Re: [ccp4bb] Is there a bulletin board (similar to ccp4bb) for small molecule crystallography

2024-03-15 Thread Rangana Warshamanage 
The line causing troubles is SFAC, I think


On Thu, 14 Mar 2024, 22:44 Navdeep Sidhu,  wrote:

> Dear Fred,
>
> I hope you'd agree that another good way to bypass similar issues is
> that before working on data where you don't know the model, you try out
> data where you do. And so I'd recommend this book, which provides you
> with practice data and great worked tutorials:
>
> Peter Müller (Ed.). Crystal Structure Refinement: A Crystallographer's
> Guide to SHELXL.  IUCr/Oxford, 2006
> .
>
> The book uses XP for visualization (which I guess some people still use)
> but, as Tim suggested, you should certainly also try out ShelXle or
> Olex2. (I think it's fair to say that we couldn't have identified some
> density issues just using XP.)
>
> (A 2nd edition of the book would also be a great idea.)
>
> Best regards,
> Navdeep
>
> ---
> Navdeep Sidhu
> Germany
> Web: https://scholar.google.de/citations?user=ZqU1AE0J=de
> ---
>
>
> ---
> On 12.03.24 16:42, Frederic Vellieux wrote:
> > Hi,
> >
> > In fact the problem was solved with the help of Ivica Dilovic from
> > Zagreb who suggested some changes to the shelxl .ins file. After these
> > modifications the cryptic error message was still there, but the
> > modifications made me try to remove one card. That did it.
> >
> > So the part that is concerned with this error in the .ins file is as
> > follows:
> >
> > did not work and gave the cryptic error message:
> > TITL 240223Ru_complex_0m_5 in P1
> > CELL 1.34139  10.36240  11.17780  13.19300  80.8589  73.7519  71.3166
> > ZERR2.00   0.00070   0.00080   0.00090   0.0026   0.0023   0.0023
> > LATT -1
> > SFAC C H N O CL RU
> > UNIT 62 64 2 10 2 2
> > TEMP -163.150
> > TREF
> > L.S. 10
> > EXTI 0.001
> > WGHT 0.0617
> > BOND $H
> > CONF
> > HTAB
> > FMAP 2
> > PLAN 20
> > FVAR 0.75351
> >
> > worked and gave no error:
> > TITL 240223Ru_complex_0m_5 in P1
> > CELL 1.34139 10.3624 11.1778 13.193 80.8589 73.7519 71.3166
> > ZERR 2 0.0007 0.0008 0.0009 0.0026 0.0023 0.0023
> > LATT -1
> > SFAC C H N O Cl Ru
> > DISP C 0.0137 0.0067 57.1
> > DISP Cl 0.3281 0.5435 4162.2
> > DISP H 0 0 0.6
> > DISP N 0.0241 0.0134 109.9
> > DISP O 0.0389 0.0241 193.4
> > DISP Ru -0.076 2.5955 20068.6
> > UNIT 62 64 2 10 2 2
> > L.S. 10
> > PLAN  10
> > TEMP -163.15
> > CONF
> > BOND $H
> > HTAB
> > MORE -1
> > fmap 2
> > WGHT 0.1
> > FVAR 0.25491
> >
> > I guess it would be much better (from the user's point of view) if
> > SHELXL would write on the output what the offending line is.
> >
> > Also, no indications are given on the SHELX site where the Windows .exe
> > files are supposed to go. They must be placed in the directory where the
> > GUI (olex2 or WingX) stores its exe file (olex2.exe or wingx.exe). I
> > just tried to place them there because I was desperate and it worked.
> >
> > Cheers, and thanks to everyone for their suggestions.
> >
> > Fred.
> >
> > On 2024-03-12 16:12, Kay Diederichs wrote:
> >> Fred,
> >>
> >> nobody would be offended if you'd just post your SHELXL .ins file
> >> here; there are enough experienced crystallographers to spot the
> mistake.
> >> Best would be if you could pare it down to small size, but such that
> >> it is still reproducible (my own experience is that this almost always
> >> makes me find my own mistakes).
> >>
> >> But to try and answer your title question, there is the
> >> bruker-...@g-groups.wisc.edu mailing list.
> >>
> >> Best wishes,
> >> Kay
> >>
> >> 
> >>
> >> To unsubscribe from the CCP4BB list, click the following link:
> >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> >>
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> >> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> >> available at https://www.jiscmail.ac.uk/policyandsecurity/
> >
> > 
> >
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Re: [ccp4bb] Is there a bulletin board (similar to ccp4bb) for small molecule crystallography

2024-03-14 Thread Navdeep Sidhu 

Dear Fred,

I hope you'd agree that another good way to bypass similar issues is 
that before working on data where you don't know the model, you try out 
data where you do. And so I'd recommend this book, which provides you 
with practice data and great worked tutorials:


Peter Müller (Ed.). Crystal Structure Refinement: A Crystallographer's 
Guide to SHELXL.  IUCr/Oxford, 2006 
.


The book uses XP for visualization (which I guess some people still use) 
but, as Tim suggested, you should certainly also try out ShelXle or 
Olex2. (I think it's fair to say that we couldn't have identified some 
density issues just using XP.)


(A 2nd edition of the book would also be a great idea.)

Best regards,
Navdeep

---
Navdeep Sidhu
Germany
Web: https://scholar.google.de/citations?user=ZqU1AE0J=de
---


---
On 12.03.24 16:42, Frederic Vellieux wrote:

Hi,

In fact the problem was solved with the help of Ivica Dilovic from 
Zagreb who suggested some changes to the shelxl .ins file. After these 
modifications the cryptic error message was still there, but the 
modifications made me try to remove one card. That did it.


So the part that is concerned with this error in the .ins file is as 
follows:


did not work and gave the cryptic error message:
TITL 240223Ru_complex_0m_5 in P1
CELL 1.34139  10.36240  11.17780  13.19300  80.8589  73.7519  71.3166
ZERR    2.00   0.00070   0.00080   0.00090   0.0026   0.0023   0.0023
LATT -1
SFAC C H N O CL RU
UNIT 62 64 2 10 2 2
TEMP -163.150
TREF
L.S. 10
EXTI 0.001
WGHT 0.0617
BOND $H
CONF
HTAB
FMAP 2
PLAN 20
FVAR 0.75351

worked and gave no error:
TITL 240223Ru_complex_0m_5 in P1
CELL 1.34139 10.3624 11.1778 13.193 80.8589 73.7519 71.3166
ZERR 2 0.0007 0.0008 0.0009 0.0026 0.0023 0.0023
LATT -1
SFAC C H N O Cl Ru
DISP C 0.0137 0.0067 57.1
DISP Cl 0.3281 0.5435 4162.2
DISP H 0 0 0.6
DISP N 0.0241 0.0134 109.9
DISP O 0.0389 0.0241 193.4
DISP Ru -0.076 2.5955 20068.6
UNIT 62 64 2 10 2 2
L.S. 10
PLAN  10
TEMP -163.15
CONF
BOND $H
HTAB
MORE -1
fmap 2
WGHT 0.1
FVAR 0.25491

I guess it would be much better (from the user's point of view) if 
SHELXL would write on the output what the offending line is.


Also, no indications are given on the SHELX site where the Windows .exe 
files are supposed to go. They must be placed in the directory where the 
GUI (olex2 or WingX) stores its exe file (olex2.exe or wingx.exe). I 
just tried to place them there because I was desperate and it worked.


Cheers, and thanks to everyone for their suggestions.

Fred.

On 2024-03-12 16:12, Kay Diederichs wrote:

Fred,

nobody would be offended if you'd just post your SHELXL .ins file 
here; there are enough experienced crystallographers to spot the mistake.
Best would be if you could pare it down to small size, but such that 
it is still reproducible (my own experience is that this almost always 
makes me find my own mistakes).


But to try and answer your title question, there is the 
bruker-...@g-groups.wisc.edu mailing list.


Best wishes,
Kay



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Re: [ccp4bb] Is there a bulletin board (similar to ccp4bb) for small molecule crystallography

2024-03-12 Thread Tim Gruene 
Hi Fred,

You can place the SHELXL binary anywhere, but you need to tell OLEX2,
e.g. by modifying the PATH-variable (search for 'ENVIRONMENT' in the
WINDOWS search field. The current working directory (CWD) is part of
the PATH in Windows by default, hence by copying shelxl.exe to where
you installed the olex2-binary is also a solution, but in case you need
shelxl.exe for several programs, the PATH variable but circumvent that
you need to copy shelxl.exe in all the different directories one by one.

The SHELXL download page
http://shelx.uni-goettingen.de/download.php tells you exactly that, and,
in addition, provides a link how to modify the PATH in Windows. Your
claim of the opposite is a bit illiterate.

TREF is an instruction for SHELXS and SHELXT to solve a structure,
hence not a SHELXL instruction. I am very sure the LST-file would stop
right there. When you work more with SHELXL you will notice how useful
the concise output to the terminal is, and how useful the separation
between logfile and terminal output.

Best,
Tim

On Tue, 12 Mar 2024 16:42:16 +0100 Frederic Vellieux
 wrote:

> Hi,
> 
> In fact the problem was solved with the help of Ivica Dilovic from 
> Zagreb who suggested some changes to the shelxl .ins file. After
> these modifications the cryptic error message was still there, but
> the modifications made me try to remove one card. That did it.
> 
> So the part that is concerned with this error in the .ins file is as 
> follows:
> 
> did not work and gave the cryptic error message:
> TITL 240223Ru_complex_0m_5 in P1
> CELL 1.34139  10.36240  11.17780  13.19300  80.8589  73.7519  71.3166
> ZERR2.00   0.00070   0.00080   0.00090   0.0026   0.0023   0.0023
> LATT -1
> SFAC C H N O CL RU
> UNIT 62 64 2 10 2 2
> TEMP -163.150
> TREF
> L.S. 10
> EXTI 0.001
> WGHT 0.0617
> BOND $H
> CONF
> HTAB
> FMAP 2
> PLAN 20
> FVAR 0.75351
> 
> worked and gave no error:
> TITL 240223Ru_complex_0m_5 in P1
> CELL 1.34139 10.3624 11.1778 13.193 80.8589 73.7519 71.3166
> ZERR 2 0.0007 0.0008 0.0009 0.0026 0.0023 0.0023
> LATT -1
> SFAC C H N O Cl Ru
> DISP C 0.0137 0.0067 57.1
> DISP Cl 0.3281 0.5435 4162.2
> DISP H 0 0 0.6
> DISP N 0.0241 0.0134 109.9
> DISP O 0.0389 0.0241 193.4
> DISP Ru -0.076 2.5955 20068.6
> UNIT 62 64 2 10 2 2
> L.S. 10
> PLAN  10
> TEMP -163.15
> CONF
> BOND $H
> HTAB
> MORE -1
> fmap 2
> WGHT 0.1
> FVAR 0.25491
> 
> I guess it would be much better (from the user's point of view) if 
> SHELXL would write on the output what the offending line is.
> 
> Also, no indications are given on the SHELX site where the Windows
> .exe files are supposed to go. They must be placed in the directory
> where the GUI (olex2 or WingX) stores its exe file (olex2.exe or
> wingx.exe). I just tried to place them there because I was desperate
> and it worked.
> 
> Cheers, and thanks to everyone for their suggestions.
> 
> Fred.
> 
> On 2024-03-12 16:12, Kay Diederichs wrote:
>  [...]  
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/



-- 
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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Re: [ccp4bb] Is there a bulletin board (similar to ccp4bb) for small molecule crystallography

2024-03-12 Thread Frederic Vellieux 

Hi,

In fact the problem was solved with the help of Ivica Dilovic from 
Zagreb who suggested some changes to the shelxl .ins file. After these 
modifications the cryptic error message was still there, but the 
modifications made me try to remove one card. That did it.


So the part that is concerned with this error in the .ins file is as 
follows:


did not work and gave the cryptic error message:
TITL 240223Ru_complex_0m_5 in P1
CELL 1.34139  10.36240  11.17780  13.19300  80.8589  73.7519  71.3166
ZERR2.00   0.00070   0.00080   0.00090   0.0026   0.0023   0.0023
LATT -1
SFAC C H N O CL RU
UNIT 62 64 2 10 2 2
TEMP -163.150
TREF
L.S. 10
EXTI 0.001
WGHT 0.0617
BOND $H
CONF
HTAB
FMAP 2
PLAN 20
FVAR 0.75351

worked and gave no error:
TITL 240223Ru_complex_0m_5 in P1
CELL 1.34139 10.3624 11.1778 13.193 80.8589 73.7519 71.3166
ZERR 2 0.0007 0.0008 0.0009 0.0026 0.0023 0.0023
LATT -1
SFAC C H N O Cl Ru
DISP C 0.0137 0.0067 57.1
DISP Cl 0.3281 0.5435 4162.2
DISP H 0 0 0.6
DISP N 0.0241 0.0134 109.9
DISP O 0.0389 0.0241 193.4
DISP Ru -0.076 2.5955 20068.6
UNIT 62 64 2 10 2 2
L.S. 10
PLAN  10
TEMP -163.15
CONF
BOND $H
HTAB
MORE -1
fmap 2
WGHT 0.1
FVAR 0.25491

I guess it would be much better (from the user's point of view) if 
SHELXL would write on the output what the offending line is.


Also, no indications are given on the SHELX site where the Windows .exe 
files are supposed to go. They must be placed in the directory where the 
GUI (olex2 or WingX) stores its exe file (olex2.exe or wingx.exe). I 
just tried to place them there because I was desperate and it worked.


Cheers, and thanks to everyone for their suggestions.

Fred.

On 2024-03-12 16:12, Kay Diederichs wrote:

Fred,

nobody would be offended if you'd just post your SHELXL .ins file here; 
there are enough experienced crystallographers to spot the mistake.
Best would be if you could pare it down to small size, but such that it 
is still reproducible (my own experience is that this almost always 
makes me find my own mistakes).


But to try and answer your title question, there is the 
bruker-...@g-groups.wisc.edu mailing list.


Best wishes,
Kay



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Re: [ccp4bb] Is there a bulletin board (similar to ccp4bb) for small molecule crystallography

2024-03-12 Thread Kay Diederichs 
Fred,

nobody would be offended if you'd just post your SHELXL .ins file here; there 
are enough experienced crystallographers to spot the mistake. 
Best would be if you could pare it down to small size, but such that it is 
still reproducible (my own experience is that this almost always makes me find 
my own mistakes).

But to try and answer your title question, there is the 
bruker-...@g-groups.wisc.edu mailing list.

Best wishes,
Kay



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Re: [ccp4bb] Is there a bulletin board (similar to ccp4bb) for small molecule crystallography

2024-03-12 Thread Tim Gruene 
Dear Fred,

there is a Bruker mailing list (bruker-...@g-groups.wisc.edu), that
acts as a ccp4bb for small molecule crystallography.
As far as I know, there is no automatic inscription, and you should
write to Ilia Guzei 

It is good you are on linux, that's one thing less to worry about.
If you want to use SHELXL with Olex2, you need to add SHELXL to your
PATH environment, either in a terminal from which you start Olex2, or
into the 'start' script for Olex2. In SHELXLE, you can add the SHELXL
command from the last menu item in the menu 'SHELX'

SHELXL typically writes these types of error into the lst-file,
underneath the line in question. If you copy the line, you most likely
will get a quick answer. It probably refers to a line that starts with
4 characters which are neither a recognised SHELXL command
(http://shelx.uni-goettingen.de/shelxl_html.php) nor a qualified atom
line.

Best,
Tim


On Tue, 12 Mar 2024 10:00:36 +0100 Fred Vellieux
 wrote:

> Hi folks,
> 
> I have a simple question: is there an electronic bulletin board for 
> small-molecule crystallography? I have checked the list of CCP
> projects and there is no CCP-project for small molecule
> crystallography in the list.
> 
> I am trying to run SHELXL, and it fails with the cryptic message "**
> BAD ATOM OR UNKNOWN INSTRUCTION **".
> 
> The alternative for me would be of course to use software meant for 
> macromolecular cystallography (that I know) on small molecule 
> diffraction data. And using the small molecule coordinate files 
> transformed to a suitable format. I don't know if this is feasible or 
> even advised. Probably not.
> 
> Thanks,
> 
> Fred.
> 



-- 
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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Description: OpenPGP digital signature

Re: [ccp4bb] Is there a bulletin board (similar to ccp4bb) for small molecule crystallography

2024-03-12 Thread Harry Powell 
Hi Fred

There *used* to be CCP14 (for small molecules and powders), but this lost 
funding many years ago.

In the UK, I’d contact the National Crystallography Service at Southampton to 
see if they have any pointers to bulletin boards - I have a vague recollection 
of one but can’t remember the details. Simon Coles is in charge there and may 
be able to help.

John Warren (now at Manchester) used to be very active on the BB I remember 
existing - he may be able to help directly with things like this.

As for your particular question, someone here may be familiar with SHELXL .ins 
files and be able to answer you directly - 30 years ago I *would* have been 
able to spot problems in these files at a glance, but lack of practice means 
that I doubt I could do the same these days!

best wishes

Harry

> On 12 Mar 2024, at 09:00, Fred Vellieux  wrote:
> 
> Hi folks,
> 
> I have a simple question: is there an electronic bulletin board for 
> small-molecule crystallography? I have checked the list of CCP projects and 
> there is no CCP-project for small molecule crystallography in the list.
> 
> I am trying to run SHELXL, and it fails with the cryptic message "** BAD ATOM 
> OR UNKNOWN INSTRUCTION **".
> 
> The alternative for me would be of course to use software meant for 
> macromolecular cystallography (that I know) on small molecule diffraction 
> data. And using the small molecule coordinate files transformed to a suitable 
> format. I don't know if this is feasible or even advised. Probably not.
> 
> Thanks,
> 
> Fred.
> 
> -- 
> MedChem, 1st F. Medicine, Charles University
> BIOCEV, Vestec, Czech Republic
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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> 
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
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Re: [ccp4bb] Is there a bulletin board (similar to ccp4bb) for small molecule crystallography

2024-03-12 Thread Andy Purkiss 
Dear Fred,

You need to register for the Windows (and other OS) installers if you want the 
stand-alone version of Shelx.

The form is at https://shelx.uni-goettingen.de/register.php

We have it running on Windows, although this version came with our Bruker X-ray 
generator.

Hope this helps,

Andy



From: CCP4 bulletin board  on behalf of Fred Vellieux 

Sent: 12 March 2024 09:38
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Is there a bulletin board (similar to ccp4bb) for small 
molecule crystallography


External Sender: Use caution.


Hello and thanks for the reply.

My input file came from my checking SHELX manuals and SHELX instructions on the 
web, and trying to modify them to suit my case.

I tried olex2 on a Windows computer (somehow olex2 did not run on my Linux box, 
and only v1.3 was able to install on that Windows machine and not the latest 
v1.5). However, olex2 (the installation program) does not come with Shelx 
program executables, and I could not locate the installers for the shelx 
software on Windows.

Hence I am running SHELXL in line command mode on my Linux box.

Thank you again,

Fred.

On 12/03/2024 10:12, David Waterman wrote:
Hi Fred,

I find Olex2 and shelxle are both convenient interfaces to SHELXL refinement, 
that take care of some of the details of .ins file format for you. However, 
maybe you are stuck in the starting gate, depending on what is malformed in 
your input file. Where did your input files come from?

Cheers
-- David


On Tue, 12 Mar 2024 at 09:01, Fred Vellieux 
mailto:frederic.velli...@lf1.cuni.cz>> wrote:
Hi folks,

I have a simple question: is there an electronic bulletin board for
small-molecule crystallography? I have checked the list of CCP projects
and there is no CCP-project for small molecule crystallography in the list.

I am trying to run SHELXL, and it fails with the cryptic message "** BAD
ATOM OR UNKNOWN INSTRUCTION **".

The alternative for me would be of course to use software meant for
macromolecular cystallography (that I know) on small molecule
diffraction data. And using the small molecule coordinate files
transformed to a suitable format. I don't know if this is feasible or
even advised. Probably not.

Thanks,

Fred.

--
MedChem, 1st F. Medicine, Charles University
BIOCEV, Vestec, Czech Republic



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Re: [ccp4bb] Is there a bulletin board (similar to ccp4bb) for small molecule crystallography

2024-03-12 Thread Fred Vellieux 

Hello again,

I'll try ccp4 for Windows when I am back at home (where Windows "lives" 
in my case).


I have certainly tried shelxle. If I remember well what is provided is a 
.deb file. I used alien to convert that to a .rpm file, and installation 
failed because of issues I can't remember (the Linux flavour here is 
Alma Linux 9, not Debian).


Fred.

On 12/03/2024 10:56, David Waterman wrote:

Hi Fred,

CCP4 distributes the shelxl binary on Linux. I've not checked yet, but 
perhaps it is also part of CCP4 on Windows?


Cheers
-- David


On Tue, 12 Mar 2024 at 09:38, Fred Vellieux 
 wrote:


Hello and thanks for the reply.

My input file came from my checking SHELX manuals and SHELX
instructions on the web, and trying to modify them to suit my case.

I tried olex2 on a Windows computer (somehow olex2 did not run on
my Linux box, and only v1.3 was able to install on that Windows
machine and not the latest v1.5). However, olex2 (the installation
program) does not come with Shelx program executables, and I could
not locate the installers for the shelx software on Windows.

Hence I am running SHELXL in line command mode on my Linux box.

Thank you again,

Fred.

On 12/03/2024 10:12, David Waterman wrote:

Hi Fred,

I find Olex2 and shelxle are both convenient interfaces to SHELXL
refinement, that take care of some of the details of .ins file
format for you. However, maybe you are stuck in the starting
gate, depending on what is malformed in your input file. Where
did your input files come from?

Cheers
-- David


On Tue, 12 Mar 2024 at 09:01, Fred Vellieux
 wrote:

Hi folks,

I have a simple question: is there an electronic bulletin
board for
small-molecule crystallography? I have checked the list of
CCP projects
and there is no CCP-project for small molecule
crystallography in the list.

I am trying to run SHELXL, and it fails with the cryptic
message "** BAD
ATOM OR UNKNOWN INSTRUCTION **".

The alternative for me would be of course to use software
meant for
macromolecular cystallography (that I know) on small molecule
diffraction data. And using the small molecule coordinate files
transformed to a suitable format. I don't know if this is
feasible or
even advised. Probably not.

Thanks,

Fred.

-- 
MedChem, 1st F. Medicine, Charles University

BIOCEV, Vestec, Czech Republic



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, terms & conditions are available
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-- 
MedChem, 1st F. Medicine, Charles University

BIOCEV, Vestec, Czech Republic


--
MedChem, 1st F. Medicine, Charles University
BIOCEV, Vestec, Czech Republic



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Re: [ccp4bb] Is there a bulletin board (similar to ccp4bb) for small molecule crystallography

2024-03-12 Thread David Waterman 
Hi Fred,

CCP4 distributes the shelxl binary on Linux. I've not checked yet, but
perhaps it is also part of CCP4 on Windows?

Cheers
-- David


On Tue, 12 Mar 2024 at 09:38, Fred Vellieux 
wrote:

> Hello and thanks for the reply.
>
> My input file came from my checking SHELX manuals and SHELX instructions
> on the web, and trying to modify them to suit my case.
>
> I tried olex2 on a Windows computer (somehow olex2 did not run on my Linux
> box, and only v1.3 was able to install on that Windows machine and not the
> latest v1.5). However, olex2 (the installation program) does not come with
> Shelx program executables, and I could not locate the installers for the
> shelx software on Windows.
>
> Hence I am running SHELXL in line command mode on my Linux box.
>
> Thank you again,
>
> Fred.
> On 12/03/2024 10:12, David Waterman wrote:
>
> Hi Fred,
>
> I find Olex2 and shelxle are both convenient interfaces to SHELXL
> refinement, that take care of some of the details of .ins file format for
> you. However, maybe you are stuck in the starting gate, depending on what
> is malformed in your input file. Where did your input files come from?
>
> Cheers
> -- David
>
>
> On Tue, 12 Mar 2024 at 09:01, Fred Vellieux 
> wrote:
>
>> Hi folks,
>>
>> I have a simple question: is there an electronic bulletin board for
>> small-molecule crystallography? I have checked the list of CCP projects
>> and there is no CCP-project for small molecule crystallography in the
>> list.
>>
>> I am trying to run SHELXL, and it fails with the cryptic message "** BAD
>> ATOM OR UNKNOWN INSTRUCTION **".
>>
>> The alternative for me would be of course to use software meant for
>> macromolecular cystallography (that I know) on small molecule
>> diffraction data. And using the small molecule coordinate files
>> transformed to a suitable format. I don't know if this is feasible or
>> even advised. Probably not.
>>
>> Thanks,
>>
>> Fred.
>>
>> --
>> MedChem, 1st F. Medicine, Charles University
>> BIOCEV, Vestec, Czech Republic
>>
>> 
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>
>> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
>> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
>> available at https://www.jiscmail.ac.uk/policyandsecurity/
>>
> --
> MedChem, 1st F. Medicine, Charles University
> BIOCEV, Vestec, Czech Republic
>
>



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Re: [ccp4bb] Is there a bulletin board (similar to ccp4bb) for small molecule crystallography

2024-03-12 Thread Fred Vellieux 

Hello and thanks for the reply.

My input file came from my checking SHELX manuals and SHELX instructions 
on the web, and trying to modify them to suit my case.


I tried olex2 on a Windows computer (somehow olex2 did not run on my 
Linux box, and only v1.3 was able to install on that Windows machine and 
not the latest v1.5). However, olex2 (the installation program) does not 
come with Shelx program executables, and I could not locate the 
installers for the shelx software on Windows.


Hence I am running SHELXL in line command mode on my Linux box.

Thank you again,

Fred.

On 12/03/2024 10:12, David Waterman wrote:

Hi Fred,

I find Olex2 and shelxle are both convenient interfaces to SHELXL 
refinement, that take care of some of the details of .ins file format 
for you. However, maybe you are stuck in the starting gate, depending 
on what is malformed in your input file. Where did your input files 
come from?


Cheers
-- David


On Tue, 12 Mar 2024 at 09:01, Fred Vellieux 
 wrote:


Hi folks,

I have a simple question: is there an electronic bulletin board for
small-molecule crystallography? I have checked the list of CCP
projects
and there is no CCP-project for small molecule crystallography in
the list.

I am trying to run SHELXL, and it fails with the cryptic message
"** BAD
ATOM OR UNKNOWN INSTRUCTION **".

The alternative for me would be of course to use software meant for
macromolecular cystallography (that I know) on small molecule
diffraction data. And using the small molecule coordinate files
transformed to a suitable format. I don't know if this is feasible or
even advised. Probably not.

Thanks,

Fred.

-- 
MedChem, 1st F. Medicine, Charles University

BIOCEV, Vestec, Czech Republic



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1


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--
MedChem, 1st F. Medicine, Charles University
BIOCEV, Vestec, Czech Republic



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Re: [ccp4bb] Is there a bulletin board (similar to ccp4bb) for small molecule crystallography

2024-03-12 Thread David Waterman 
Hi Fred,

I find Olex2 and shelxle are both convenient interfaces to SHELXL
refinement, that take care of some of the details of .ins file format for
you. However, maybe you are stuck in the starting gate, depending on what
is malformed in your input file. Where did your input files come from?

Cheers
-- David


On Tue, 12 Mar 2024 at 09:01, Fred Vellieux 
wrote:

> Hi folks,
>
> I have a simple question: is there an electronic bulletin board for
> small-molecule crystallography? I have checked the list of CCP projects
> and there is no CCP-project for small molecule crystallography in the list.
>
> I am trying to run SHELXL, and it fails with the cryptic message "** BAD
> ATOM OR UNKNOWN INSTRUCTION **".
>
> The alternative for me would be of course to use software meant for
> macromolecular cystallography (that I know) on small molecule
> diffraction data. And using the small molecule coordinate files
> transformed to a suitable format. I don't know if this is feasible or
> even advised. Probably not.
>
> Thanks,
>
> Fred.
>
> --
> MedChem, 1st F. Medicine, Charles University
> BIOCEV, Vestec, Czech Republic
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/
>



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[ccp4bb] Is there a bulletin board (similar to ccp4bb) for small molecule crystallography

2024-03-12 Thread Fred Vellieux 

Hi folks,

I have a simple question: is there an electronic bulletin board for 
small-molecule crystallography? I have checked the list of CCP projects 
and there is no CCP-project for small molecule crystallography in the list.


I am trying to run SHELXL, and it fails with the cryptic message "** BAD 
ATOM OR UNKNOWN INSTRUCTION **".


The alternative for me would be of course to use software meant for 
macromolecular cystallography (that I know) on small molecule 
diffraction data. And using the small molecule coordinate files 
transformed to a suitable format. I don't know if this is feasible or 
even advised. Probably not.


Thanks,

Fred.

--
MedChem, 1st F. Medicine, Charles University
BIOCEV, Vestec, Czech Republic



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

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