it? 

Thank you 

Freia Krause 

Christian-Albrechts Universit?t zu Kiel,Germany
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From mohamed_nafie at science.suez.edu.eg  Sun Jan  7 05:33:56 2018
From: mohamed_nafie at science.suez.edu.eg (Mohamed S. Nafie)
Date: Sun, 7 Jan 2018 13:33:56 +0000
Subject: [Chimera-users] Inquiry about hydrogen bond analysis- important
Message-ID: <VI1PR0102MB26229780AD44EE2D10A6713B92120@VI1PR0102MB2622.eurprd01.prod.exchangelabs.com>

Chimera team.

I made the hydrogen bond analysis for the co-crystallized ligand for 1DB1 receptor. it makes on the PDB 6 hydrogen bonds through both oxygen and hydrogen of the hydroxyl group (three of both) with the amino acids residues in the binding site, Also chimera forms 6 but through oxygen of hydroxyl group only. This my first question why?

The second question is the structure of the Co crystallized Ligand is not correct, when I adjust the bond order of it by Maestro and save it as pdb and reopen it by Chimera, it forms only two hydrogen binds why?

Please try to help me in this question, because I need it necessary

Thanks

Mohamed S. Nafie
Assistant lecturer Chemistry Department,
Faculty of Science,  Suez Canal University
Ismailia, P.O(41522), Egypt
Mobile: +201065072524
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From meng at cgl.ucsf.edu  Mon Jan  8 09:14:21 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 8 Jan 2018 09:14:21 -0800
Subject: [Chimera-users] Inquiry about hydrogen bond analysis- important
In-Reply-To: <VI1PR0102MB26229780AD44EE2D10A6713B92120@VI1PR0102MB2622.eurprd01.prod.exchangelabs.com>
References: <VI1PR0102MB26229780AD44EE2D10A6713B92120@VI1PR0102MB2622.eurprd01.prod.exchangelabs.com>
Message-ID: <0246DE55-9D04-4963-A3D8-04337581D03C@cgl.ucsf.edu>

Dear Mohamed,
Different hydrogen bond calculations use different methods and parameters, so it is not surprising to get small differences unless you use exactly the same method and parameter values.   Some methods care about the angles, some only care about distances, sometimes it depends on the atom types, and the distance and angle cutoffs can vary.  The Chimera method is described here:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html#criteria>

However, I don?t see any reason to prefer different results than in Chimera, because when I use Chimera to calculate ligand-receptor H-bonds on 1DB1 with the default parameters, I get the same H-bonds as shown in Fig 3D of the paper describing this structure:

<http://www.sciencedirect.com/science/article/pii/S109727650080413X?via%3Dihub>

Secondly, 1DB1 does not have hydrogens in it.   If you use Chimera to find H-bonds on a structure without hydrogens, it will imagine their possible positions when doing the calculation.  If you add hydrogens before doing the calculation, it may decrease the number of H-bonds found because then it only uses the hydrogen positions given, instead of imagining multiple possible positions.

Thirdly, PDB format does not contain bond orders, and I have no idea what Maestro may have done to change the file or why you think it is incorrect.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jan 7, 2018, at 5:33 AM, Mohamed S. Nafie <mohamed_nafie at science.suez.edu.eg> wrote:
> 
> Chimera team.
> 
> I made the hydrogen bond analysis for the co-crystallized ligand for 1DB1 receptor. it makes on the PDB 6 hydrogen bonds through both oxygen and hydrogen of the hydroxyl group (three of both) with the amino acids residues in the binding site, Also chimera forms 6 but through oxygen of hydroxyl group only. This my first question why? 
> 
> The second question is the structure of the Co crystallized Ligand is not correct, when I adjust the bond order of it by Maestro and save it as pdb and reopen it by Chimera, it forms only two hydrogen binds why? 
> 
> Please try to help me in this question, because I need it necessary
> 
> Thanks
> 
> Mohamed S. Nafie 
> Assistant lecturer Chemistry Department,  
> Faculty of Science,  Suez Canal University 
> Ismailia, P.O(41522), Egypt
> Mobile: +201065072524




From pett at cgl.ucsf.edu  Mon Jan  8 11:39:43 2018
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Mon, 8 Jan 2018 11:39:43 -0800
Subject: [Chimera-users] write prmtop, source leaprc.ff14SB
In-Reply-To: <0de40ac8bca3498b056326fc4c702aec@mail.uni-kiel.de>
References: <0de40ac8bca3498b056326fc4c702aec@mail.uni-kiel.de>
Message-ID: <ACC3687E-8E12-4487-BE22-341152E45DF1@cgl.ucsf.edu>

Hi Freia,
	When I upgraded Chimera to use Ambertools17 in October, I changed Add Ions and Add Solvent to account for the fact that the ff14SB leaprc file had moved into that ?oldff? folder, but missed the fact that WritePrmtop needed the same thing.  I have now corrected that, and a fixed version will be in tomorrow?s daily build (look for a daily build dated Jan 6 or newer).  Let me know if you run into any other problems?

?Eric

	Eric Pettersen
	UCSF Computer Graphics Lab

> On Jan 8, 2018, at 5:51 AM, stu118506 <stu118506 at mail.uni-kiel.de> wrote:
> 
> Dear Chimera users,
> 
> I'd like to save a prmtop file of my protein after preparation for molecular dynamics simulation.
> 
> I tried to do it by using Tools - Amber - write Prmtop .
> 
> I get this reply log entry:
> 
> command: ['/gpfs/fs5/home-sh/sumbi463/.local/UCSF-Chimera64-2017-12-05/bin/amber16/bin/sleap', '-f', '/scratch/tmpOlw0GO/solvate.cmd']
> Running sleap command: /gpfs/fs5/home-sh/sumbi463/.local/UCSF-Chimera64-2017-12-05/bin/amber16/bin/sleap -f /scratch/tmpOlw0GO/solvate.cmd
> (writeprmtop) [gtkleap]$ source leaprc.ff14SB
> 
> (writeprmtop) Error: can not find file leaprc.ff14SB in all the search path.
> 
> Failure running sleap
> 
>  
> I guess that it should source oldff/leaprc.ff14SB because the file seems to be in the directory oldff. But I don't know if that is right and were I have to change the path.
> 
> Additionally, addions works perfectly although leaprc.ff14SB is also needed. So there the path seems to be set correctly.
> 
> Is there anything I can do about it?
> 
>  
> Thank you
> 
> Freia Krause
> 
> Christian-Albrechts Universit?t zu Kiel,Germany
> 
>  
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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From rowanlodge19 at gmail.com  Tue Jan  9 01:30:38 2018
From: rowanlodge19 at gmail.com (simon chapman)
Date: Tue, 9 Jan 2018 09:30:38 +0000
Subject: [Chimera-users] substituting atoms
In-Reply-To: <22F2B48B-4F2B-4AF1-9DC4-D345A604826B@cgl.ucsf.edu>
References: <CAJPu8_4BERfN66uP9s4eNa0Drw4MvAzwyDEcJKpB8uQjSMyKDQ@mail.gmail.com>
 <D54630F4-AFE0-4AE7-8BC8-20DAE3F5F8CF@cgl.ucsf.edu>
 <CAJPu8_63fUvHZTybU-zzNz6dOa+kXY91LH32_-+_fYidGh+5cQ@mail.gmail.com>
 <22F2B48B-4F2B-4AF1-9DC4-D345A604826B@cgl.ucsf.edu>
Message-ID: <CAJPu8_6=8XarBYK3qWUnx1dEDxDdajBEbY5VbMV-4eT=CCSUow@mail.gmail.com>

Hello Elaine, sorry to bother you again.

Chimera has been a real treat so far, but I have hit a problem. I've
struggled for a week now, and finally given up!

I am incrementally substituting S for O on four guanines in a regular
complex. 3 substitutions work fine in a simulation and producing very
encouraging data (attachment 1) But 4 substitutions (attachment 2) triggers
a load of error messages. The first is attachment 3. After solvation,
attachment 4 appears and the solvation box is removed if neutralising ions
are added. If ions not added, attachment 5 warning appears.  Not sure if
attachment 6 is relevant.

Hope you can help/advise?

Best wishes   Simon

On 1 January 2018 at 19:33, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Simon,
> The calculation runs on your own computer and as far as I know, there
> isn?t a limit on the run time.  The  ?Run Parameters? section of the
> Molecular Dynamics SImulation dialog allows you to enter the numbers of
> steps for minimization, equilibration, and production.  If you click on
> ?minimization? you can see it is actually a little a menu that can switch
> to ?equilibration? and ?production? subsections.
>
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/md/md.html#run>
>
> You can also specify a restart file for the production run, for
> subsequently doing another production run starting from the endpoint of the
> current one.  As far as I know, there isn?t an upper limit to the number of
> steps per run, but it might be wiser to do multiple production runs anyway
> (so that if something happens, you don?t lose so much prior computation).
>
> The tool was intended more to make MD simulations accessible to many
> people without too steep of a learning curve, rather than for very
> large-scale, long simulations which might be accomplished more efficiently
> with a dedicated MD package (AMBER, GROMACS, etc.), but you can certainly
> try.
>
> 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 30, 2017, at 4:10 AM, simon chapman <rowanlodge19 at gmail.com>
> wrote:
> >
> > Hello Elaine. Yes,remiss of me to leave out so much info! I'm new-ish
> to Chimera and wasn't really sure if there would be a reply (as has
> happened with some other MD products)
> >
> > So thanks for your prompt response.
> >
> > I had no problems with Build Structure after being pointed in the right
> direction. I will try text editor eventually just for the experience.  I
> have successfully substituted S for O in a guanine complex, and will extend
> that to a Se substitution later.
> >
> > The MD simulation runs much  faster if I exclude the Periodic Boundary
> Conditions option.  Is there a way to extend the run-time?  Currently  it
> covers 1000fs. Is getting to picosecond region a possibility?
> >
> > Best wishes and congrats to whoever put Chimera MD together!    Simon
> >
> > On 28 December 2017 at 17:09, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> > Hi Simon,
> > It would have been helpful if you said how you substituted S for O and
> what the error messages were.  I have no idea what you did.
> >
> > You can change atom type and element inside of Chimera or use a text
> editor (not in Chimera) to change the PDB file before opening it in Chimera.
> >
> > The way to change the atom inside of Chimera is to select the atom and
> then use Build Structure (in menu under Tools? Structure Editing), the
> Modify Structure section. Use the option to change the name of the residue
> since if you keep the name the same, Chimera is expecting that residue, not
> something different with a sulphur in it.
> > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/
> editing.html#modify>
> >
> > If you try text-editing instead, remember spacing is important in PDB
> files, so don?t change the spacing. There's a summary of PDB format here:
> > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/
> tutorials/framepdbintro.html>
> >
> > In the text-editor of your choice, in the ATOM line for that atom, I
> would change the atom name, the element symbol (if present, would be near
> the end of the line), and in the ATOM lines for the whole residue, change
> the residue name.
> >
> > Regardless of how you change the atom, however, another problem is that
> this nonstandard residue must be parametrized if you are going to run MD.
> Chimera will try to do this automatically using AMBER?s Antechamber module,
> but especially with highly charged residues such as nucleotides it may
> fail.  In that case, I don?t really have any solution other than to try the
> simpler Gasteiger charges if it gives you a choice of Gasteiger or AM1-BCC.
> > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/
> addcharge.html#antechamber>
> >
> > 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 27, 2017, at 1:49 PM, simon chapman <rowanlodge19 at gmail.com>
> wrote:
> > >
> > > Hello...for my Master's dissertation, I need to substitute a sulphur
> atom for an oxygen in a Molecular Dynamics simulation. The run works fine
> with my target molecule 1KF1.pdb uploaded into Chimera, but the substituted
> version sends quite a few error messages and won't run. It doesn't appear
> to recognise the novel S atom.
> > >
> > > Any help would be much appreciated...I've been stuck on this for
> nearly a week!
> > >
> > > Best wishes   Simon
> >
> >
> > _______________________________________________
> > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> > Manage subscription: http://plato.cgl.ucsf.edu/
> mailman/listinfo/chimera-users
>
>
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From meng at cgl.ucsf.edu  Tue Jan  9 10:24:09 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 9 Jan 2018 10:24:09 -0800
Subject: [Chimera-users] substituting atoms
In-Reply-To: <CAJPu8_6=8XarBYK3qWUnx1dEDxDdajBEbY5VbMV-4eT=CCSUow@mail.gmail.com>
References: <CAJPu8_4BERfN66uP9s4eNa0Drw4MvAzwyDEcJKpB8uQjSMyKDQ@mail.gmail.com>
 <D54630F4-AFE0-4AE7-8BC8-20DAE3F5F8CF@cgl.ucsf.edu>
 <CAJPu8_63fUvHZTybU-zzNz6dOa+kXY91LH32_-+_fYidGh+5cQ@mail.gmail.com>
 <22F2B48B-4F2B-4AF1-9DC4-D345A604826B@cgl.ucsf.edu>
 <CAJPu8_6=8XarBYK3qWUnx1dEDxDdajBEbY5VbMV-4eT=CCSUow@mail.gmail.com>
Message-ID: <E4A29D03-3EB7-4E5C-B3F2-2E64C054C4D1@cgl.ucsf.edu>

Hi Simon,
I think you may be stretching the tools beyond their intended purposes: Chimera?s minimization, molecular dynamics interface, and automatic parametrization of nonstandard residues with Antechamber are meant to provide relatively simple access to such calculations by noncomputational scientists, given the large learning curves of dedicated simulation packages like GROMACS, AMBER, etc. These tools can be highly useful to clean up structures or suggest additional reasonable conformations. However, they are not meant for precise quantification of energies or for very long simulations, especially not in conjunction with nonstandard residues with parameters estimated by Antechamber.  The Gasteiger charges are very quick-and-dirty, so I would caution against overinterpreting simulations that employ them.  Further, Antechember is meant to cover most small organic molecules but not every possible molecule.

It seems that the modified UNK residues fall into two structural types (as per the ?specify net charges? dialog), and that one (maybe just the 4th?) fails in parametrization by Antechamber, and then the Solvate or Add Ions tool cannot find some parameter needed for its calculation. These tools come from the Ambertools package even though they are included with Chimera and Chimera has interfaces to them.  I don?t know exactly what the problem is, nor do I have a solution, sorry.  
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Jan 9, 2018, at 1:30 AM, simon chapman <rowanlodge19 at gmail.com> wrote:
> 
> Hello Elaine, sorry to bother you again.
> 
> Chimera has been a real treat so far, but I have hit a problem. I've struggled for a week now, and finally given up!
> 
> I am incrementally substituting S for O on four guanines in a regular complex. 3 substitutions work fine in a simulation and producing very encouraging data (attachment 1) But 4 substitutions (attachment 2) triggers a load of error messages. The first is attachment 3. After solvation, attachment 4 appears and the solvation box is removed if neutralising ions are added. If ions not added, attachment 5 warning appears.  Not sure if attachment 6 is relevant.
> 
> Hope you can help/advise?
> 
> Best wishes   Simon
> 




From pett at cgl.ucsf.edu  Tue Jan  9 11:31:51 2018
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Tue, 9 Jan 2018 11:31:51 -0800
Subject: [Chimera-users] substituting atoms
In-Reply-To: <E4A29D03-3EB7-4E5C-B3F2-2E64C054C4D1@cgl.ucsf.edu>
References: <CAJPu8_4BERfN66uP9s4eNa0Drw4MvAzwyDEcJKpB8uQjSMyKDQ@mail.gmail.com>
 <D54630F4-AFE0-4AE7-8BC8-20DAE3F5F8CF@cgl.ucsf.edu>
 <CAJPu8_63fUvHZTybU-zzNz6dOa+kXY91LH32_-+_fYidGh+5cQ@mail.gmail.com>
 <22F2B48B-4F2B-4AF1-9DC4-D345A604826B@cgl.ucsf.edu>
 <CAJPu8_6=8XarBYK3qWUnx1dEDxDdajBEbY5VbMV-4eT=CCSUow@mail.gmail.com>
 <E4A29D03-3EB7-4E5C-B3F2-2E64C054C4D1@cgl.ucsf.edu>
Message-ID: <55D62632-F2CD-448C-9924-F1D5DA2A26D8@cgl.ucsf.edu>

Hi Simon,
	Everything Elaine says is true.  I do have some last ditch suggestions for you though.  One thing is that the fourth guanine differs in protonation state from the others in that the fourth one either has or lacks an HO3? whereas the others don?t.  You should investigate why this is the case.  The two possibilities are then:

1) The protonation difference is an error.  You would need to correct the structure so that all four guanines start with the same protonation.
2) For some reason the protonation difference is okay.  You then need to give the modified version of the fourth guanine a different name from the others, e.g. ?UK2? instead of ?UNK?.  Not guaranteeing this will work, but it might.

?Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


On Jan 9, 2018, at 10:24 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi Simon,
> I think you may be stretching the tools beyond their intended purposes: Chimera?s minimization, molecular dynamics interface, and automatic parametrization of nonstandard residues with Antechamber are meant to provide relatively simple access to such calculations by noncomputational scientists, given the large learning curves of dedicated simulation packages like GROMACS, AMBER, etc. These tools can be highly useful to clean up structures or suggest additional reasonable conformations. However, they are not meant for precise quantification of energies or for very long simulations, especially not in conjunction with nonstandard residues with parameters estimated by Antechamber.  The Gasteiger charges are very quick-and-dirty, so I would caution against overinterpreting simulations that employ them.  Further, Antechember is meant to cover most small organic molecules but not every possible molecule.
> 
> It seems that the modified UNK residues fall into two structural types (as per the ?specify net charges? dialog), and that one (maybe just the 4th?) fails in parametrization by Antechamber, and then the Solvate or Add Ions tool cannot find some parameter needed for its calculation. These tools come from the Ambertools package even though they are included with Chimera and Chimera has interfaces to them.  I don?t know exactly what the problem is, nor do I have a solution, sorry.  
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
>> On Jan 9, 2018, at 1:30 AM, simon chapman <rowanlodge19 at gmail.com> wrote:
>> 
>> Hello Elaine, sorry to bother you again.
>> 
>> Chimera has been a real treat so far, but I have hit a problem. I've struggled for a week now, and finally given up!
>> 
>> I am incrementally substituting S for O on four guanines in a regular complex. 3 substitutions work fine in a simulation and producing very encouraging data (attachment 1) But 4 substitutions (attachment 2) triggers a load of error messages. The first is attachment 3. After solvation, attachment 4 appears and the solvation box is removed if neutralising ions are added. If ions not added, attachment 5 warning appears.  Not sure if attachment 6 is relevant.
>> 
>> Hope you can help/advise?
>> 
>> Best wishes   Simon
>> 
> 
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 

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From rowanlodge19 at gmail.com  Wed Jan 10 04:09:37 2018
From: rowanlodge19 at gmail.com (simon chapman)
Date: Wed, 10 Jan 2018 12:09:37 +0000
Subject: [Chimera-users] substituting atoms
In-Reply-To: <55D62632-F2CD-448C-9924-F1D5DA2A26D8@cgl.ucsf.edu>
References: <CAJPu8_4BERfN66uP9s4eNa0Drw4MvAzwyDEcJKpB8uQjSMyKDQ@mail.gmail.com>
 <D54630F4-AFE0-4AE7-8BC8-20DAE3F5F8CF@cgl.ucsf.edu>
 <CAJPu8_63fUvHZTybU-zzNz6dOa+kXY91LH32_-+_fYidGh+5cQ@mail.gmail.com>
 <22F2B48B-4F2B-4AF1-9DC4-D345A604826B@cgl.ucsf.edu>
 <CAJPu8_6=8XarBYK3qWUnx1dEDxDdajBEbY5VbMV-4eT=CCSUow@mail.gmail.com>
 <E4A29D03-3EB7-4E5C-B3F2-2E64C054C4D1@cgl.ucsf.edu>
 <55D62632-F2CD-448C-9924-F1D5DA2A26D8@cgl.ucsf.edu>
Message-ID: <CAJPu8_5tTDM7vXKp5eJUtBnc4i-Lt1WNwP5kJMt0x_+VoOBE8Q@mail.gmail.com>

Hello Elaine and Eric. Thankyou for the prompt reply....and I'm very
impressed! Eric's suggestion #2 worked!

I assumed the protonation was OK as I ran the PDB downloaded structure
through a protonation webserver (H++).  So I just changed the name of the
novel substitution. It looks like additional alterations will also need
renaming: I ran the next substitution in the incremental progression( #5)
as "UNK3",and that is just about to complete.

I am especially pleased as the data are definitely tending to support my
hypothesis. You will acknowledged in the Methodology section of my
dissertation.

So, thanks again. There's a charming 14th century pub just down the lane
from me...buy you both a pint next time you're passing through

Best wishes   Simon

On 9 January 2018 at 19:31, Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> Hi Simon,
> Everything Elaine says is true.  I do have some last ditch suggestions for
> you though.  One thing is that the fourth guanine differs in protonation
> state from the others in that the fourth one either has or lacks an HO3?
> whereas the others don?t.  You should investigate why this is the case.
> The two possibilities are then:
>
> 1) The protonation difference is an error.  You would need to correct the
> structure so that all four guanines start with the same protonation.
> 2) For some reason the protonation difference is okay.  You then need to
> give the modified version of the fourth guanine a different name from the
> others, e.g. ?UK2? instead of ?UNK?.  Not guaranteeing this will work, but
> it might.
>
> ?Eric
>
> Eric Pettersen
> UCSF Computer Graphics Lab
>
>
> On Jan 9, 2018, at 10:24 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>
>
> Hi Simon,
> I think you may be stretching the tools beyond their intended purposes:
> Chimera?s minimization, molecular dynamics interface, and automatic
> parametrization of nonstandard residues with Antechamber are meant to
> provide relatively simple access to such calculations by noncomputational
> scientists, given the large learning curves of dedicated simulation
> packages like GROMACS, AMBER, etc. These tools can be highly useful to
> clean up structures or suggest additional reasonable conformations.
> However, they are not meant for precise quantification of energies or for
> very long simulations, especially not in conjunction with nonstandard
> residues with parameters estimated by Antechamber.  The Gasteiger charges
> are very quick-and-dirty, so I would caution against overinterpreting
> simulations that employ them.  Further, Antechember is meant to cover most
> small organic molecules but not every possible molecule.
>
> It seems that the modified UNK residues fall into two structural types (as
> per the ?specify net charges? dialog), and that one (maybe just the 4th?)
> fails in parametrization by Antechamber, and then the Solvate or Add Ions
> tool cannot find some parameter needed for its calculation. These tools
> come from the Ambertools package even though they are included with Chimera
> and Chimera has interfaces to them.  I don?t know exactly what the problem
> is, nor do I have a solution, sorry.
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
> On Jan 9, 2018, at 1:30 AM, simon chapman <rowanlodge19 at gmail.com> wrote:
>
> Hello Elaine, sorry to bother you again.
>
> Chimera has been a real treat so far, but I have hit a problem. I've
> struggled for a week now, and finally given up!
>
> I am incrementally substituting S for O on four guanines in a regular
> complex. 3 substitutions work fine in a simulation and producing very
> encouraging data (attachment 1) But 4 substitutions (attachment 2) triggers
> a load of error messages. The first is attachment 3. After solvation,
> attachment 4 appears and the solvation box is removed if neutralising ions
> are added. If ions not added, attachment 5 warning appears.  Not sure if
> attachment 6 is relevant.
>
> Hope you can help/advise?
>
> Best wishes   Simon
>
>
>
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/
> mailman/listinfo/chimera-users
>
>
>
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From mysterayrice at yahoo.com  Wed Jan 10 07:39:14 2018
From: mysterayrice at yahoo.com (Mysteray Rice)
Date: Wed, 10 Jan 2018 15:39:14 +0000 (UTC)
Subject: [Chimera-users] importing chimera module question
References: <1191158523.444088.1515598754887.ref@mail.yahoo.com>
Message-ID: <1191158523.444088.1515598754887@mail.yahoo.com>



Get organized with Yahoo Mail
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From pett at cgl.ucsf.edu  Wed Jan 10 11:01:17 2018
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Wed, 10 Jan 2018 11:01:17 -0800
Subject: [Chimera-users] substituting atoms
In-Reply-To: <CAJPu8_5tTDM7vXKp5eJUtBnc4i-Lt1WNwP5kJMt0x_+VoOBE8Q@mail.gmail.com>
References: <CAJPu8_4BERfN66uP9s4eNa0Drw4MvAzwyDEcJKpB8uQjSMyKDQ@mail.gmail.com>
 <D54630F4-AFE0-4AE7-8BC8-20DAE3F5F8CF@cgl.ucsf.edu>
 <CAJPu8_63fUvHZTybU-zzNz6dOa+kXY91LH32_-+_fYidGh+5cQ@mail.gmail.com>
 <22F2B48B-4F2B-4AF1-9DC4-D345A604826B@cgl.ucsf.edu>
 <CAJPu8_6=8XarBYK3qWUnx1dEDxDdajBEbY5VbMV-4eT=CCSUow@mail.gmail.com>
 <E4A29D03-3EB7-4E5C-B3F2-2E64C054C4D1@cgl.ucsf.edu>
 <55D62632-F2CD-448C-9924-F1D5DA2A26D8@cgl.ucsf.edu>
 <CAJPu8_5tTDM7vXKp5eJUtBnc4i-Lt1WNwP5kJMt0x_+VoOBE8Q@mail.gmail.com>
Message-ID: <68D0300F-B133-45A3-A73B-4E7C44FCB479@cgl.ucsf.edu>

Great!  If we?re in the neighborhood I?ll take a pint of ginger ale. :-)

?Eric

> On Jan 10, 2018, at 4:09 AM, simon chapman <rowanlodge19 at gmail.com> wrote:
> 
> Hello Elaine and Eric. Thankyou for the prompt reply....and I'm very impressed! Eric's suggestion #2 worked!
> 
> I assumed the protonation was OK as I ran the PDB downloaded structure through a protonation webserver (H++).  So I just changed the name of the novel substitution. It looks like additional alterations will also need renaming: I ran the next substitution in the incremental progression( #5) as "UNK3",and that is just about to complete. 
> 
> I am especially pleased as the data are definitely tending to support my hypothesis. You will acknowledged in the Methodology section of my dissertation.
> 
> So, thanks again. There's a charming 14th century pub just down the lane from me...buy you both a pint next time you're passing through
> 
> Best wishes   Simon
> 
> On 9 January 2018 at 19:31, Eric Pettersen <pett at cgl.ucsf.edu <mailto:pett at cgl.ucsf.edu>> wrote:
> Hi Simon,
> 	Everything Elaine says is true.  I do have some last ditch suggestions for you though.  One thing is that the fourth guanine differs in protonation state from the others in that the fourth one either has or lacks an HO3? whereas the others don?t.  You should investigate why this is the case.  The two possibilities are then:
> 
> 1) The protonation difference is an error.  You would need to correct the structure so that all four guanines start with the same protonation.
> 2) For some reason the protonation difference is okay.  You then need to give the modified version of the fourth guanine a different name from the others, e.g. ?UK2? instead of ?UNK?.  Not guaranteeing this will work, but it might.
> 
> ?Eric
> 
>  	Eric Pettersen
> 	UCSF Computer Graphics Lab
> 
> 
> On Jan 9, 2018, at 10:24 AM, Elaine Meng <meng at cgl.ucsf.edu <mailto:meng at cgl.ucsf.edu>> wrote:
>> 
>> Hi Simon,
>> I think you may be stretching the tools beyond their intended purposes: Chimera?s minimization, molecular dynamics interface, and automatic parametrization of nonstandard residues with Antechamber are meant to provide relatively simple access to such calculations by noncomputational scientists, given the large learning curves of dedicated simulation packages like GROMACS, AMBER, etc. These tools can be highly useful to clean up structures or suggest additional reasonable conformations. However, they are not meant for precise quantification of energies or for very long simulations, especially not in conjunction with nonstandard residues with parameters estimated by Antechamber.  The Gasteiger charges are very quick-and-dirty, so I would caution against overinterpreting simulations that employ them.  Further, Antechember is meant to cover most small organic molecules but not every possible molecule.
>> 
>> It seems that the modified UNK residues fall into two structural types (as per the ?specify net charges? dialog), and that one (maybe just the 4th?) fails in parametrization by Antechamber, and then the Solvate or Add Ions tool cannot find some parameter needed for its calculation. These tools come from the Ambertools package even though they are included with Chimera and Chimera has interfaces to them.  I don?t know exactly what the problem is, nor do I have a solution, sorry.  
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.                       
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> 
>> 
>>> On Jan 9, 2018, at 1:30 AM, simon chapman <rowanlodge19 at gmail.com <mailto:rowanlodge19 at gmail.com>> wrote:
>>> 
>>> Hello Elaine, sorry to bother you again.
>>> 
>>> Chimera has been a real treat so far, but I have hit a problem. I've struggled for a week now, and finally given up!
>>> 
>>> I am incrementally substituting S for O on four guanines in a regular complex. 3 substitutions work fine in a simulation and producing very encouraging data (attachment 1) But 4 substitutions (attachment 2) triggers a load of error messages. The first is attachment 3. After solvation, attachment 4 appears and the solvation box is removed if neutralising ions are added. If ions not added, attachment 5 warning appears.  Not sure if attachment 6 is relevant.
>>> 
>>> Hope you can help/advise?
>>> 
>>> Best wishes   Simon
>>> 
>> 
>> 
>> _______________________________________________
>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu <mailto:Chimera-users at cgl.ucsf.edu>
>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
>> 
> 
> 

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From nguyen.henry.c at gmail.com  Wed Jan 10 14:24:46 2018
From: nguyen.henry.c at gmail.com (Henry Nguyen)
Date: Wed, 10 Jan 2018 14:24:46 -0800
Subject: [Chimera-users] Pseudobonds in mmCIF
Message-ID: <CADbM=U50kSJ5WZVsK_r3BCZRZFyOkNnmtGk+P2=h5Q+yPb9L9Q@mail.gmail.com>

Hi,

I am trying to disable all pseudobonds between gaps in my structure in an
mmCIF file. I've tried:

In the Pseudobond Panel, there is only one group (distance monitor) and it
has 0 pseudobonds in the group.  Hiding that group doesn't change anything.

I also tried disabling them using setattrr ("setattr p display false"/
"setattr p display false") but neither didn't change anything.

If I select a psuedobond and examine it using the Selection Inspector, the
Pseudobond tab is unselectable under Inspect. Only if I go to the Bond tab
can I hide it.

I have to use mmCIF format as I have too many chains for a pdb.

Thanks,
Henry
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From meng at cgl.ucsf.edu  Wed Jan 10 16:00:53 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 10 Jan 2018 16:00:53 -0800
Subject: [Chimera-users] Pseudobonds in mmCIF
In-Reply-To: <CADbM=U50kSJ5WZVsK_r3BCZRZFyOkNnmtGk+P2=h5Q+yPb9L9Q@mail.gmail.com>
References: <CADbM=U50kSJ5WZVsK_r3BCZRZFyOkNnmtGk+P2=h5Q+yPb9L9Q@mail.gmail.com>
Message-ID: <DA43877C-3D03-41C0-AE30-CC7161AAC5B2@cgl.ucsf.edu>

Hi Henry,
The simpler command is

~longbond

? but I am confused because in my tests of opening 1www.cif  (which has examples of missing segments pseudobonds) they are listed in the Pseudobond Panel as ?missing segments? and these commands also work:

setattr p display false
setattr g display false

I?m testing with Chimera version 1.12.

Your description makes me think the offending connections may actually be bonds, not pseudobonds.  To say any more, we?d have to see the file? maybe something in there is wrong.  

If they are bonds, you can delete them with the ~bond command or in the Build Structure tool (in menu under Tools? Structure Editing) Adjust Bonds section.

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/bond.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#bond>

My only other idea is that they result from autochaining, which you can turn off with command:

setattr m autochain 0

(that?s a zero)

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Jan 10, 2018, at 2:24 PM, Henry Nguyen <nguyen.henry.c at gmail.com> wrote:
> 
> Hi,
> 
> I am trying to disable all pseudobonds between gaps in my structure in an mmCIF file. I've tried: 
> 
> In the Pseudobond Panel, there is only one group (distance monitor) and it has 0 pseudobonds in the group.  Hiding that group doesn't change anything.
> 
> I also tried disabling them using setattrr ("setattr p display false"/ "setattr p display false") but neither didn't change anything.
> 
> If I select a psuedobond and examine it using the Selection Inspector, the Pseudobond tab is unselectable under Inspect. Only if I go to the Bond tab can I hide it.
> 
> I have to use mmCIF format as I have too many chains for a pdb.
> 
> Thanks,
> Henry






From sette at uniroma2.it  Thu Jan 11 02:17:44 2018
From: sette at uniroma2.it (Marco Sette)
Date: Thu, 11 Jan 2018 11:17:44 +0100
Subject: [Chimera-users] Output of distance measurements
Message-ID: <a12856fb-9dc8-6fd3-54d8-a0bab1f3e1d0@uniroma2.it>

Dear all,

I have a very primitive script to measure distances, like
distance :1.a at ha :5.b at ha
distance :1.a at ha :4.b at ha
distance ....
etc.
I run the script in File --> Open and get the distances in the Structure 
Measurements panel and then Save.
The output file list all the distances but, for my analysis, it would be 
better to keep the lines separated by a blank line, or something like this.
Maybe this is possible by some change in my primtive script but I have 
no idea...

Thanks for your help,
Marco



From meng at cgl.ucsf.edu  Thu Jan 11 10:07:16 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 11 Jan 2018 10:07:16 -0800
Subject: [Chimera-users] Output of distance measurements
In-Reply-To: <a12856fb-9dc8-6fd3-54d8-a0bab1f3e1d0@uniroma2.it>
References: <a12856fb-9dc8-6fd3-54d8-a0bab1f3e1d0@uniroma2.it>
Message-ID: <86B46222-6250-4AC8-BA02-7885BEA384C7@cgl.ucsf.edu>

Hi Marco,
If you put the command

echo

between the distance commands, it will put a blank line in the Log. It worked when I tried it, at least!
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jan 11, 2018, at 2:17 AM, Marco Sette <sette at uniroma2.it> wrote:
> 
> Dear all,
> 
> I have a very primitive script to measure distances, like
> distance :1.a at ha :5.b at ha
> distance :1.a at ha :4.b at ha
> distance ....
> etc.
> I run the script in File --> Open and get the distances in the Structure Measurements panel and then Save.
> The output file list all the distances but, for my analysis, it would be better to keep the lines separated by a blank line, or something like this.
> Maybe this is possible by some change in my primtive script but I have no idea...
> 
> Thanks for your help,
> Marco



From pett at cgl.ucsf.edu  Thu Jan 11 11:23:35 2018
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Thu, 11 Jan 2018 11:23:35 -0800
Subject: [Chimera-users] Output of distance measurements
In-Reply-To: <86B46222-6250-4AC8-BA02-7885BEA384C7@cgl.ucsf.edu>
References: <a12856fb-9dc8-6fd3-54d8-a0bab1f3e1d0@uniroma2.it>
 <86B46222-6250-4AC8-BA02-7885BEA384C7@cgl.ucsf.edu>
Message-ID: <08928C6B-5B4D-4768-A884-ABEDCA92C115@cgl.ucsf.edu>

To use Elaine?s suggestion you have to use the Save button on the Reply Log, not the Save button on the Distances dialog.  The only way to get blanks lines in that is to change Chimera?s Python code.

?Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Jan 11, 2018, at 10:07 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi Marco,
> If you put the command
> 
> echo
> 
> between the distance commands, it will put a blank line in the Log. It worked when I tried it, at least!
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
>> On Jan 11, 2018, at 2:17 AM, Marco Sette <sette at uniroma2.it> wrote:
>> 
>> Dear all,
>> 
>> I have a very primitive script to measure distances, like
>> distance :1.a at ha :5.b at ha
>> distance :1.a at ha :4.b at ha
>> distance ....
>> etc.
>> I run the script in File --> Open and get the distances in the Structure Measurements panel and then Save.
>> The output file list all the distances but, for my analysis, it would be better to keep the lines separated by a blank line, or something like this.
>> Maybe this is possible by some change in my primtive script but I have no idea...
>> 
>> Thanks for your help,
>> Marco
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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From xzhang1999 at zju.edu.cn  Thu Jan 11 18:43:23 2018
From: xzhang1999 at zju.edu.cn (xzhang1999 at zju.edu.cn)
Date: Fri, 12 Jan 2018 10:43:23 +0800
Subject: [Chimera-users] Does Chimera support stereo with a Nvidia Quadro
	M4000 graphics card?
Message-ID: <2018011205572596561616@zju.edu.cn>

Hi, 

Does Chimera support stereo on the Nvidia Quadro M4000 graphics card? I have a workstation with a Nvidia Quadro M4000 graphcs card (64bit, win10&ubantu), but cannot successfully have Chimera displaying sequential stereo? Any suggestion would be greatly appreciated. Thanks a lot.



Best regards,
Xing

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From gregc at cgl.ucsf.edu  Thu Jan 11 22:02:15 2018
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Thu, 11 Jan 2018 22:02:15 -0800
Subject: [Chimera-users] Does Chimera support stereo with a Nvidia
 Quadro M4000 graphics card?
In-Reply-To: <2018011205572596561616@zju.edu.cn>
References: <2018011205572596561616@zju.edu.cn>
Message-ID: <48148feb-16b6-76d6-68d0-9d1bc31dc37b@cgl.ucsf.edu>

Yes, Chimera supports stereo on the NVidia Quadro M4000 graphics care.? 
A simple test to see if you have configured your system correctly is to 
run the stereotest program from 
https://www.cgl.ucsf.edu/Overview/stereotest.html.? In your case, I 
expect that it would show that stereo isn't working.

To fix it depends on which OS you're using:

On Linux, you'll need to configure the X11 display server to show 
stereo.? See the NVidia release notes in 
/usr/share/doc/nvidia-x11-drv-*/.? In the appendix on X Config Options, 
it says how to set the Stereo option.? Pick the Stereo option that 
matches the 3D stereo display setup that you are using -- you most 
likely have a 3D TV that came with stereo glasses, or a 120hz+ gaming 
monitor with NVidia 3D Vision support and associated glasses, those 
would be options 12 or 10, respectively.? If you are using the 3D Vision 
emitter, I'd recommend connecting the 3-pin DIN cable from the M4000's 
daughter card.

On WIndows, you need to go to the NVidia control panel, and choose 
"Manage 3D settings", not the Stereoscopic settings.? There you need to 
set "Stereo - Enable" to on, and "Stereo - Display mode" to match your 
3D stereo display setup.? Again, I'd recommend using the 3-pin DIN cable 
with the NVidia 3D Vision emitter if you are using that.

 ??? Hope this helps,

 ??? Greg

On 1/11/2018 6:43 PM, xzhang1999 at zju.edu.cn wrote:
> Hi,
>
> Does Chimera support stereo on the Nvidia Quadro M4000 graphics card? 
> I have a workstation with a Nvidia Quadro M4000 graphcs card (64bit, 
> win10&ubantu), but cannot successfully have Chimera displaying 
> sequential stereo? Any suggestion would be greatly appreciated. Thanks 
> a lot.
>
> ------------------------------------------------------------------------
> Best regards,
> Xing
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From batra1 at niehs.nih.gov  Fri Jan 12 11:22:44 2018
From: batra1 at niehs.nih.gov (Batra, Vinod (NIH/NIEHS) [C])
Date: Fri, 12 Jan 2018 19:22:44 +0000
Subject: [Chimera-users] Adding Menu items to Python Shell
Message-ID: <99953286-2997-465D-BC86-BE24540ED148@niehs.nih.gov>

Hi
How to add menu items to IDLE-> Python Shell opened with Chimera 1:1x running on OS X.

Vinod Batra
NIEHS
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From sette at uniroma2.it  Sat Jan 13 13:27:19 2018
From: sette at uniroma2.it (Marco Sette)
Date: Sat, 13 Jan 2018 22:27:19 +0100
Subject: [Chimera-users] Output of distance measurements
In-Reply-To: <08928C6B-5B4D-4768-A884-ABEDCA92C115@cgl.ucsf.edu>
References: <a12856fb-9dc8-6fd3-54d8-a0bab1f3e1d0@uniroma2.it>
 <86B46222-6250-4AC8-BA02-7885BEA384C7@cgl.ucsf.edu>
 <08928C6B-5B4D-4768-A884-ABEDCA92C115@cgl.ucsf.edu>
Message-ID: <ece3a5ee-4216-3fc3-37e8-c2cd74fb8cce@uniroma2.it>

Thanks Elaine and Eric,

it works fine :)

Best

Marco


Il 11/01/2018 20:23, Eric Pettersen ha scritto:
> To use Elaine?s suggestion you have to use the Save button on the 
> Reply Log, not the Save button on the Distances dialog. ?The only way 
> to get blanks lines in that is to change Chimera?s Python code.
>
> ?Eric
>
> Eric Pettersen
> UCSF Computer Graphics Lab
>
>
>> On Jan 11, 2018, at 10:07 AM, Elaine Meng <meng at cgl.ucsf.edu 
>> <mailto:meng at cgl.ucsf.edu>> wrote:
>>
>> Hi Marco,
>> If you put the command
>>
>> echo
>>
>> between the distance commands, it will put a blank line in the Log. 
>> It worked when I tried it, at least!
>> Best,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.
>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>>
>>> On Jan 11, 2018, at 2:17 AM, Marco Sette <sette at uniroma2.it 
>>> <mailto:sette at uniroma2.it>> wrote:
>>>
>>> Dear all,
>>>
>>> I have a very primitive script to measure distances, like
>>> distance :1.a at ha :5.b at ha
>>> distance :1.a at ha :4.b at ha
>>> distance ....
>>> etc.
>>> I run the script in File --> Open and get the distances in the 
>>> Structure Measurements panel and then Save.
>>> The output file list all the distances but, for my analysis, it 
>>> would be better to keep the lines separated by a blank line, or 
>>> something like this.
>>> Maybe this is possible by some change in my primtive script but I 
>>> have no idea...
>>>
>>> Thanks for your help,
>>> Marco
>>
>> _______________________________________________
>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu 
>> <mailto:Chimera-users at cgl.ucsf.edu>
>> Manage subscription: 
>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>

-- 
Dr.Marco Sette, Ph.D.
Department of Chemical Sciences and Technology
University of Rome, "Tor Vergata"
via della Ricerca Scientifica, 00133, Rome, Italy
e-mail: sette at uniroma2.it
e-mail: m77it at yahoo.it
Tel.: +39-0672594424
Fax: +39-0672594328
http://stc.uniroma2.it/?page_id=622&cn-entry-slug=marco-sette

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From xzhang1999 at zju.edu.cn  Sat Jan 13 18:48:34 2018
From: xzhang1999 at zju.edu.cn (xzhang1999 at zju.edu.cn)
Date: Sun, 14 Jan 2018 10:48:34 +0800
Subject: [Chimera-users] Does Chimera support stereo with a Nvidia
	Quadro M4000 graphics card?
References: <2018011205572596561616@zju.edu.cn>, 
 <48148feb-16b6-76d6-68d0-9d1bc31dc37b@cgl.ucsf.edu>
Message-ID: <201801141048341221744@zju.edu.cn>

Thanks much for help, Greg,

We now have it working on Linux, but the stereo display in win10 is still not as good as that on linux! and we will play the configuations on win10. Thanks.



Best regards,
Xing
 
From: Greg Couch
Date: 2018-01-12 14:02
To: xzhang1999 at zju.edu.cn; chimera-users
Subject: Re: [Chimera-users] Does Chimera support stereo with a Nvidia Quadro M4000 graphics card?
Yes, Chimera supports stereo on the NVidia Quadro M4000 graphics care.  A simple test to see if you have configured your system correctly is to run the stereotest program from https://www.cgl.ucsf.edu/Overview/stereotest.html.  In your case, I expect that it would show that stereo isn't working.
To fix it depends on which OS you're using:
On Linux, you'll need to configure the X11 display server to show stereo.  See the NVidia release notes in /usr/share/doc/nvidia-x11-drv-*/.  In the appendix on X Config Options, it says how to set the Stereo option.  Pick the Stereo option that matches the 3D stereo display setup that you are using -- you most likely have a 3D TV that came with stereo glasses, or a 120hz+ gaming monitor with NVidia 3D Vision support and associated glasses, those would be options 12 or 10, respectively.  If you are using the 3D Vision emitter, I'd recommend connecting the 3-pin DIN cable from the M4000's daughter card.
On WIndows, you need to go to the NVidia control panel, and choose "Manage 3D settings", not the Stereoscopic settings.  There you need to set "Stereo - Enable" to on, and "Stereo - Display mode" to match your 3D stereo display setup.  Again, I'd recommend using the 3-pin DIN cable with the NVidia 3D Vision emitter if you are using that.
    Hope this helps,
    Greg
On 1/11/2018 6:43 PM, xzhang1999 at zju.edu.cn wrote:
Hi, 

Does Chimera support stereo on the Nvidia Quadro M4000 graphics card? I have a workstation with a Nvidia Quadro M4000 graphcs card (64bit, win10&ubantu), but cannot successfully have Chimera displaying sequential stereo? Any suggestion would be greatly appreciated. Thanks a lot.



Best regards, 
Xing
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From meng at cgl.ucsf.edu  Tue Jan 16 09:40:05 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 16 Jan 2018 09:40:05 -0800
Subject: [Chimera-users] Pseudobonds in mmCIF
In-Reply-To: <CADbM=U7en=9kJRV=SNCFmC9hwmb+hs-+Yjz94FGufXT0B67+Jg@mail.gmail.com>
References: <CADbM=U7rEwcX8+eF6Ksidu6COkb4JUOsa49EEu=_dTAc9j3jYA@mail.gmail.com>
 <512DCFBC-D4BB-4639-BDA6-6FC935475EA9@cgl.ucsf.edu>
 <b5ae50cb-8b62-0675-344b-e66b46b42616@cgl.ucsf.edu>
 <CADbM=U7nYtKEk_7WaLb9aByQ-imy_d-ACympTVAryH1taLcWeg@mail.gmail.com>
 <680DB50A-21D8-43B8-86F1-810F1C67F8C4@cgl.ucsf.edu>
 <CADbM=U7en=9kJRV=SNCFmC9hwmb+hs-+Yjz94FGufXT0B67+Jg@mail.gmail.com>
Message-ID: <297F26E6-6ECD-4E75-833D-9E78CD812B19@cgl.ucsf.edu>

Just for the benefit of the list, the problem with spurious bonds between residues in Chimera was solved by adding sequence information to the input mmCIF file.
Elaine

> > On Jan 11, 2018, at 1:35 PM, Henry Nguyen <nguyen.henry.c at gmail.com> wrote:
> >
> > Thanks everyone for all the help. My problem is fixed by running mmtbx.prepare_pdb_deposition with the sequence information. The new cif file is displaying pseudobonds correctly and can be toggled on/off.
> >
> > Thanks again!
> > Henry
> >
> > On Thu, Jan 11, 2018 at 11:43 AM, Greg Couch <gregc at cgl.ucsf.edu> wrote:
> > Hi Henry,
> >
> > Sorry about the problems with mmCIF in Chimera.  Those problems are a major reason why we wrote ChimeraX.  So please check out ChimeraX, http://www.rbvi.ucsf.edu/chimerax/.  The mmCIF reader is several orders of magnitude faster than Chimera's and presents the author numbering to identify residues instead of the internal mmCIF numbering.  The graphics in ChimeraX are better too.  If there is some feature in Chimera that isn't in ChimeraX yet that you need, please let us know.  ChimeraX also works with VR headsets.
> > And while ChimeraX shows your structure "correctly".  It could do a much better job if the missing sequence information were in the mmCIF file.  In Phenix, that is done by running the mmtbx.prepare_pdb_deposition program, i.e, by preparing the mmCIF file so that is suitable for submission to the PDB.  That would probably help Chimera too.
> >
> >     HTH,
> >     Greg




From jerryeuhonts at gmail.com  Fri Jan 12 11:42:44 2018
From: jerryeuhonts at gmail.com (Jerry Honts)
Date: Fri, 12 Jan 2018 13:42:44 -0600
Subject: [Chimera-users] Command line selection in Chimera
Message-ID: <CABx+PAiO3NWNbB8qn1cpiZZW+NK=LUmy0kYa6y2Wmty-vFw0hQ@mail.gmail.com>

Is there any easy way to select *a range of chains* in complex models like
the ribosome in Chimera at the command line?  I haven't been able to work
out the syntax for this type of complex selection at the command line.  For
example, what is the syntax of the command to select chains 1G through 1Z
and chains 10 through 19 in PDB file 5DOY [without explicitly listing them
one by one]?  I may be missing something simple, and I have not been able
to get it to work or find an example in documentation.

I have been able to do this in Chimera X but not the current version of
Chimera.

Thanks,

Jerry E. Honts

-- 
Jerry E. Honts, Ph. D.
Associate Professor of Biology
Drake University
2507 University Avenue
Des Moines, IA 50311-4505
Science Connector Building 210 (faculty office)
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From meng at cgl.ucsf.edu  Tue Jan 16 11:49:23 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 16 Jan 2018 11:49:23 -0800
Subject: [Chimera-users] Command line selection in Chimera
In-Reply-To: <CABx+PAiO3NWNbB8qn1cpiZZW+NK=LUmy0kYa6y2Wmty-vFw0hQ@mail.gmail.com>
References: <CABx+PAiO3NWNbB8qn1cpiZZW+NK=LUmy0kYa6y2Wmty-vFw0hQ@mail.gmail.com>
Message-ID: <C789FD59-C622-40D1-A435-2F8518E081BC@cgl.ucsf.edu>

Hi Jerry,
Chimera does not support 2-character chain IDs, likely the root problem.  On the laptop I?m using today, I can?t even open something as large as 5doy in Chimera (although it?s fine in ChimeraX), but I recall recently testing this with a different structure that had chains A1, A2, ? and I was unable to specify them uniquely in Chimera.  I could specify chain A in Chimera, but it only mapped to one of those 2-letter chains starting with A.
I hope this clarifies the situation,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Jan 12, 2018, at 11:42 AM, Jerry Honts <jerryeuhonts at gmail.com> wrote:
> 
> Is there any easy way to select a range of chains in complex models like the ribosome in Chimera at the command line?  I haven't been able to work out the syntax for this type of complex selection at the command line.  For example, what is the syntax of the command to select chains 1G through 1Z and chains 10 through 19 in PDB file 5DOY [without explicitly listing them one by one]?  I may be missing something simple, and I have not been able to get it to work or find an example in documentation.
> 
> I have been able to do this in Chimera X but not the current version of Chimera.
> 
> Thanks,
> 
> Jerry E. Honts
> -- 
> Jerry E. Honts, Ph. D.
> Associate Professor of Biology
> Drake University
> 2507 University Avenue
> Des Moines, IA 50311-4505
> Science Connector Building 210 (faculty office)




From pett at cgl.ucsf.edu  Tue Jan 16 13:03:19 2018
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Tue, 16 Jan 2018 13:03:19 -0800
Subject: [Chimera-users] Adding Menu items to Python Shell
In-Reply-To: <99953286-2997-465D-BC86-BE24540ED148@niehs.nih.gov>
References: <99953286-2997-465D-BC86-BE24540ED148@niehs.nih.gov>
Message-ID: <34FD8533-7FD2-49D5-9950-1362D8C6A8DE@cgl.ucsf.edu>

Hi Vinod,
	Chimera just adds a thin layer over the Python IDLE shell that is a standard module of Python 2.  So, to add a menu to it you would modify the IDLE code found in Chimera.app/Contents/Resources/lib/python2.7/idlelib.  Keep in mind that new downloads of Chimera won?t have your changes, so you might want to note what changes you made so you could reapply them to newer versions you get.

?Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Jan 12, 2018, at 11:22 AM, Batra, Vinod (NIH/NIEHS) [C] <batra1 at niehs.nih.gov> wrote:
> 
> Hi 
> How to add menu items to IDLE-> Python Shell opened with Chimera 1:1x running on OS X.
>  
> Vinod Batra
> NIEHS
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu <mailto:Chimera-users at cgl.ucsf.edu>
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>

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From rowanlodge19 at gmail.com  Wed Jan 17 04:33:18 2018
From: rowanlodge19 at gmail.com (simon chapman)
Date: Wed, 17 Jan 2018 12:33:18 +0000
Subject: [Chimera-users] substituting atoms
In-Reply-To: <68D0300F-B133-45A3-A73B-4E7C44FCB479@cgl.ucsf.edu>
References: <CAJPu8_4BERfN66uP9s4eNa0Drw4MvAzwyDEcJKpB8uQjSMyKDQ@mail.gmail.com>
 <D54630F4-AFE0-4AE7-8BC8-20DAE3F5F8CF@cgl.ucsf.edu>
 <CAJPu8_63fUvHZTybU-zzNz6dOa+kXY91LH32_-+_fYidGh+5cQ@mail.gmail.com>
 <22F2B48B-4F2B-4AF1-9DC4-D345A604826B@cgl.ucsf.edu>
 <CAJPu8_6=8XarBYK3qWUnx1dEDxDdajBEbY5VbMV-4eT=CCSUow@mail.gmail.com>
 <E4A29D03-3EB7-4E5C-B3F2-2E64C054C4D1@cgl.ucsf.edu>
 <55D62632-F2CD-448C-9924-F1D5DA2A26D8@cgl.ucsf.edu>
 <CAJPu8_5tTDM7vXKp5eJUtBnc4i-Lt1WNwP5kJMt0x_+VoOBE8Q@mail.gmail.com>
 <68D0300F-B133-45A3-A73B-4E7C44FCB479@cgl.ucsf.edu>
Message-ID: <CAJPu8_7Fr59u6srp0QHUy-PYRv8c2kuuRXaMY-UHxtL6+WKYLg@mail.gmail.com>

Hello Eric and Elaine. Chance of earning a second pint of ginger beer if
you wish...

Simulations and analysis going very well, I have substituted all 12 oxygens
for sulphur. Each requires a new name: UNK I, UNK2 etc. Advice for
others...naming will only alow digits 1 to 9. so for 12 iterations, I used
zero and the original unappended "UNK". Which makes 12. I have also
successfully set production for 50000steps, equivalent to 8ps.

However, there appears to be an option for continuation from one run to a
subsequent one. I've tried for a few days now, but get the same error
message every time ('continuation2 attachment').  Changing file names as
described in the message doesn't work. It's probably something simple
(probably me in fact), but would really appreciate your comments.

Best wishes   Simon



On 10 January 2018 at 19:01, Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> Great!  If we?re in the neighborhood I?ll take a pint of ginger ale. :-)
>
> ?Eric
>
>
> On Jan 10, 2018, at 4:09 AM, simon chapman <rowanlodge19 at gmail.com> wrote:
>
> Hello Elaine and Eric. Thankyou for the prompt reply....and I'm very
> impressed! Eric's suggestion #2 worked!
>
> I assumed the protonation was OK as I ran the PDB downloaded structure
> through a protonation webserver (H++).  So I just changed the name of the
> novel substitution. It looks like additional alterations will also need
> renaming: I ran the next substitution in the incremental progression( #5)
> as "UNK3",and that is just about to complete.
>
> I am especially pleased as the data are definitely tending to support my
> hypothesis. You will acknowledged in the Methodology section of my
> dissertation.
>
> So, thanks again. There's a charming 14th century pub just down the lane
> from me...buy you both a pint next time you're passing through
>
> Best wishes   Simon
>
> On 9 January 2018 at 19:31, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
>
>> Hi Simon,
>> Everything Elaine says is true.  I do have some last ditch suggestions
>> for you though.  One thing is that the fourth guanine differs in
>> protonation state from the others in that the fourth one either has or
>> lacks an HO3? whereas the others don?t.  You should investigate why this is
>> the case.  The two possibilities are then:
>>
>> 1) The protonation difference is an error.  You would need to correct the
>> structure so that all four guanines start with the same protonation.
>> 2) For some reason the protonation difference is okay.  You then need to
>> give the modified version of the fourth guanine a different name from the
>> others, e.g. ?UK2? instead of ?UNK?.  Not guaranteeing this will work, but
>> it might.
>>
>> ?Eric
>>
>> Eric Pettersen
>> UCSF Computer Graphics Lab
>>
>>
>> On Jan 9, 2018, at 10:24 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>>
>>
>> Hi Simon,
>> I think you may be stretching the tools beyond their intended purposes:
>> Chimera?s minimization, molecular dynamics interface, and automatic
>> parametrization of nonstandard residues with Antechamber are meant to
>> provide relatively simple access to such calculations by noncomputational
>> scientists, given the large learning curves of dedicated simulation
>> packages like GROMACS, AMBER, etc. These tools can be highly useful to
>> clean up structures or suggest additional reasonable conformations.
>> However, they are not meant for precise quantification of energies or for
>> very long simulations, especially not in conjunction with nonstandard
>> residues with parameters estimated by Antechamber.  The Gasteiger charges
>> are very quick-and-dirty, so I would caution against overinterpreting
>> simulations that employ them.  Further, Antechember is meant to cover most
>> small organic molecules but not every possible molecule.
>>
>> It seems that the modified UNK residues fall into two structural types
>> (as per the ?specify net charges? dialog), and that one (maybe just the
>> 4th?) fails in parametrization by Antechamber, and then the Solvate or Add
>> Ions tool cannot find some parameter needed for its calculation. These
>> tools come from the Ambertools package even though they are included with
>> Chimera and Chimera has interfaces to them.  I don?t know exactly what the
>> problem is, nor do I have a solution, sorry.
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>>
>>
>> On Jan 9, 2018, at 1:30 AM, simon chapman <rowanlodge19 at gmail.com> wrote:
>>
>> Hello Elaine, sorry to bother you again.
>>
>> Chimera has been a real treat so far, but I have hit a problem. I've
>> struggled for a week now, and finally given up!
>>
>> I am incrementally substituting S for O on four guanines in a regular
>> complex. 3 substitutions work fine in a simulation and producing very
>> encouraging data (attachment 1) But 4 substitutions (attachment 2) triggers
>> a load of error messages. The first is attachment 3. After solvation,
>> attachment 4 appears and the solvation box is removed if neutralising ions
>> are added. If ions not added, attachment 5 warning appears.  Not sure if
>> attachment 6 is relevant.
>>
>> Hope you can help/advise?
>>
>> Best wishes   Simon
>>
>>
>>
>> _______________________________________________
>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
>> Manage subscription: http://plato.cgl.ucsf.edu/mail
>> man/listinfo/chimera-users
>>
>>
>>
>
>
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From meng at cgl.ucsf.edu  Wed Jan 17 10:38:32 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 17 Jan 2018 10:38:32 -0800
Subject: [Chimera-users] substituting atoms
In-Reply-To: <CAJPu8_7Fr59u6srp0QHUy-PYRv8c2kuuRXaMY-UHxtL6+WKYLg@mail.gmail.com>
References: <CAJPu8_4BERfN66uP9s4eNa0Drw4MvAzwyDEcJKpB8uQjSMyKDQ@mail.gmail.com>
 <D54630F4-AFE0-4AE7-8BC8-20DAE3F5F8CF@cgl.ucsf.edu>
 <CAJPu8_63fUvHZTybU-zzNz6dOa+kXY91LH32_-+_fYidGh+5cQ@mail.gmail.com>
 <22F2B48B-4F2B-4AF1-9DC4-D345A604826B@cgl.ucsf.edu>
 <CAJPu8_6=8XarBYK3qWUnx1dEDxDdajBEbY5VbMV-4eT=CCSUow@mail.gmail.com>
 <E4A29D03-3EB7-4E5C-B3F2-2E64C054C4D1@cgl.ucsf.edu>
 <55D62632-F2CD-448C-9924-F1D5DA2A26D8@cgl.ucsf.edu>
 <CAJPu8_5tTDM7vXKp5eJUtBnc4i-Lt1WNwP5kJMt0x_+VoOBE8Q@mail.gmail.com>
 <68D0300F-B133-45A3-A73B-4E7C44FCB479@cgl.ucsf.edu>
 <CAJPu8_7Fr59u6srp0QHUy-PYRv8c2kuuRXaMY-UHxtL6+WKYLg@mail.gmail.com>
Message-ID: <97A73AA4-B685-4DEC-A8E6-E3811A47153B@cgl.ucsf.edu>

As I understand it, the message is that the molecules in the input restart file are not the same as the current molecules (not exactly the same set of residues, atoms, bonds).  Changing the filenames would allow for a completely separate run, but it would not solve the problem of continuing the same simulation if the chemical system is different.   How it might be different, I don?t know.  All I can say is if you changed something between the runs, don?t do that.
Elaine


> On Jan 17, 2018, at 4:33 AM, simon chapman <rowanlodge19 at gmail.com> wrote:
> 
> Hello Eric and Elaine. Chance of earning a second pint of ginger beer if you wish...
> 
> Simulations and analysis going very well, I have substituted all 12 oxygens for sulphur. Each requires a new name: UNK I, UNK2 etc. Advice for others...naming will only alow digits 1 to 9. so for 12 iterations, I used zero and the original unappended "UNK". Which makes 12. I have also successfully set production for 50000steps, equivalent to 8ps. 
> 
> However, there appears to be an option for continuation from one run to a subsequent one. I've tried for a few days now, but get the same error message every time ('continuation2 attachment').  Changing file names as described in the message doesn't work. It's probably something simple (probably me in fact), but would really appreciate your comments.
> 
> Best wishes   Simon
> 
> 
> 
> On 10 January 2018 at 19:01, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> Great!  If we?re in the neighborhood I?ll take a pint of ginger ale. :-)
> 
> ?Eric
> 
> 
>> On Jan 10, 2018, at 4:09 AM, simon chapman <rowanlodge19 at gmail.com> wrote:
>> 
>> Hello Elaine and Eric. Thankyou for the prompt reply....and I'm very impressed! Eric's suggestion #2 worked!
>> 
>> I assumed the protonation was OK as I ran the PDB downloaded structure through a protonation webserver (H++).  So I just changed the name of the novel substitution. It looks like additional alterations will also need renaming: I ran the next substitution in the incremental progression( #5) as "UNK3",and that is just about to complete. 
>> 
>> I am especially pleased as the data are definitely tending to support my hypothesis. You will acknowledged in the Methodology section of my dissertation.
>> 
>> So, thanks again. There's a charming 14th century pub just down the lane from me...buy you both a pint next time you're passing through
>> 
>> Best wishes   Simon
>> 
>> On 9 January 2018 at 19:31, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
>> Hi Simon,
>> 	Everything Elaine says is true.  I do have some last ditch suggestions for you though.  One thing is that the fourth guanine differs in protonation state from the others in that the fourth one either has or lacks an HO3? whereas the others don?t.  You should investigate why this is the case.  The two possibilities are then:
>> 
>> 1) The protonation difference is an error.  You would need to correct the structure so that all four guanines start with the same protonation.
>> 2) For some reason the protonation difference is okay.  You then need to give the modified version of the fourth guanine a different name from the others, e.g. ?UK2? instead of ?UNK?.  Not guaranteeing this will work, but it might.
>> 
>> ?Eric
>> 
>>  	Eric Pettersen
>> 	UCSF Computer Graphics Lab
>> 
>> 
>> On Jan 9, 2018, at 10:24 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>>> 
>>> Hi Simon,
>>> I think you may be stretching the tools beyond their intended purposes: Chimera?s minimization, molecular dynamics interface, and automatic parametrization of nonstandard residues with Antechamber are meant to provide relatively simple access to such calculations by noncomputational scientists, given the large learning curves of dedicated simulation packages like GROMACS, AMBER, etc. These tools can be highly useful to clean up structures or suggest additional reasonable conformations. However, they are not meant for precise quantification of energies or for very long simulations, especially not in conjunction with nonstandard residues with parameters estimated by Antechamber.  The Gasteiger charges are very quick-and-dirty, so I would caution against overinterpreting simulations that employ them.  Further, Antechember is meant to cover most small organic molecules but not every possible molecule.
>>> 
>>> It seems that the modified UNK residues fall into two structural types (as per the ?specify net charges? dialog), and that one (maybe just the 4th?) fails in parametrization by Antechamber, and then the Solvate or Add Ions tool cannot find some parameter needed for its calculation. These tools come from the Ambertools package even though they are included with Chimera and Chimera has interfaces to them.  I don?t know exactly what the problem is, nor do I have a solution, sorry.  
>>> Elaine
>>> -----
>>> Elaine C. Meng, Ph.D.                       
>>> UCSF Chimera(X) team
>>> Department of Pharmaceutical Chemistry
>>> University of California, San Francisco
>>> 
>>> 
>>>> On Jan 9, 2018, at 1:30 AM, simon chapman <rowanlodge19 at gmail.com> wrote:
>>>> 
>>>> Hello Elaine, sorry to bother you again.
>>>> 
>>>> Chimera has been a real treat so far, but I have hit a problem. I've struggled for a week now, and finally given up!
>>>> 
>>>> I am incrementally substituting S for O on four guanines in a regular complex. 3 substitutions work fine in a simulation and producing very encouraging data (attachment 1) But 4 substitutions (attachment 2) triggers a load of error messages. The first is attachment 3. After solvation, attachment 4 appears and the solvation box is removed if neutralising ions are added. If ions not added, attachment 5 warning appears.  Not sure if attachment 6 is relevant.
>>>> 
>>>> Hope you can help/advise?
>>>> 
>>>> Best wishes   Simon
>>>> 




From n.gandhiau at gmail.com  Thu Jan 18 23:24:21 2018
From: n.gandhiau at gmail.com (Neha Gandhi)
Date: Fri, 19 Jan 2018 17:24:21 +1000
Subject: [Chimera-users] MD movie residue network analysis
Message-ID: <CA+Hq8HygMW7rWTntiTg=MyP8W8xf-+vbML1-+6gALaX_4WNSUA@mail.gmail.com>

Dear List,

I am loading gromacs trajectory in Chimera using .tpr and .xtc files. The
residue number in gro file starts from 83 and not from 1. When I perform
residue network analyis using chimera and cytoscape, the numbering of
residues starts from 1. Is there a way to change the residue numbers either
in .tpr file or in cytoscape? Changing the residue numbering after the
trajectory is loaded doesn't help.

Thank you for your attention.

Regards,
Neha

-- 
Regards,
Dr. Neha S. Gandhi,
Vice Chancellor's Research Fellow,
Queensland University of Technology,
2 George Street, Brisbane, QLD 4000
Australia
LinkedIn
Research Gate

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From 519198561 at 163.com  Thu Jan 18 20:29:00 2018
From: 519198561 at 163.com (=?GBK?B?s8LB+Mfg?=)
Date: Fri, 19 Jan 2018 12:29:00 +0800 (GMT+08:00)
Subject: [Chimera-users] chimera website
Message-ID: <4bba43e9.238a.1610cad510d.Coremail.519198561@163.com>


hi
i  can not  log  chimera  website .  can not  download  the  software.  what's problem?
sincerely
liuqing  chen

| |
???
???519198561 at 163.com
|

??? ?????? ??
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From meng at cgl.ucsf.edu  Fri Jan 19 09:04:58 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 19 Jan 2018 09:04:58 -0800
Subject: [Chimera-users] chimera website
In-Reply-To: <4bba43e9.238a.1610cad510d.Coremail.519198561@163.com>
References: <4bba43e9.238a.1610cad510d.Coremail.519198561@163.com>
Message-ID: <77D0F33D-CD1D-4123-8CE8-BFE08BF40EA9@cgl.ucsf.edu>

Hi,
As far as I can tell, the Chimera website is functioning normally.  From an off-campus location, I tried viewing it and downloading Chimera, without problems.

Maybe it was temporary, or a problem on your side?
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Jan 18, 2018, at 8:29 PM, ??? <519198561 at 163.com> wrote:
> hi
> i  can not  log  chimera  website .  can not  download  the  software.  what's problem?
> sincerely
> liuqing  chen
> 	




From meng at cgl.ucsf.edu  Fri Jan 19 16:28:20 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 19 Jan 2018 16:28:20 -0800
Subject: [Chimera-users] question about AutodockVina /CHIMERA
In-Reply-To: <d8d2dac408c0278d2ec23c40080d7516@ibt.unam.mx>
References: <d8d2dac408c0278d2ec23c40080d7516@ibt.unam.mx>
Message-ID: <61AD1D23-C3C7-4DE1-90DB-08A58FDD8CA1@cgl.ucsf.edu>

Hi Osvaldo,
Without more information, I have no idea, sorry.  If you are sure that the process finished (click the ?i? icon near the bottom right corner of the Chimera window to make sure), I can only say to check in the Reply Log (open from Chimera Favorites menu) and see if it says anything else useful.  The Autodock Vina process does not run on our system, so there is nothing I can check here; Chimera just has an interface to send and receive results from a web service that is run by another lab, as explained in the help page:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>

For the future, please send Chimera questions to the chimera-users at cgl.ucsf.edu address (CC?d here) to ensure they come to our attention.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Jan 19, 2018, at 4:04 PM, ogs <ogs at ibt.unam.mx> wrote:
> 
> to whom it may concern,
> 
> hi!
> I am having some problems using AUTODOCK-VINA / CHIMERA.
> 
> I recently docked a linand, but I did not get the name.pdbqt file as result (I only got the name.receptor.pdb and pdbqt and the name.ligand.pdb and pdbqt)
> 
> The software show a message telling me that the process has ended and I need to check the files (but I did not see the name.pdbqt file)
> 
> What is happening? What could I do to solve this problem?
> Thanks a lot.
> Osvaldo G?mez Secundino




From meng at cgl.ucsf.edu  Fri Jan 19 18:31:07 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 19 Jan 2018 18:31:07 -0800
Subject: [Chimera-users] question about AutodockVina /CHIMERA
In-Reply-To: <61AD1D23-C3C7-4DE1-90DB-08A58FDD8CA1@cgl.ucsf.edu>
References: <d8d2dac408c0278d2ec23c40080d7516@ibt.unam.mx>
 <61AD1D23-C3C7-4DE1-90DB-08A58FDD8CA1@cgl.ucsf.edu>
Message-ID: <DCA4E7D7-0ADD-4A9B-8DE6-7D508813A894@cgl.ucsf.edu>

A few more points:

If there is docking output, it would appear automatically in Chimera.  That is, you would see docked structure(s) in the 3D graphics window, and a ViewDock dialog listing these results and their scores.  I guess you didn?t get that either.  Some things to check are that your receptor and ligand pdbqt files seem reasonable (do they contain the expected atoms?) and that the search box is a reasonable size and location.  If the search box is completely filled with receptor atoms, there might not be any space to put the ligand, for example.

These are all just guesses of possible things that could go wrong. I don?t know if they apply to you or not.
Best,
Elaine
 
> On Jan 19, 2018, at 4:28 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi Osvaldo,
> Without more information, I have no idea, sorry.  If you are sure that the process finished (click the ?i? icon near the bottom right corner of the Chimera window to make sure), I can only say to check in the Reply Log (open from Chimera Favorites menu) and see if it says anything else useful.  The Autodock Vina process does not run on our system, so there is nothing I can check here; Chimera just has an interface to send and receive results from a web service that is run by another lab, as explained in the help page:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>
> 
> For the future, please send Chimera questions to the chimera-users at cgl.ucsf.edu address (CC?d here) to ensure they come to our attention.
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
>> On Jan 19, 2018, at 4:04 PM, ogs <ogs at ibt.unam.mx> wrote:
>> 
>> to whom it may concern,
>> 
>> hi!
>> I am having some problems using AUTODOCK-VINA / CHIMERA.
>> 
>> I recently docked a linand, but I did not get the name.pdbqt file as result (I only got the name.receptor.pdb and pdbqt and the name.ligand.pdb and pdbqt)
>> 
>> The software show a message telling me that the process has ended and I need to check the files (but I did not see the name.pdbqt file)
>> 
>> What is happening? What could I do to solve this problem?
>> Thanks a lot.
>> Osvaldo G?mez Secundino




From vamseedharr at gmail.com  Fri Jan 19 14:34:48 2018
From: vamseedharr at gmail.com (vamsee)
Date: Fri, 19 Jan 2018 15:34:48 -0700
Subject: [Chimera-users] Pipes command deletes the previous pipes model
Message-ID: <CA+Oyf__-EZKhGcbiH3L3HNx3uGzcg-fSjLNkm-iLw0BZtBPPtg@mail.gmail.com>

Hello Elaine,


I'm trying to create pipes models with different edge colors for 2 models.
I use the following command for the first model (model # - 0.11).

*pipes #0.11 helixArrow false helixSplit false helixSplitRatio 7.0
helixEdgeColor blue*

Then I try to create the second pipes model using the same command with the
model number changed (model number #0.12)


*pipes #0.12 helixArrow false helixSplit false helixSplitRatio 7.0
helixEdgeColor red*


Basically the difference between the two pipes models is the edge color.
But, when I run the second command, it deletes the first pipes model
(#0.11). I'm not sure what is going on. I'm attaching the whole code here.
Please advise.


*open 0 4G80.pdb*
*split*
*delete #0.1-10*

*focus*
*color white,r #*

*pipes #0.11 helixArrow false helixSplit false helixSplitRatio 7.0
helixEdgeColor blue*
*pipes #0.12 helixArrow false helixSplit false helixSplitRatio 7.0
helixEdgeColor blue*


Thank you,

Vamsee
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From agas at nicd.ac.za  Fri Jan 19 21:52:52 2018
From: agas at nicd.ac.za (Aga Szydlik)
Date: Sat, 20 Jan 2018 05:52:52 +0000
Subject: [Chimera-users] emails
Message-ID: <1673ae0a4adf4b42b52f2bc36cded60c@NICDSANDEXCH02.NICD.local>



May I please ask to be unsubscribe from all "chimera users questions" emails, thank you
Aga Szydlik
PhD Candidate, School of Pathology, University of the Witwatersrand

National Institute for Communicable Diseases,
a Division of the National Health Laboratory Service
Centre for HIV & STI's: HIV Virology Section (Morris Laboratory)
1 Modderfontein Road
Sandringham, 2131
South Africa
email: agas at nicd.ac.za<mailto:agas at nicd.ac.za> | www.nicd.ac.za<http://www.nicd.ac.za/>

[cid:image003.png at 01D2F0EE.60CC2540]
Practice Number: 5200296



The views expressed in this email are, unless otherwise stated, those of the author and not those of the National Health Laboratory Service or its management. The information in this e-mail is confidential and is intended solely for the addressee.
Access to this e-mail by anyone else is unauthorized. If you are not the intended recipient, any disclosure, copying, distribution or any action taken or omitted in reliance on this, is prohibited and may be unlawful.
Whilst all reasonable steps are taken to ensure the accuracy and integrity of information and data transmitted electronically and to preserve the confidentiality thereof, no liability or responsibility whatsoever is accepted if information or data is, for whatever reason, corrupted or does not reach its intended destination.
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From meng at cgl.ucsf.edu  Sat Jan 20 08:22:11 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Sat, 20 Jan 2018 08:22:11 -0800
Subject: [Chimera-users] emails
In-Reply-To: <1673ae0a4adf4b42b52f2bc36cded60c@NICDSANDEXCH02.NICD.local>
References: <1673ae0a4adf4b42b52f2bc36cded60c@NICDSANDEXCH02.NICD.local>
Message-ID: <8730C4FD-C123-4DFF-88A3-4FAD1FE4A8F0@cgl.ucsf.edu>

People on this email list can unsubscribe by using the ?manage subscription? link at the bottom of each email message to the list.  I?m not the manager, sorry.
Elaine

> On Jan 19, 2018, at 9:52 PM, Aga Szydlik <agas at nicd.ac.za> wrote:
> 
>  
> May I please ask to be unsubscribe from all ?chimera users questions? emails, thank you
> Aga Szydlik 
> PhD Candidate, School of Pathology, University of the Witwatersrand
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users




From meng at cgl.ucsf.edu  Sat Jan 20 08:44:52 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Sat, 20 Jan 2018 08:44:52 -0800
Subject: [Chimera-users] Pipes command deletes the previous pipes model
In-Reply-To: <CA+Oyf__-EZKhGcbiH3L3HNx3uGzcg-fSjLNkm-iLw0BZtBPPtg@mail.gmail.com>
References: <CA+Oyf__-EZKhGcbiH3L3HNx3uGzcg-fSjLNkm-iLw0BZtBPPtg@mail.gmail.com>
Message-ID: <96728977-7D41-4238-9524-850A628C20AE@cgl.ucsf.edu>

Hi Vamsee,
Seems like a little bug, probably thinks it?s the same model because they have the same major model number.  However, the workaround is simple? just open the structure twice (in that case, no need to bother splitting), remove the chains you don?t want, and run pipe-and-planks on the different major model numbers.  For example:

open 4g80
open 4g80
del #0:.A-J:.T
del #1:.A-J:.S
focus
color white,r 
pipes #0 helixArrow false helixSplit false helixSplitRatio 7.0 helixEdgeColor blue
pipes #1 helixArrow false helixSplit false helixSplitRatio 7.0 helixEdgeColor red

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jan 19, 2018, at 2:34 PM, vamsee <vamseedharr at gmail.com> wrote:
> 
> Hello Elaine,
> I'm trying to create pipes models with different edge colors for 2 models. I use the following command for the first model (model # - 0.11). 
> 
> pipes #0.11 helixArrow false helixSplit false helixSplitRatio 7.0 helixEdgeColor blue
> 
> Then I try to create the second pipes model using the same command with the model number changed (model number #0.12)
> 
> pipes #0.12 helixArrow false helixSplit false helixSplitRatio 7.0 helixEdgeColor red
> 
> Basically the difference between the two pipes models is the edge color. But, when I run the second command, it deletes the first pipes model (#0.11). I'm not sure what is going on. I'm attaching the whole code here. Please advise. 
> 
> open 0 4G80.pdb
> split
> delete #0.1-10
> 
> focus
> color white,r #
> 
> pipes #0.11 helixArrow false helixSplit false helixSplitRatio 7.0 helixEdgeColor blue
> pipes #0.12 helixArrow false helixSplit false helixSplitRatio 7.0 helixEdgeColor blue
> 
> Thank you,
> Vamsee




From 519198561 at 163.com  Fri Jan 19 23:30:45 2018
From: 519198561 at 163.com (=?utf-8?B?6ZmI5p+z6Z2S?=)
Date: Sat, 20 Jan 2018 15:30:45 +0800 (CST)
Subject: [Chimera-users] chimera website
In-Reply-To: <77D0F33D-CD1D-4123-8CE8-BFE08BF40EA9@cgl.ucsf.edu>
References: <4bba43e9.238a.1610cad510d.Coremail.519198561@163.com>
 <77D0F33D-CD1D-4123-8CE8-BFE08BF40EA9@cgl.ucsf.edu>
Message-ID: <4a9c6c44.3204.161127a133e.Coremail.519198561@163.com>

Hi<br/>thanks,  it's should be my computers problem.   but i can login  google,  gmail,  and others,   only can't  login  chimera  related website  for several months.  <br/>best<br/>liuqing chen
At 2018-01-20 01:04:58, "Elaine Meng" <meng at cgl.ucsf.edu> wrote:
>Hi,
>As far as I can tell, the Chimera website is functioning normally.  From an off-campus location, I tried viewing it and downloading Chimera, without problems.
>
>Maybe it was temporary, or a problem on your side?
>Best,
>Elaine
>-----
>Elaine C. Meng, Ph.D.                       
>UCSF Chimera(X) team
>Department of Pharmaceutical Chemistry
>University of California, San Francisco
>
>
>> On Jan 18, 2018, at 8:29 PM, ??? <519198561 at 163.com> wrote:
>> hi
>> i  can not  log  chimera  website .  can not  download  the  software.  what's problem?
>> sincerely
>> liuqing  chen
>> 	



From 527655229 at qq.com  Sat Jan 20 20:38:17 2018
From: 527655229 at qq.com (=?gb18030?B?tPPLpw==?=)
Date: Sun, 21 Jan 2018 12:38:17 +0800
Subject: [Chimera-users] Rotate and transform command
Message-ID: <tencent_D3C89859C503928EE06A0154C7BD4A355B08@qq.com>

Hi,


Therefore, we used UCSF Chimera to have a map's smmetry axes (approximately) parallel to the XYZ axes. The procedure followed by the relion tutorial we used for that was to
read in InitialModel/symC1/run_it003_class001.mrc; use the duplicate
option under the File menu of the Volume viewer. Then to deactivate map
#1 on the Model Panel; rotate map #0 to have it?s symmetry axis more or
less parallel to the XYZ axes; and then to use in the Command Line entry field:
run_it003_class001.mrc; and save this model in the InitialModel/symC1/
directory with the name inimodel.mrc



I have done as the above tutorial in relion, but the saved inimodel.mrc file does not change its position or  orientation at all. So, my question is what commend can save a map after rotating or transforming its  x,y,z coordinate ? What is the procedures to do so ?




                                                                                               Thanks


                                                                                                 Dashuai
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From gregc at cgl.ucsf.edu  Sun Jan 21 22:06:13 2018
From: gregc at cgl.ucsf.edu (Greg Couch)
Date: Sun, 21 Jan 2018 22:06:13 -0800
Subject: [Chimera-users] chimera website
In-Reply-To: <4a9c6c44.3204.161127a133e.Coremail.519198561@163.com>
References: <4bba43e9.238a.1610cad510d.Coremail.519198561@163.com>
 <77D0F33D-CD1D-4123-8CE8-BFE08BF40EA9@cgl.ucsf.edu>
 <4a9c6c44.3204.161127a133e.Coremail.519198561@163.com>
Message-ID: <7c85884b-b198-9f8f-105b-aadfce1a1156@cgl.ucsf.edu>

You shouldn't need to login to use the chimera website.? Let's take this 
off the mailing list to debug it.? Please email me directly with the URL 
that you are using that you are trying to login to.

 ?? -- Greg


On 1/19/2018 11:30 PM, ??? wrote:
> Hi<br/>thanks,  it's should be my computers problem.   but i can login  google,  gmail,  and others,   only can't  login  chimera  related website  for several months.  <br/>best<br/>liuqing chen
> At 2018-01-20 01:04:58, "Elaine Meng" <meng at cgl.ucsf.edu> wrote:
>> Hi,
>> As far as I can tell, the Chimera website is functioning normally.  From an off-campus location, I tried viewing it and downloading Chimera, without problems.
>>
>> Maybe it was temporary, or a problem on your side?
>> Best,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>>
>>
>>> On Jan 18, 2018, at 8:29 PM, ??? <519198561 at 163.com> wrote:
>>> hi
>>> i  can not  log  chimera  website .  can not  download  the  software.  what's problem?
>>> sincerely
>>> liuqing  chen
>>> 	
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>



From nazaahmadrodzli at gmail.com  Mon Jan 22 03:58:03 2018
From: nazaahmadrodzli at gmail.com (Nazahiyah Rodzli)
Date: Mon, 22 Jan 2018 19:58:03 +0800
Subject: [Chimera-users] Inactive atoms
Message-ID: <7E2FDB97-909B-4D0F-80DF-DEE58AA22152@gmail.com>

Dear Chimera Users, 

My Chimera seems to display atoms and side chains in dimmed dark colour (picture below). I?ve tried to change the colour but they don?t work. I also can?t select any of the atoms/sidechains by mouse click+ctrl unless I pick select all from the select menu. I am using Chimera 1.10 version. Could you help me how I can change the settings perhaps?

Best regards,
Naza
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From fglaser at technion.ac.il  Mon Jan 22 07:13:39 2018
From: fglaser at technion.ac.il (Fabian Glaser)
Date: Mon, 22 Jan 2018 15:13:39 +0000
Subject: [Chimera-users] mouse hovering not working
Message-ID: <5FF550FF-B64C-44D6-9BBE-5B822F24C6AF@technion.ac.il>

Dear all,

The mouse hovering is not working for me, I use a Mac, and tried several version of Chimera, but the residue / atom number automatic labelling does not appear when hovering over.

Any suggestion?

Thanks a lot ,

Best,

Fabian

Fabian Glaser PhD

Head of the Structural  Bioinformatics section
Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Interdisciplinary 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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From sheng.zhong at yale.edu  Mon Jan 22 08:50:04 2018
From: sheng.zhong at yale.edu (Zhong, Sheng)
Date: Mon, 22 Jan 2018 16:50:04 +0000
Subject: [Chimera-users] mouse hovering not working
In-Reply-To: <5FF550FF-B64C-44D6-9BBE-5B822F24C6AF@technion.ac.il>
References: <5FF550FF-B64C-44D6-9BBE-5B822F24C6AF@technion.ac.il>
Message-ID: <SN4PR0801MB369573DA4FBC0A7F3FE535029CEC0@SN4PR0801MB3695.namprd08.prod.outlook.com>

Use a Bluetooth mouse.

It works well in Mac.


Sheng

________________________________
From: Chimera-users <chimera-users-bounces at cgl.ucsf.edu> on behalf of Fabian Glaser <fglaser at technion.ac.il>
Sent: Monday, January 22, 2018 10:13:39 AM
To: Chimera BB
Subject: [Chimera-users] mouse hovering not working

Dear all,

The mouse hovering is not working for me, I use a Mac, and tried several version of Chimera, but the residue / atom number automatic labelling does not appear when hovering over.

Any suggestion?

Thanks a lot ,

Best,

Fabian

Fabian Glaser PhD

Head of the Structural  Bioinformatics section
Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering
Technion - Israel Institute of Technology, Haifa, Israel
Web http://bku.technion.ac.il/<https://urldefense.proofpoint.com/v2/url?u=http-3A__bku.technion.ac.il_&d=DwMBAg&c=cjytLXgP8ixuoHflwc-poQ&r=ZRSEBeiYmgRFrwpeyy9Kgg8yeqswuhQe3EINonUZbFI&m=wv57_O2od6oV_Ou6CXjZh3uQOfUcIDOpjZ3NokmIvqI&s=8KJ4SSpNnKAY3YdZq0S-EGWxNRaJztkVb8SulSH2H0s&e=>
Tel +972 (0) 4 8293701


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From meng at cgl.ucsf.edu  Mon Jan 22 10:14:34 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 22 Jan 2018 10:14:34 -0800
Subject: [Chimera-users] Rotate and transform command
In-Reply-To: <tencent_D3C89859C503928EE06A0154C7BD4A355B08@qq.com>
References: <tencent_D3C89859C503928EE06A0154C7BD4A355B08@qq.com>
Message-ID: <18757EF0-B117-46EA-B536-0CCB8A8A3E5C@cgl.ucsf.edu>

Hi Dashuai,
This is a frequently asked question? the reason is that map files do not contain rotation information. 

If the map was fitted to another map, the solution would be to resample the rotated map on the grid of the other to create a third map,  see ?saving maps after fitting":
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#afterfitting>

if you don?t have another map grid already, one idea is to make new zero-valued map with ?vop new? and then resample your rotated map on the grid of that zero-valued map. However, you?d have to create the new map so that it encloses your existing rotated map (show box outlines with Volume Viewer).
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#new>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#resample>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jan 20, 2018, at 8:38 PM, ?? <527655229 at qq.com> wrote:
> 
> Hi,
> 
> Therefore, we used UCSF Chimera to have a map's smmetry axes (approximately) parallel to the XYZ axes. The procedure followed by the relion tutorial we used for that was to
> read in InitialModel/symC1/run_it003_class001.mrc; use the duplicate
> option under the File menu of the Volume viewer. Then to deactivate map
> #1 on the Model Panel; rotate map #0 to have it?s symmetry axis more or
> less parallel to the XYZ axes; and then to use in the Command Line entry field:
> run_it003_class001.mrc; and save this model in the InitialModel/symC1/
> directory with the name inimodel.mrc
> 
> I have done as the above tutorial in relion, but the saved inimodel.mrc file does not change its position or  orientation at all. So, my question is what commend can save a map after rotating or transforming its  x,y,z coordinate ? What is the procedures to do so ?
> 
>                                                                                                Thanks
>                                                                                                  Dashuai




From meng at cgl.ucsf.edu  Mon Jan 22 10:33:11 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 22 Jan 2018 10:33:11 -0800
Subject: [Chimera-users] Inactive atoms
In-Reply-To: <7E2FDB97-909B-4D0F-80DF-DEE58AA22152@gmail.com>
References: <7E2FDB97-909B-4D0F-80DF-DEE58AA22152@gmail.com>
Message-ID: <25EC2684-E977-46A5-AA60-514259CADAA4@cgl.ucsf.edu>

Dear Naza,
Try using a newer Chimera (1.12 release or newer).  If I remember correctly, this dark sticks issue occurred on some systems with older Chimera but has been fixed.
<http://www.rbvi.ucsf.edu/chimera/download.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 Jan 22, 2018, at 3:58 AM, Nazahiyah Rodzli <nazaahmadrodzli at gmail.com> wrote:
> 
> Dear Chimera Users, 
> My Chimera seems to display atoms and side chains in dimmed dark colour (picture below). I?ve tried to change the colour but they don?t work. I also can?t select any of the atoms/sidechains by mouse click+ctrl unless I pick select all from the select menu. I am using Chimera 1.10 version. Could you help me how I can change the settings perhaps?
> Best regards,
> Naza




From meng at cgl.ucsf.edu  Mon Jan 22 10:38:32 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 22 Jan 2018 10:38:32 -0800
Subject: [Chimera-users] mouse hovering not working
In-Reply-To: <SN4PR0801MB369573DA4FBC0A7F3FE535029CEC0@SN4PR0801MB3695.namprd08.prod.outlook.com>
References: <5FF550FF-B64C-44D6-9BBE-5B822F24C6AF@technion.ac.il>
 <SN4PR0801MB369573DA4FBC0A7F3FE535029CEC0@SN4PR0801MB3695.namprd08.prod.outlook.com>
Message-ID: <D37EEF25-0F85-4134-9E1B-33C91D0AC8C6@cgl.ucsf.edu>

Dear Fabian,
I don?t think the kind of mouse is that important? I use a plug-in one myself.  

If you were using some other application you may need to click back into the Chimera window first.  Other than that, my only idea is to check your Preferences settings, menu: Favorites? Preferences, category ?Labels? and make sure ?Show atomspec balloon? is ?true? (and click Save if you had to change it from false to true).
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#Labels>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jan 22, 2018, at 8:50 AM, Zhong, Sheng <sheng.zhong at yale.edu> wrote:
> 
> Use a Bluetooth mouse.
> It works well in Mac.
> 
> Sheng
> From: Chimera-users <chimera-users-bounces at cgl.ucsf.edu> on behalf of Fabian Glaser <fglaser at technion.ac.il>
> Sent: Monday, January 22, 2018 10:13:39 AM
> To: Chimera BB
> Subject: [Chimera-users] mouse hovering not working
>  
> Dear all,
> 
> The mouse hovering is not working for me, I use a Mac, and tried several version of Chimera, but the residue / atom number automatic labelling does not appear when hovering over.
> 
> Any suggestion?
> 
> Thanks a lot ,
> 
> Best,
> 
> Fabian
> 
> Fabian Glaser PhD
> 
> Head of the Structural  Bioinformatics section 
> Bioinformatics Knowledge Unit - BKU
> The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering
> Technion - Israel Institute of Technology, Haifa, Israel
> Web http://bku.technion.ac.il/
> Tel +972 (0) 4 8293701
> 
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users




From meng at cgl.ucsf.edu  Mon Jan 22 10:40:36 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 22 Jan 2018 10:40:36 -0800
Subject: [Chimera-users] chimera website
In-Reply-To: <7c85884b-b198-9f8f-105b-aadfce1a1156@cgl.ucsf.edu>
References: <4bba43e9.238a.1610cad510d.Coremail.519198561@163.com>
 <77D0F33D-CD1D-4123-8CE8-BFE08BF40EA9@cgl.ucsf.edu>
 <4a9c6c44.3204.161127a133e.Coremail.519198561@163.com>
 <7c85884b-b198-9f8f-105b-aadfce1a1156@cgl.ucsf.edu>
Message-ID: <93E20B8E-D0B3-44F8-A6D7-19B61900C894@cgl.ucsf.edu>

As Greg said, there is no login to the UCSF Chimera website: 
<http://www.rbvi.ucsf.edu/chimera/index.html>

Best,
Elaine

> On Jan 21, 2018, at 10:06 PM, Greg Couch <gregc at cgl.ucsf.edu> wrote:
> 
> You shouldn't need to login to use the chimera website.  Let's take this off the mailing list to debug it.  Please email me directly with the URL that you are using that you are trying to login to.
> 
>    -- Greg
> 
> 
> On 1/19/2018 11:30 PM, ??? wrote:
>> Hi<br/>thanks,  it's should be my computers problem.   but i can login  google,  gmail,  and others,   only can't  login  chimera  related website  for several months.  <br/>best<br/>liuqing chen
>> At 2018-01-20 01:04:58, "Elaine Meng" <meng at cgl.ucsf.edu> wrote:
>>> Hi,
>>> As far as I can tell, the Chimera website is functioning normally.  From an off-campus location, I tried viewing it and downloading Chimera, without problems.
>>> 
>>> Maybe it was temporary, or a problem on your side?
>>> Best,
>>> Elaine
>>> -----
>>> Elaine C. Meng, Ph.D.
>>> UCSF Chimera(X) team
>>> Department of Pharmaceutical Chemistry
>>> University of California, San Francisco
>>> 
>>> 
>>>> On Jan 18, 2018, at 8:29 PM, ??? <519198561 at 163.com> wrote:
>>>> hi
>>>> i  can not  log  chimera  website .  can not  download  the  software.  what's problem?
>>>> sincerely
>>>> liuqing  chen
>>>> 	




From ogs at ibt.unam.mx  Mon Jan 22 12:25:47 2018
From: ogs at ibt.unam.mx (ogs)
Date: Mon, 22 Jan 2018 14:25:47 -0600
Subject: [Chimera-users] question about AutodockVina /CHIMERA
In-Reply-To: <DCA4E7D7-0ADD-4A9B-8DE6-7D508813A894@cgl.ucsf.edu>
References: <d8d2dac408c0278d2ec23c40080d7516@ibt.unam.mx>
 <61AD1D23-C3C7-4DE1-90DB-08A58FDD8CA1@cgl.ucsf.edu>
 <DCA4E7D7-0ADD-4A9B-8DE6-7D508813A894@cgl.ucsf.edu>
Message-ID: <bb4a769bf712f9b8c8aad2fbbf471161@ibt.unam.mx>

 Thank you so much for your answer.

 I tried to repeat docking I did before (when I got output) and I did 
 not see the output this time.
 I only get: receptor.pdbqt and ligand.pdbqt as output. I did not get 
 the name.pdbqt file. The software did not show any warm message or 
 something like that.

 THANKS
 Osvaldo G?mez




 On Fri, 19 Jan 2018 18:31:07 -0800, Elaine Meng <meng at cgl.ucsf.edu> 
 wrote:
> A few more points:
>
> If there is docking output, it would appear automatically in Chimera.
> That is, you would see docked structure(s) in the 3D graphics window,
> and a ViewDock dialog listing these results and their scores.  I 
> guess
> you didn?t get that either.  Some things to check are that your
> receptor and ligand pdbqt files seem reasonable (do they contain the
> expected atoms?) and that the search box is a reasonable size and
> location.  If the search box is completely filled with receptor 
> atoms,
> there might not be any space to put the ligand, for example.
>
> These are all just guesses of possible things that could go wrong. I
> don?t know if they apply to you or not.
> Best,
> Elaine
>
>> On Jan 19, 2018, at 4:28 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>>
>> Hi Osvaldo,
>> Without more information, I have no idea, sorry.  If you are sure 
>> that the process finished (click the ?i? icon near the bottom right 
>> corner of the Chimera window to make sure), I can only say to check in 
>> the Reply Log (open from Chimera Favorites menu) and see if it says 
>> anything else useful.  The Autodock Vina process does not run on our 
>> system, so there is nothing I can check here; Chimera just has an 
>> interface to send and receive results from a web service that is run 
>> by another lab, as explained in the help page:
>> 
>> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>
>>
>> For the future, please send Chimera questions to the 
>> chimera-users at cgl.ucsf.edu address (CC?d here) to ensure they come to 
>> our attention.
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>>
>>
>>> On Jan 19, 2018, at 4:04 PM, ogs <ogs at ibt.unam.mx> wrote:
>>>
>>> to whom it may concern,
>>>
>>> hi!
>>> I am having some problems using AUTODOCK-VINA / CHIMERA.
>>>
>>> I recently docked a linand, but I did not get the name.pdbqt file 
>>> as result (I only got the name.receptor.pdb and pdbqt and the 
>>> name.ligand.pdb and pdbqt)
>>>
>>> The software show a message telling me that the process has ended 
>>> and I need to check the files (but I did not see the name.pdbqt file)
>>>
>>> What is happening? What could I do to solve this problem?
>>> Thanks a lot.
>>> Osvaldo G?mez Secundino


From pett at cgl.ucsf.edu  Mon Jan 22 14:03:26 2018
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Mon, 22 Jan 2018 14:03:26 -0800
Subject: [Chimera-users] MD movie residue network analysis
In-Reply-To: <CA+Hq8HygMW7rWTntiTg=MyP8W8xf-+vbML1-+6gALaX_4WNSUA@mail.gmail.com>
References: <CA+Hq8HygMW7rWTntiTg=MyP8W8xf-+vbML1-+6gALaX_4WNSUA@mail.gmail.com>
Message-ID: <A30ED55C-D9A3-4C40-A758-F3DD4BE9D1DB@cgl.ucsf.edu>

Hi,
	If I open a trajectory and delete the starting residues before generating the Cytoscape RIN, the numbering does not start at 1 for me.  Perhaps you need to use Chimera?s Help->Report A Bug menu item to start a bug report so that we can investigate your problem without involving everyone on the mailing list?.

?Eric

	Eric Pettersen
	UCSF Computer Graphics Lab

> On Jan 18, 2018, at 11:24 PM, Neha Gandhi <n.gandhiau at gmail.com> wrote:
> 
> Dear List,
> 
> I am loading gromacs trajectory in Chimera using .tpr and .xtc files. The residue number in gro file starts from 83 and not from 1. When I perform residue network analyis using chimera and cytoscape, the numbering of residues starts from 1. Is there a way to change the residue numbers either in .tpr file or in cytoscape? Changing the residue numbering after the trajectory is loaded doesn't help.
> 
> Thank you for your attention.
> 
> Regards,
> Neha
> 
> -- 
> Regards,
> Dr. Neha S. Gandhi,
> Vice Chancellor's Research Fellow,
> Queensland University of Technology,
> 2 George Street, Brisbane, QLD 4000
> Australia
> LinkedIn <>
> Research Gate <>
> 
>  <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail>	Virus-free. www.avg.com <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> <x-msg://25/#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>_______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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From meng at cgl.ucsf.edu  Mon Jan 22 14:20:34 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 22 Jan 2018 14:20:34 -0800
Subject: [Chimera-users] question about AutodockVina /CHIMERA
In-Reply-To: <bb4a769bf712f9b8c8aad2fbbf471161@ibt.unam.mx>
References: <d8d2dac408c0278d2ec23c40080d7516@ibt.unam.mx>
 <61AD1D23-C3C7-4DE1-90DB-08A58FDD8CA1@cgl.ucsf.edu>
 <DCA4E7D7-0ADD-4A9B-8DE6-7D508813A894@cgl.ucsf.edu>
 <bb4a769bf712f9b8c8aad2fbbf471161@ibt.unam.mx>
Message-ID: <87B1421E-85C8-4273-984C-FE8F1BB77278@cgl.ucsf.edu>

Hi Osvaldo,
First, make sure what you enter as ?Output file? in the AutoDock Vina dialog is a location you can find and have permission to write files.

Second, make sure the job is really finished (click blue ?i? icon near bottom right corner of Chimera).  The receptor and ligand pdbqt files are made very quickly at the beginning of the job.  They do not mean that the whole job is finished.

Third, see if any results are automatically shown in the Chimera 3D window and ViewDock dialog.  If you can see the results in Chimera, there is an output file somewhere.  It is possible the output file is just named ?name? without the pdbqt part.  For example, in my test I entered ?~/Desktop/junk? and the results file I got was on my Desktop and named ?junk?.

If no output, I already gave all my ideas in the previous message.

Elaine

On Jan 22, 2018, at 12:25 PM, ogs <ogs at ibt.unam.mx> wrote:
> 
> 
> Thank you so much for your answer.
> 
> I tried to repeat docking I did before (when I got output) and I did not see the output this time.
> I only get: receptor.pdbqt and ligand.pdbqt as output. I did not get the name.pdbqt file. The software did not show any warm message or something like that.
> 
> THANKS
> Osvaldo G?mez
> 
> On Fri, 19 Jan 2018 18:31:07 -0800, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> A few more points:
>> 
>> If there is docking output, it would appear automatically in Chimera.
>> That is, you would see docked structure(s) in the 3D graphics window,
>> and a ViewDock dialog listing these results and their scores.  I guess
>> you didn?t get that either.  Some things to check are that your
>> receptor and ligand pdbqt files seem reasonable (do they contain the
>> expected atoms?) and that the search box is a reasonable size and
>> location.  If the search box is completely filled with receptor atoms,
>> there might not be any space to put the ligand, for example.
>> 
>> These are all just guesses of possible things that could go wrong. I
>> don?t know if they apply to you or not.
>> Best,
>> Elaine
>> 
>>> On Jan 19, 2018, at 4:28 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>>> 
>>> Hi Osvaldo,
>>> Without more information, I have no idea, sorry.  If you are sure that the process finished (click the ?i? icon near the bottom right corner of the Chimera window to make sure), I can only say to check in the Reply Log (open from Chimera Favorites menu) and see if it says anything else useful.  The Autodock Vina process does not run on our system, so there is nothing I can check here; Chimera just has an interface to send and receive results from a web service that is run by another lab, as explained in the help page:
>>> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>
>>> 
>>> For the future, please send Chimera questions to the chimera-users at cgl.ucsf.edu address (CC?d here) to ensure they come to our attention.
>>> I hope this helps,
>>> Elaine
>>> -----
>>> Elaine C. Meng, Ph.D.
>>> UCSF Chimera(X) team
>>> Department of Pharmaceutical Chemistry
>>> University of California, San Francisco
>>> 
>>> 
>>>> On Jan 19, 2018, at 4:04 PM, ogs <ogs at ibt.unam.mx> wrote:
>>>> 
>>>> to whom it may concern,
>>>> 
>>>> hi!
>>>> I am having some problems using AUTODOCK-VINA / CHIMERA.
>>>> 
>>>> I recently docked a linand, but I did not get the name.pdbqt file as result (I only got the name.receptor.pdb and pdbqt and the name.ligand.pdb and pdbqt)
>>>> 
>>>> The software show a message telling me that the process has ended and I need to check the files (but I did not see the name.pdbqt file)
>>>> 
>>>> What is happening? What could I do to solve this problem?
>>>> Thanks a lot.
>>>> Osvaldo G?mez Secundino
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 




From 519198561 at 163.com  Mon Jan 22 16:44:05 2018
From: 519198561 at 163.com (=?GBK?B?s8LB+Mfg?=)
Date: Tue, 23 Jan 2018 08:44:05 +0800 (CST)
Subject: [Chimera-users] chimera website
In-Reply-To: <93E20B8E-D0B3-44F8-A6D7-19B61900C894@cgl.ucsf.edu>
References: <4bba43e9.238a.1610cad510d.Coremail.519198561@163.com>
 <77D0F33D-CD1D-4123-8CE8-BFE08BF40EA9@cgl.ucsf.edu>
 <4a9c6c44.3204.161127a133e.Coremail.519198561@163.com>
 <7c85884b-b198-9f8f-105b-aadfce1a1156@cgl.ucsf.edu>
 <93E20B8E-D0B3-44F8-A6D7-19B61900C894@cgl.ucsf.edu>
Message-ID: <ff86ab7.cd8.1612078d4c9.Coremail.519198561@163.com>

Hi
thanks,  it's my computer problem,  i have enter in the homepage of chimera  by another computer!
best
Liuqing chen








At 2018-01-23 02:40:36, "Elaine Meng" <meng at cgl.ucsf.edu> wrote:
>As Greg said, there is no login to the UCSF Chimera website: 
><http://www.rbvi.ucsf.edu/chimera/index.html>
>
>Best,
>Elaine
>
>> On Jan 21, 2018, at 10:06 PM, Greg Couch <gregc at cgl.ucsf.edu> wrote:
>> 
>> You shouldn't need to login to use the chimera website.  Let's take this off the mailing list to debug it.  Please email me directly with the URL that you are using that you are trying to login to.
>> 
>>    -- Greg
>> 
>> 
>> On 1/19/2018 11:30 PM, ??? wrote:
>>> Hi<br/>thanks,  it's should be my computers problem.   but i can login  google,  gmail,  and others,   only can't  login  chimera  related website  for several months.  <br/>best<br/>liuqing chen
>>> At 2018-01-20 01:04:58, "Elaine Meng" <meng at cgl.ucsf.edu> wrote:
>>>> Hi,
>>>> As far as I can tell, the Chimera website is functioning normally.  From an off-campus location, I tried viewing it and downloading Chimera, without problems.
>>>> 
>>>> Maybe it was temporary, or a problem on your side?
>>>> Best,
>>>> Elaine
>>>> -----
>>>> Elaine C. Meng, Ph.D.
>>>> UCSF Chimera(X) team
>>>> Department of Pharmaceutical Chemistry
>>>> University of California, San Francisco
>>>> 
>>>> 
>>>>> On Jan 18, 2018, at 8:29 PM, ??? <519198561 at 163.com> wrote:
>>>>> hi
>>>>> i  can not  log  chimera  website .  can not  download  the  software.  what's problem?
>>>>> sincerely
>>>>> liuqing  chen
>>>>> 	
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From fglaser at technion.ac.il  Tue Jan 23 00:26:00 2018
From: fglaser at technion.ac.il (Fabian Glaser)
Date: Tue, 23 Jan 2018 08:26:00 +0000
Subject: [Chimera-users] mouse hovering not working
In-Reply-To: <D37EEF25-0F85-4134-9E1B-33C91D0AC8C6@cgl.ucsf.edu>
References: <5FF550FF-B64C-44D6-9BBE-5B822F24C6AF@technion.ac.il>
 <SN4PR0801MB369573DA4FBC0A7F3FE535029CEC0@SN4PR0801MB3695.namprd08.prod.outlook.com>
 <D37EEF25-0F85-4134-9E1B-33C91D0AC8C6@cgl.ucsf.edu>
Message-ID: <29D7BECB-A6A8-4D2F-9FE1-B24364AB094B@technion.ac.il>

It worked!

Thanks a lot,

Best,

Fabian

Fabian Glaser PhD

Head of the Structural  Bioinformatics section
Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering
Technion - Israel Institute of Technology, Haifa, Israel
Web http://bku.technion.ac.il/
Tel +972 (0) 4 8293701


On 22 Jan 2018, at 20:38, Elaine Meng <meng at cgl.ucsf.edu<mailto:meng at cgl.ucsf.edu>> wrote:

Dear Fabian,
I don?t think the kind of mouse is that important? I use a plug-in one myself.

If you were using some other application you may need to click back into the Chimera window first.  Other than that, my only idea is to check your Preferences settings, menu: Favorites? Preferences, category ?Labels? and make sure ?Show atomspec balloon? is ?true? (and click Save if you had to change it from false to true).
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#Labels>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jan 22, 2018, at 8:50 AM, Zhong, Sheng <sheng.zhong at yale.edu<mailto:sheng.zhong at yale.edu>> wrote:

Use a Bluetooth mouse.
It works well in Mac.

Sheng
From: Chimera-users <chimera-users-bounces at cgl.ucsf.edu<mailto:chimera-users-bounces at cgl.ucsf.edu>> on behalf of Fabian Glaser <fglaser at technion.ac.il<mailto:fglaser at technion.ac.il>>
Sent: Monday, January 22, 2018 10:13:39 AM
To: Chimera BB
Subject: [Chimera-users] mouse hovering not working

Dear all,

The mouse hovering is not working for me, I use a Mac, and tried several version of Chimera, but the residue / atom number automatic labelling does not appear when hovering over.

Any suggestion?

Thanks a lot ,

Best,

Fabian

Fabian Glaser PhD

Head of the Structural  Bioinformatics section
Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering
Technion - Israel Institute of Technology, Haifa, Israel
Web http://bku.technion.ac.il/
Tel +972 (0) 4 8293701


_______________________________________________
Chimera-users mailing list: Chimera-users at cgl.ucsf.edu<mailto:Chimera-users at cgl.ucsf.edu>
Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users


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From niash.t24 at gmail.com  Wed Jan 24 05:19:37 2018
From: niash.t24 at gmail.com (Niasha Tauro)
Date: Wed, 24 Jan 2018 15:19:37 +0200
Subject: [Chimera-users] How do i rectify this error
Message-ID: <CAKDEksZMsNqn4=nN579=qa30AQ+JNr78c0D7b_9MrtbeppARaQ@mail.gmail.com>

Hello Chimera Users

Can you please help me rectify the following error showing on chimera
(1.11.2 version) during molecular docking:

'C:\molecular' is not recognized as an internal or external command,
operable program or batch file.
-----
Application stdout
-----
[no output]
-----
 I have installed Autodock Vina and i am using the local executable
location: vina.exe
your assistance will be greatly appreciated

kind regards

Nyasha Tauro

<https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail>
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From meng at cgl.ucsf.edu  Wed Jan 24 09:51:01 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 24 Jan 2018 09:51:01 -0800
Subject: [Chimera-users] How do i rectify this error
In-Reply-To: <CAKDEksZMsNqn4=nN579=qa30AQ+JNr78c0D7b_9MrtbeppARaQ@mail.gmail.com>
References: <CAKDEksZMsNqn4=nN579=qa30AQ+JNr78c0D7b_9MrtbeppARaQ@mail.gmail.com>
Message-ID: <2C0F5D8D-4DD7-48CA-AFC6-956DE2415544@cgl.ucsf.edu>

Hello Nyasha,
I?m guessing it is because the local executable location has a space in it.  You may need to put it in a path that does not contain a space. (I don?t know if putting quotation marks around the current location would work, although you could try it.)
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Jan 24, 2018, at 5:19 AM, Niasha Tauro <niash.t24 at gmail.com> wrote:
> 
> Hello Chimera Users
> Can you please help me rectify the following error showing on chimera (1.11.2 version) during molecular docking:
> 
> 'C:\molecular' is not recognized as an internal or external command,
> operable program or batch file.
> -----
> Application stdout
> -----
> [no output]
> -----
>  I have installed Autodock Vina and i am using the local executable location: vina.exe
> your assistance will be greatly appreciated
> 
> kind regards 
> Nyasha Tauro




From esserlo at mail.nih.gov  Wed Jan 24 08:58:45 2018
From: esserlo at mail.nih.gov (Esser, Lothar (NIH/NCI) [E])
Date: Wed, 24 Jan 2018 16:58:45 +0000
Subject: [Chimera-users] Turning models on/off on a perframe basis
Message-ID: <MW2PR0901MB248969F3B33CF61398B9A5BE93E20@MW2PR0901MB2489.namprd09.prod.outlook.com>

Hi,


   in a short animation I would like to turn on/off a second model that is overlapping with the main model. The idea is to show differences by showing/hiding side chains of the second model.

I know I can turn off models with ~modeldisp #1  but I don't know how to do that properly in a perframe statement


turn y 2 180

perframe  "modeldisp #1 "  range 0,1 frames 180  # pseudo code

wait


clearly range does not quite work and $1 is presumably not setup to be ~ or nothing.

I want to turn #1 on/off say every 6 degrees. How can this be done ?


Thanks,


  Lothar


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From meng at cgl.ucsf.edu  Wed Jan 24 12:42:36 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 24 Jan 2018 12:42:36 -0800
Subject: [Chimera-users] Turning models on/off on a perframe basis
In-Reply-To: <MW2PR0901MB248969F3B33CF61398B9A5BE93E20@MW2PR0901MB2489.namprd09.prod.outlook.com>
References: <MW2PR0901MB248969F3B33CF61398B9A5BE93E20@MW2PR0901MB2489.namprd09.prod.outlook.com>
Message-ID: <D18FD308-184C-4824-A91F-1A0ECD10AD55@cgl.ucsf.edu>

Hi Lothar,
The perframe command does have an ?interval? option to do something only at every Nth frame (N >1), but then how to interleave modeldisplay and ~modeldisplay?
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/perframe.html>

Here?s a possibly crazy idea, and I really don?t know if it would work: make an alias that hides the model, waits N frames (e.g. 6 frames), and then shows it again.  Then use perframe to execute this alias every 2N frames (e.g. 12).  I guess it?s worth a try?
I hope this helps,
Elaine  
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jan 24, 2018, at 8:58 AM, Esser, Lothar (NIH/NCI) [E] <esserlo at mail.nih.gov> wrote:
> 
> Hi, 
>    in a short animation I would like to turn on/off a second model that is overlapping with the main model. The idea is to show differences by showing/hiding side chains of the second model. 
> I know I can turn off models with ~modeldisp #1  but I don't know how to do that properly in a perframe statement
> 
> turn y 2 180
> perframe  "modeldisp #1 "  range 0,1 frames 180  # pseudo code 
> wait
> 
> clearly range does not quite work and $1 is presumably not setup to be ~ or nothing.
> I want to turn #1 on/off say every 6 degrees. How can this be done ? 
> 
> Thanks, 
>   Lothar 




From esserlo at mail.nih.gov  Wed Jan 24 13:10:02 2018
From: esserlo at mail.nih.gov (Esser, Lothar (NIH/NCI) [E])
Date: Wed, 24 Jan 2018 21:10:02 +0000
Subject: [Chimera-users] Turning models on/off on a perframe basis
In-Reply-To: <D18FD308-184C-4824-A91F-1A0ECD10AD55@cgl.ucsf.edu>
References: <MW2PR0901MB248969F3B33CF61398B9A5BE93E20@MW2PR0901MB2489.namprd09.prod.outlook.com>,
 <D18FD308-184C-4824-A91F-1A0ECD10AD55@cgl.ucsf.edu>
Message-ID: <MW2PR0901MB2489C3827DBC00F7AFA2FF4A93E20@MW2PR0901MB2489.namprd09.prod.outlook.com>

Hi Elaine,


  thanks for the fast reply. After I sent off the question I wrote a script to generate a bunch of simple turn y 2 3 statements in a row with interspersed modeldisp #1 and ~modeldisp #1 statement. That worked. Only I found out that I did not like the abruptness. So I did the reasonable thing as to change the transparency ! perframe "transparency $1,a" range 100,50 frames 10 ... or something like this. That gave a smooth transition that looks good.


Thanks again.


Lothar


P.S. I apologize for any inconvenience, but recently my mail server was moved and I still have to update my subscription.


________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Wednesday, January 24, 2018 3:42:36 PM
To: Esser, Lothar (NIH/NCI) [E]
Cc: chimeraBB
Subject: Re: [Chimera-users] Turning models on/off on a perframe basis

Hi Lothar,
The perframe command does have an ?interval? option to do something only at every Nth frame (N >1), but then how to interleave modeldisplay and ~modeldisplay?
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/perframe.html>

Here?s a possibly crazy idea, and I really don?t know if it would work: make an alias that hides the model, waits N frames (e.g. 6 frames), and then shows it again.  Then use perframe to execute this alias every 2N frames (e.g. 12).  I guess it?s worth a try?
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jan 24, 2018, at 8:58 AM, Esser, Lothar (NIH/NCI) [E] <esserlo at mail.nih.gov> wrote:
>
> Hi,
>    in a short animation I would like to turn on/off a second model that is overlapping with the main model. The idea is to show differences by showing/hiding side chains of the second model.
> I know I can turn off models with ~modeldisp #1  but I don't know how to do that properly in a perframe statement
>
> turn y 2 180
> perframe  "modeldisp #1 "  range 0,1 frames 180  # pseudo code
> wait
>
> clearly range does not quite work and $1 is presumably not setup to be ~ or nothing.
> I want to turn #1 on/off say every 6 degrees. How can this be done ?
>
> Thanks,
>   Lothar

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From niash.t24 at gmail.com  Thu Jan 25 00:57:34 2018
From: niash.t24 at gmail.com (Niasha Tauro)
Date: Thu, 25 Jan 2018 10:57:34 +0200
Subject: [Chimera-users] How do i rectify this error
In-Reply-To: <2C0F5D8D-4DD7-48CA-AFC6-956DE2415544@cgl.ucsf.edu>
References: <CAKDEksZMsNqn4=nN579=qa30AQ+JNr78c0D7b_9MrtbeppARaQ@mail.gmail.com>
 <2C0F5D8D-4DD7-48CA-AFC6-956DE2415544@cgl.ucsf.edu>
Message-ID: <CAKDEksYussZELyJ4MjO63oTygPLBjD4n33GatSma8drbq2Ar1Q@mail.gmail.com>

Good day

Thank you for your timely response. Let me try doing what you said and I
will get back to you.

Regards

On Wed, Jan 24, 2018 at 7:51 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hello Nyasha,
> I?m guessing it is because the local executable location has a space in
> it.  You may need to put it in a path that does not contain a space. (I
> don?t know if putting quotation marks around the current location would
> work, although you could try it.)
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
> > On Jan 24, 2018, at 5:19 AM, Niasha Tauro <niash.t24 at gmail.com> wrote:
> >
> > Hello Chimera Users
> > Can you please help me rectify the following error showing on chimera
> (1.11.2 version) during molecular docking:
> >
> > 'C:\molecular' is not recognized as an internal or external command,
> > operable program or batch file.
> > -----
> > Application stdout
> > -----
> > [no output]
> > -----
> >  I have installed Autodock Vina and i am using the local executable
> location: vina.exe
> > your assistance will be greatly appreciated
> >
> > kind regards
> > Nyasha Tauro
>
>
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From fran.benitez at botany.ubc.ca  Fri Jan 26 12:15:37 2018
From: fran.benitez at botany.ubc.ca (Benitez De La Fuente, Francisco)
Date: Fri, 26 Jan 2018 20:15:37 +0000
Subject: [Chimera-users] Alignment of repeated domains
Message-ID: <E8B2C630839B254E8589E43937524F643A25F49D@exch-mbx03p.ead.ubc.ca>

Hello,

I'm using the tool MatchMaker to align different structures.
My reference protein has 3 domains very similar and I would like to show an alignment of other 3 proteins with each one of those 3 domains. The problem is that the 3 protein always align to the same domain (one of the 3, instead of each one with a different domain).

How can I do so I can exclude the part of the protein already aligned in new alignments?

I hope I explained myself and thank you in advance.
Francisco Benitez.
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From meng at cgl.ucsf.edu  Fri Jan 26 14:49:38 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 26 Jan 2018 14:49:38 -0800
Subject: [Chimera-users] Alignment of repeated domains
In-Reply-To: <E8B2C630839B254E8589E43937524F643A25F49D@exch-mbx03p.ead.ubc.ca>
References: <E8B2C630839B254E8589E43937524F643A25F49D@exch-mbx03p.ead.ubc.ca>
Message-ID: <198B2437-AC17-4A61-8954-F3E6336DE46E@cgl.ucsf.edu>

Hello Francisco,
You can specify just the part to use for the alignment. In the graphical interface (MatchMaker dialog), you would select the part of the structure you want to use and then turn on the option to "Further restrict matching to current selection,? described here:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html#initial>

? or if using the ?matchmaker? command, you could specify residue number range directly in that command to restrict the fit, as described here:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html#restrict>

Example: mm #0:50-100.A  #1
? will only use residues 50-100 in chain A of the reference structure #0

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Jan 26, 2018, at 12:15 PM, Benitez De La Fuente, Francisco <fran.benitez at botany.ubc.ca> wrote:
> 
> Hello,
> I'm using the tool MatchMaker to align different structures. 
> My reference protein has 3 domains very similar and I would like to show an alignment of other 3 proteins with each one of those 3 domains. The problem is that the 3 protein always align to the same domain (one of the 3, instead of each one with a different domain).
> 
> How can I do so I can exclude the part of the protein already aligned in new alignments?
> 
> I hope I explained myself and thank you in advance.
> Francisco Benitez.



From fran.benitez at botany.ubc.ca  Fri Jan 26 15:17:59 2018
From: fran.benitez at botany.ubc.ca (Benitez De La Fuente, Francisco)
Date: Fri, 26 Jan 2018 23:17:59 +0000
Subject: [Chimera-users] Alignment of repeated domains
In-Reply-To: <198B2437-AC17-4A61-8954-F3E6336DE46E@cgl.ucsf.edu>
References: <E8B2C630839B254E8589E43937524F643A25F49D@exch-mbx03p.ead.ubc.ca>,
 <198B2437-AC17-4A61-8954-F3E6336DE46E@cgl.ucsf.edu>
Message-ID: <E8B2C630839B254E8589E43937524F643A25F4DD@exch-mbx03p.ead.ubc.ca>

It perfectly solved my problem. 
Thanks so much Elaine for your help and quick answer.

Have a good Friday!
Francisco Benitez.
________________________________________
From: Elaine Meng [meng at cgl.ucsf.edu]
Sent: Friday, January 26, 2018 14:49
To: Benitez De La Fuente, Francisco
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Alignment of repeated domains

Hello Francisco,
You can specify just the part to use for the alignment. In the graphical interface (MatchMaker dialog), you would select the part of the structure you want to use and then turn on the option to "Further restrict matching to current selection,? described here:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html#initial>

? or if using the ?matchmaker? command, you could specify residue number range directly in that command to restrict the fit, as described here:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html#restrict>

Example: mm #0:50-100.A  #1
? will only use residues 50-100 in chain A of the reference structure #0

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Jan 26, 2018, at 12:15 PM, Benitez De La Fuente, Francisco <fran.benitez at botany.ubc.ca> wrote:
>
> Hello,
> I'm using the tool MatchMaker to align different structures.
> My reference protein has 3 domains very similar and I would like to show an alignment of other 3 proteins with each one of those 3 domains. The problem is that the 3 protein always align to the same domain (one of the 3, instead of each one with a different domain).
>
> How can I do so I can exclude the part of the protein already aligned in new alignments?
>
> I hope I explained myself and thank you in advance.
> Francisco Benitez.



From pacharya at nysbc.org  Fri Jan 26 23:30:39 2018
From: pacharya at nysbc.org (Priyamvada Acharya)
Date: Sat, 27 Jan 2018 07:30:39 +0000
Subject: [Chimera-users] Quantification of electron density volume
Message-ID: <BLUPR14MB01782A3AFD66D5F213373E22DAE70@BLUPR14MB0178.namprd14.prod.outlook.com>

Hi everyone,


I am wondering if there is a way to extract the values plotted under Tools > Volume Data > Values at Atom Positions?


Specifically, I would like to quantify the electron density surrounding a domain and compare it to another domain. This can be easily done if the values in the Histogram plotted under the tool mentioned above can be tabulated on a per-atom basis (perhaps within a PDB file, in the B-factor column).


If anyone knows other methods to achieve this goal, that would be helpful as well.


Thank you very much in advance for your feedback and suggestions!


Best regards,

Priyamvada
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From einavt at gmail.com  Sat Jan 27 01:56:15 2018
From: einavt at gmail.com (Einav Tayeb-Fligelman)
Date: Sat, 27 Jan 2018 11:56:15 +0200
Subject: [Chimera-users] Calculating distances in and between sheets
Message-ID: <CAHFcffwbg2utpiUc7wu+jqHxk0j5LnC4nbAEgC+2zCB4fUg6tA@mail.gmail.com>

Dear all,

I am trying to calculate distances in a unique structure in which
alpha-helices stack into sheets, as in beta-sheets. I wish to calculate the
distance between two facing sheets and between helices along each sheet.
The structure theoretically contains tens of thousands of helices in each
sheet (the content of the asymmetric unit is only one helix and the rest
are a result of symmetry operations).
I tried creating planes, one for each sheet, and calculate their distances,
but I get zero since the planes are not exactly parallel.
I also tried calculating centroid to centroid distance (I used 4 helices
for each sheet), but there is an angle between the centroids and therefore
I get a longer value then expected. Same when calculating axis to axis
distance.
Is there a good way to calculate such things with chimera? and if so, I
would appreciate an explanation for an "alpha-helical sheet" containing
structure, as well as for facing beta-sheets containing structure (in case
there is a difference in the explanation).

Thank you in advance,
Einav


-- 
PhD student at the Landau lab
Faculty of Biology
Technion, Israel Institute of Technology
Haifa, Israel
E-mail :einavtf at campus.technion.ac.il
Tel at the lab:+972-77-8871964 <+972%2077-887-1964>
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From meng at cgl.ucsf.edu  Sat Jan 27 09:06:36 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Sat, 27 Jan 2018 09:06:36 -0800
Subject: [Chimera-users] Quantification of electron density volume
In-Reply-To: <BLUPR14MB01782A3AFD66D5F213373E22DAE70@BLUPR14MB0178.namprd14.prod.outlook.com>
References: <BLUPR14MB01782A3AFD66D5F213373E22DAE70@BLUPR14MB0178.namprd14.prod.outlook.com>
Message-ID: <74A122E1-D11E-4C5A-A032-2EC13A3462A7@cgl.ucsf.edu>

Dear Priyamvada,
Yes, you can save the atom attribute values (which Values at Atom Positions assigns) from the Render/Select by Attribute dialog.  This dialog is the one showing the histogram of values, but you can also open it from the main menu: Tools? Structure Analysis? Render by Attribute. You can save the values to text file using the dialog?s menu as described here, ?saving attributes? near the bottom of the page:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#saving>

If you really wanted to overwrite the bfactor, you?d have to save the attribute file as mentioned above, text-edit it to change the name of the attribute to bfactor, and then read it back in with Define Attribute or command ?defattr? as described in this previous post to the list, and then save a copy of the PDB file now with the different bfactor values.  However, the bfactor column is narrow, so the values would get rounded off somewhat.
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-August/010235.html>

You can also calculate sums over sets of atoms with Attribute Calculator. See the list of things that can be done with attribute values:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#saving>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jan 26, 2018, at 11:30 PM, Priyamvada Acharya <pacharya at nysbc.org> wrote:
> 
> Hi everyone,
> I am wondering if there is a way to extract the values plotted under Tools > Volume Data > Values at Atom Positions?
> 
> Specifically, I would like to quantify the electron density surrounding a domain and compare it to another domain. This can be easily done if the values in the Histogram plotted under the tool mentioned above can be tabulated on a per-atom basis (perhaps within a PDB file, in the B-factor column).
> 
> If anyone knows other methods to achieve this goal, that would be helpful as well.
> 
> Thank you very much in advance for your feedback and suggestions!
> Best regards,
> Priyamvada
> 




From olibclarke at gmail.com  Sat Jan 27 09:25:58 2018
From: olibclarke at gmail.com (Oliver Clarke)
Date: Sat, 27 Jan 2018 12:25:58 -0500
Subject: [Chimera-users] launch behavior query
Message-ID: <9B4ADE73-B818-4ABA-8114-E43DBFCBBEC2@gmail.com>

Hi,

I have Chimera listed as the default app on my Mac to open MRC and PDB files. It used to be that if I double clicked on a pdb, and I had Chimera open, the pdb would open in that instance of chimera. Now, it always spawns a new instance of chimera. Is there any way to revert to the old behavior?

Cheers
Oli


From meng at cgl.ucsf.edu  Sat Jan 27 09:27:45 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Sat, 27 Jan 2018 09:27:45 -0800
Subject: [Chimera-users] Calculating distances in and between sheets
In-Reply-To: <CAHFcffwbg2utpiUc7wu+jqHxk0j5LnC4nbAEgC+2zCB4fUg6tA@mail.gmail.com>
References: <CAHFcffwbg2utpiUc7wu+jqHxk0j5LnC4nbAEgC+2zCB4fUg6tA@mail.gmail.com>
Message-ID: <6090FC30-D79E-4C31-AE0D-5223D167F4FC@cgl.ucsf.edu>

Dear Einav,
There may not be a way to do exactly what you want, since for distance measurements the planes are treated as infinite.  However, axes are treated as finite line segments for distance measurements (although infinite for angle measurements), so I would have guessed it would work, but maybe not with the specific geometry of your system.

One idea is that you can use command ?measure distance? to report the minimum distance between one set of atoms and another, and in that case I'd use only CA atoms or N,CA,C,O to avoid the variability from sidechains.  I would do it several times (say for different regions of the sheets) to see the spread of the resulting values. 
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#distance>

Oooh, I just thought of a trick: use this command to measure the minimum distance between the discs of defined planes (but treating them as finite) and to my surprise, it actually worked!!

(1) define two planes
(2) Ctrl-click one to select it, command: namesel sel1
(3) Ctrl-click the other plane to select it, command: namesel sel2
(4) command: measure distance sel1 sel2

(I thought it wouldn?t work because these plane surfaces are hidden from the model panel, but as far as I can tell, the distance reported in the status line and Reply Log is correct for my two planes)

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Jan 27, 2018, at 1:56 AM, Einav Tayeb-Fligelman <einavt at gmail.com> wrote:
> 
> Dear all,
> I am trying to calculate distances in a unique structure in which alpha-helices stack into sheets, as in beta-sheets. I wish to calculate the distance between two facing sheets and between helices along each sheet. The structure theoretically contains tens of thousands of helices in each sheet (the content of the asymmetric unit is only one helix and the rest are a result of symmetry operations). 
> I tried creating planes, one for each sheet, and calculate their distances, but I get zero since the planes are not exactly parallel. 
> I also tried calculating centroid to centroid distance (I used 4 helices for each sheet), but there is an angle between the centroids and therefore I get a longer value then expected. Same when calculating axis to axis distance. 
> Is there a good way to calculate such things with chimera? and if so, I would appreciate an explanation for an "alpha-helical sheet" containing structure, as well as for facing beta-sheets containing structure (in case there is a difference in the explanation).
> 
> Thank you in advance,
> Einav 
> 
> 
> -- 
> PhD student at the Landau lab 
> Faculty of Biology 
> Technion, Israel Institute of Technology
> Haifa, Israel
> E-mail :einavtf at campus.technion.ac.il
> Tel at the lab:+972-77-8871964
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users




From meng at cgl.ucsf.edu  Mon Jan 29 12:50:57 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 29 Jan 2018 12:50:57 -0800
Subject: [Chimera-users] launch behavior query
In-Reply-To: <9B4ADE73-B818-4ABA-8114-E43DBFCBBEC2@gmail.com>
References: <9B4ADE73-B818-4ABA-8114-E43DBFCBBEC2@gmail.com>
Message-ID: <82F6DE2F-A351-43A0-84E8-7073E83FD873@cgl.ucsf.edu>

Hi Oliver,
In my tests with the current daily build, I don?t have this problem (double-clicking PDB file in Finder opens it in the currently running Chimera).

However, I do remember a problem with Mac OS that if you have more than one Chimera copy installed, it stubbornly insists on sending the file to one of those even if you repeatedly designate opening in a different Chimera.  Could this be the problem?

If it?s starting another instance of the same copy/version of Chimera that you already have running (or you only have one version of Chimera on your computer), however, I don?t know what the issue might be.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jan 27, 2018, at 9:25 AM, Oliver Clarke <olibclarke at gmail.com> wrote:
> 
> Hi,
> I have Chimera listed as the default app on my Mac to open MRC and PDB files. It used to be that if I double clicked on a pdb, and I had Chimera open, the pdb would open in that instance of chimera. Now, it always spawns a new instance of chimera. Is there any way to revert to the old behavior?
> Cheers
> Oli




From ahodaei15 at ku.edu.tr  Mon Jan 29 13:49:37 2018
From: ahodaei15 at ku.edu.tr (ARMIN HODAEI)
Date: Mon, 29 Jan 2018 23:49:37 +0200
Subject: [Chimera-users] Adding Missing residues
Message-ID: <CAE-mGxyfyaQYsMmHqyd+xpk0hLpAoVxakXwk9u7sUzsWv1-TQw@mail.gmail.com>

Dear Chimera Users,

     I am trying to add missing residues to the protein with the ID: 1u54
But unfortunately for chain A, I cannot do the adding.

   I go to "Tools > Structure Editing > Model/Refine Loops". Then I choose
"chain A" and I select "all missing structure" and then "apply". But I got
an error. Is there any other way for it? for "chain B" it works.

Best Wishes,
Armin
-- 
Armin Hodaei
Department of Physics,
Faculty of Arts and Sciences
Koc University, Istanbul
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From pett at cgl.ucsf.edu  Mon Jan 29 17:07:38 2018
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Mon, 29 Jan 2018 17:07:38 -0800
Subject: [Chimera-users] Adding Missing residues
In-Reply-To: <CAE-mGxyfyaQYsMmHqyd+xpk0hLpAoVxakXwk9u7sUzsWv1-TQw@mail.gmail.com>
References: <CAE-mGxyfyaQYsMmHqyd+xpk0hLpAoVxakXwk9u7sUzsWv1-TQw@mail.gmail.com>
Message-ID: <D0C85AB1-5550-434F-9E4E-736D3C431E7D@cgl.ucsf.edu>

Hi Armin,
	This problem turns out to be kind of complicated to fix, but rather easy to work around.  Until I have time to actually fix the problem you can work around the problem by running this command (Favorites->Command Line) after opening 1u54 and before doing the modeling:  setattr r isHet false :ptr
	I will open a ticket in our bug database for this issue with you on the recipient list, so you will know when it is actually fixed.

?Eric

> On Jan 29, 2018, at 1:49 PM, ARMIN HODAEI <ahodaei15 at ku.edu.tr> wrote:
> 
> Dear Chimera Users,
> 
>      I am trying to add missing residues to the protein with the ID: 1u54
> But unfortunately for chain A, I cannot do the adding.
> 
>    I go to "Tools > Structure Editing > Model/Refine Loops". Then I choose "chain A" and I select "all missing structure" and then "apply". But I got an error. Is there any other way for it? for "chain B" it works.
> 
> Best Wishes,
> Armin
> -- 
> Armin Hodaei
> Department of Physics,
> Faculty of Arts and Sciences
> Koc University, Istanbul
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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From ahodaei15 at ku.edu.tr  Tue Jan 30 00:48:44 2018
From: ahodaei15 at ku.edu.tr (ARMIN HODAEI)
Date: Tue, 30 Jan 2018 10:48:44 +0200
Subject: [Chimera-users] Adding Missing residues
In-Reply-To: <D0C85AB1-5550-434F-9E4E-736D3C431E7D@cgl.ucsf.edu>
References: <CAE-mGxyfyaQYsMmHqyd+xpk0hLpAoVxakXwk9u7sUzsWv1-TQw@mail.gmail.com>
 <D0C85AB1-5550-434F-9E4E-736D3C431E7D@cgl.ucsf.edu>
Message-ID: <CAE-mGxxDt-wY0==Qgog2bzRX6FJNKgEm1rD0bqP_CXL94=VBHA@mail.gmail.com>

Dear Eric,

     Thank you very much for your time and attention. I do appreciate your
kind reply.

Best Wishes,
Armin

On Tue, Jan 30, 2018 at 3:07 AM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> Hi Armin,
> This problem turns out to be kind of complicated to fix, but rather easy
> to work around.  Until I have time to actually fix the problem you can work
> around the problem by running this command (Favorites->Command Line) after
> opening 1u54 and before doing the modeling:  setattr r isHet false :ptr
> I will open a ticket in our bug database for this issue with you on the
> recipient list, so you will know when it is actually fixed.
>
> ?Eric
>
> On Jan 29, 2018, at 1:49 PM, ARMIN HODAEI <ahodaei15 at ku.edu.tr> wrote:
>
> Dear Chimera Users,
>
>      I am trying to add missing residues to the protein with the ID: 1u54
> But unfortunately for chain A, I cannot do the adding.
>
>    I go to "Tools > Structure Editing > Model/Refine Loops". Then I choose
> "chain A" and I select "all missing structure" and then "apply". But I got
> an error. Is there any other way for it? for "chain B" it works.
>
> Best Wishes,
> Armin
> --
> Armin Hodaei
> Department of Physics,
> Faculty of Arts and Sciences
> Koc University, Istanbul
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/
> mailman/listinfo/chimera-users
>
>
>


-- 
Armin Hodaei
Department of Physics,
Faculty of Arts and Sciences
Koc University, Istanbul
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From hernando.sosa at einstein.yu.edu  Tue Jan 30 12:38:07 2018
From: hernando.sosa at einstein.yu.edu (Hernando J Sosa)
Date: Tue, 30 Jan 2018 20:38:07 +0000
Subject: [Chimera-users] computed SS
In-Reply-To: <D0C85AB1-5550-434F-9E4E-736D3C431E7D@cgl.ucsf.edu>
References: <CAE-mGxyfyaQYsMmHqyd+xpk0hLpAoVxakXwk9u7sUzsWv1-TQw@mail.gmail.com>
 <D0C85AB1-5550-434F-9E4E-736D3C431E7D@cgl.ucsf.edu>
Message-ID: <F0E461AAE34D0448B6EE7D31E433B7080123758B0F@AEWEXCPM21.yuad.uds.yu.edu>

Dear UCSF-Chimera,

I have several structures with their own defined secondary structures (SS) that are slightly different from the Chimera default assignments. I want to display them with their own assignment, not the chimera default so I am using the command mm with the option computeSS false which works as intended.   But my question is:  if at any point an alignment were done without using this option, is it possible to go back to display each structure with their own SS assignment?  I have tried but it seems that I can't go back.    Or a related question, is it possible to switch back and forth between structure-defined (when available) or Chimera-default SS assignments ?

Thank  you,

Best

H.


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From pett at cgl.ucsf.edu  Tue Jan 30 15:54:49 2018
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Tue, 30 Jan 2018 15:54:49 -0800
Subject: [Chimera-users] computed SS
In-Reply-To: <F0E461AAE34D0448B6EE7D31E433B7080123758B0F@AEWEXCPM21.yuad.uds.yu.edu>
References: <CAE-mGxyfyaQYsMmHqyd+xpk0hLpAoVxakXwk9u7sUzsWv1-TQw@mail.gmail.com>
 <D0C85AB1-5550-434F-9E4E-736D3C431E7D@cgl.ucsf.edu>
 <F0E461AAE34D0448B6EE7D31E433B7080123758B0F@AEWEXCPM21.yuad.uds.yu.edu>
Message-ID: <4F751E40-76E1-4C68-83F6-EA6DC7CF5473@cgl.ucsf.edu>

Hi Hernando,
	This is possible, but the only (non-Python) way I can think of to do it is kind of a pain.  You would use the Attribute Calculator (Tools->Structure Analysis) to define a residue attribute named ?saveHelix? using the formula ?residue.isHelix? and then the same with ?saveStrand? and ?residue.isStrand?.  After the secondary assignments were later changed, you could revert to the originals by again using the Attribute Calculator, but by defining isHelix/isStrand with the formula residue.saveHelix/saveStrand.  Ugly.  Also, the saveHelix/Strand won?t be remembered in sessions unless you get tonight?s daily build.

?Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Jan 30, 2018, at 12:38 PM, Hernando J Sosa <hernando.sosa at einstein.yu.edu> wrote:
> 
> Dear UCSF-Chimera,
>  
> I have several structures with their own defined secondary structures (SS) that are slightly different from the Chimera default assignments. I want to display them with their own assignment, not the chimera default so I am using the command mm with the option computeSS false which works as intended.   But my question is:  if at any point an alignment were done without using this option, is it possible to go back to display each structure with their own SS assignment?  I have tried but it seems that I can't go back.    Or a related question, is it possible to switch back and forth between structure-defined (when available) or Chimera-default SS assignments ?
>  
> Thank  you,
>  
> Best
>  
> H.
>  
>  
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu <mailto:Chimera-users at cgl.ucsf.edu>
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
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From elias.veijola at aalto.fi  Wed Jan 31 02:14:58 2018
From: elias.veijola at aalto.fi (Veijola Elias)
Date: Wed, 31 Jan 2018 10:14:58 +0000
Subject: [Chimera-users] Minimizing the structure in Chimera
Message-ID: <1fe51d312b4d4864b20de191d67966ed@aalto.fi>

Dear Mr. or Mrs.


I am trying to minimize a structure of mutated coEnzyme B but the program gives me this error

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From elias.veijola at aalto.fi  Wed Jan 31 02:16:28 2018
From: elias.veijola at aalto.fi (Veijola Elias)
Date: Wed, 31 Jan 2018 10:16:28 +0000
Subject: [Chimera-users] VL: Minimizing the structure in Chimera
In-Reply-To: <1fe51d312b4d4864b20de191d67966ed@aalto.fi>
References: <1fe51d312b4d4864b20de191d67966ed@aalto.fi>
Message-ID: <490669994ca74b44a7bc36e19295fe73@aalto.fi>


Dear Mr. or Mrs.


I am trying to minimize a structure of mutated coEnzyme B but the program gives me this error


Element Ni (atom #0:700.A at NI) is not currently supported [no GAFF type]


Best regards,


Elias Veijola
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From meng at cgl.ucsf.edu  Wed Jan 31 08:10:12 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 31 Jan 2018 08:10:12 -0800
Subject: [Chimera-users] computed SS
In-Reply-To: <4F751E40-76E1-4C68-83F6-EA6DC7CF5473@cgl.ucsf.edu>
References: <CAE-mGxyfyaQYsMmHqyd+xpk0hLpAoVxakXwk9u7sUzsWv1-TQw@mail.gmail.com>
 <D0C85AB1-5550-434F-9E4E-736D3C431E7D@cgl.ucsf.edu>
 <F0E461AAE34D0448B6EE7D31E433B7080123758B0F@AEWEXCPM21.yuad.uds.yu.edu>
 <4F751E40-76E1-4C68-83F6-EA6DC7CF5473@cgl.ucsf.edu>
Message-ID: <8E8BF31F-0832-46AC-9F27-31595DB0D5F6@cgl.ucsf.edu>

Hi Hernando,
Here?s another way, slightly less painful ? make aliases to save and restore the secondary structure, commands:

alias ^sskeep sel strand;namesel ostrand;sel helix;namesel ohelix;~sel

alias ^ssrestore setattr r isHelix false;setattr r isStrand false;setattr r isHelix true ohelix;setattr r isStrand true ostrand

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/namesel.html>

Each alias command should be entered as one long line (even though the mailing-list software may decide to display them broken into multiple lines).  Then in Chimera, you have new commands ?sskeep? and ?ssrestore? that can be typed or run from the Aliases menu, and they are saved in the preferences file automatically so they should be available in later uses of Chimera.  

You would run sskeep one time before changing any assignments and then ssrestore any time you want to restore the ones that were saved with sskeep.  Matchmaker with ?computeSS true? changes secondary structure assignments by running ?ksdssp?, which you could also run separately.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html#options>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html>

The named selections (saved sets of residues) created by the aliases are saved in session files.

The approach outlined above just saves/restores secondary structure for all open models together.  A fancier appraoch would save different names for different models so they could be saved/restored independently, but that would probably require python (possibly could be done with ?perframe? command) and I did not try it.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Jan 30, 2018, at 3:54 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> 
> Hi Hernando,
> 	This is possible, but the only (non-Python) way I can think of to do it is kind of a pain.  You would use the Attribute Calculator (Tools->Structure Analysis) to define a residue attribute named ?saveHelix? using the formula ?residue.isHelix? and then the same with ?saveStrand? and ?residue.isStrand?.  After the secondary assignments were later changed, you could revert to the originals by again using the Attribute Calculator, but by defining isHelix/isStrand with the formula residue.saveHelix/saveStrand.  Ugly.  Also, the saveHelix/Strand won?t be remembered in sessions unless you get tonight?s daily build.
> ?Eric
> 	Eric Pettersen
> 	UCSF Computer Graphics Lab
> 
> 
>> On Jan 30, 2018, at 12:38 PM, Hernando J Sosa <hernando.sosa at einstein.yu.edu> wrote:
>> 
>> Dear UCSF-Chimera, 
>> I have several structures with their own defined secondary structures (SS) that are slightly different from the Chimera default assignments. I want to display them with their own assignment, not the chimera default so I am using the command mm with the option computeSS false which works as intended.   But my question is:  if at any point an alignment were done without using this option, is it possible to go back to display each structure with their own SS assignment?  I have tried but it seems that I can't go back.    Or a related question, is it possible to switch back and forth between structure-defined (when available) or Chimera-default SS assignments ?
>> Thank  you,
>> Best 
>> H.
>>  




From meng at cgl.ucsf.edu  Wed Jan 31 08:21:00 2018
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 31 Jan 2018 08:21:00 -0800
Subject: [Chimera-users] VL: Minimizing the structure in Chimera
In-Reply-To: <490669994ca74b44a7bc36e19295fe73@aalto.fi>
References: <1fe51d312b4d4864b20de191d67966ed@aalto.fi>
 <490669994ca74b44a7bc36e19295fe73@aalto.fi>
Message-ID: <168AF45C-2340-45DE-9953-A77D22F97BA3@cgl.ucsf.edu>

Dear Elias Veijola,
Sorry, there are only parameters for a certain set of elements.

>From the Minimize Structure manual page:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html>

"Monatomic ions are assigned user-specified net charges and Amber VDW parameters. The following ions are handled: Li+, Na+, K+, Rb+, Cs+, F?, Cl?, Br?, I?, Mg2+, Ca2+, Zn2+. In addition, Fe ion nonbonded parameters are taken from the heme residue in the Amber parameter database. See Limitations for how to add types.?

It is very difficult to try to add parameters yourself, but you take a look at the Limitations section if you want:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html#limitations>

If you are not trying to be highly precise or the Ni ion is not near the parts of interest, you could consider text-editing your input file to change it to a different metal (one in the list above) or even delete it entirely.

Best regards,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Jan 31, 2018, at 2:16 AM, Veijola Elias <elias.veijola at aalto.fi> wrote:
> Dear Mr. or Mrs.
> I am trying to minimize a structure of mutated coEnzyme B but the program gives me this error 
> Element Ni (atom #0:700.A at NI) is not currently supported [no GAFF type]
> Best regards,
> Elias Veijola




From elias.veijola at aalto.fi  Wed Jan 31 08:31:56 2018
From: elias.veijola at aalto.fi (Veijola Elias)
Date: Wed, 31 Jan 2018 16:31:56 +0000
Subject: [Chimera-users] VL: Minimizing the structure in Chimera
In-Reply-To: <168AF45C-2340-45DE-9953-A77D22F97BA3@cgl.ucsf.edu>
References: <1fe51d312b4d4864b20de191d67966ed@aalto.fi>
 <490669994ca74b44a7bc36e19295fe73@aalto.fi>,
 <168AF45C-2340-45DE-9953-A77D22F97BA3@cgl.ucsf.edu>
Message-ID: <fa178cbda00f4c06a25b8e581559eff4@aalto.fi>

Dear Elaine,


Thank you for the respond.


Yes I tried to overcome the problem with your suggestions but it didn't work. However I just deleted the whole metal ion complex and that solved the problem. Atleast it can be used as an visual suggestion for my future project.


Best regards,

Elias Veijola

________________________________
L?hett?j?: Elaine Meng <meng at cgl.ucsf.edu>
L?hetetty: 31. tammikuuta 2018 18:21:00
Vastaanottaja: Veijola Elias
Kopio: chimera-users at cgl.ucsf.edu
Aihe: Re: [Chimera-users] VL: Minimizing the structure in Chimera

Dear Elias Veijola,
Sorry, there are only parameters for a certain set of elements.

>From the Minimize Structure manual page:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html>

"Monatomic ions are assigned user-specified net charges and Amber VDW parameters. The following ions are handled: Li+, Na+, K+, Rb+, Cs+, F?, Cl?, Br?, I?, Mg2+, Ca2+, Zn2+. In addition, Fe ion nonbonded parameters are taken from the heme residue in the Amber parameter database. See Limitations for how to add types.?

It is very difficult to try to add parameters yourself, but you take a look at the Limitations section if you want:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html#limitations>

If you are not trying to be highly precise or the Ni ion is not near the parts of interest, you could consider text-editing your input file to change it to a different metal (one in the list above) or even delete it entirely.

Best regards,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Jan 31, 2018, at 2:16 AM, Veijola Elias <elias.veijola at aalto.fi> wrote:
> Dear Mr. or Mrs.
> I am trying to minimize a structure of mutated coEnzyme B but the program gives me this error
> Element Ni (atom #0:700.A at NI) is not currently supported [no GAFF type]
> Best regards,
> Elias Veijola

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From ajcuyegkeng at ucdavis.edu  Wed Jan 31 15:19:07 2018
From: ajcuyegkeng at ucdavis.edu (Andrew Cuyegkeng)
Date: Wed, 31 Jan 2018 15:19:07 -0800
Subject: [Chimera-users] Chimera Color Coding Chains that are Interacting
Message-ID: <CAM+b92aoKi7VOg94VKXAjm7ADMrTAM6YFSknrHNXAnd3N5UgjA@mail.gmail.com>

Hello,

I am an undergraduate researcher still learning how to use Chimera. Our lab
is exploring intramolecular bonds within a complex. I am aware of the
FindContact tool but was running into problems when it came to color coding
these interactions. I would like to color code the different chains that
are involved in these interactions and make everything that's not
interacting the color black. What would the best approach to this be?

Thanks,
Andrew
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